GISAID - gisaid.org
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134Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis
Mariana G. Ferrarini•Avantika Lal•Rita Rebollo•Andreas J. Gruber•Andrea Guarracino等 13 人
Communications Biology
2021
•2021/5/17
•Vol.4 No.1 p.1-15
The novel betacoronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic (COVID-19) after emerging in Wuhan, China. Here we analyzed public host and viral RNA sequencing data to better understand how SARS-CoV-2 interacts with human respiratory cells. We iden...
Computational biology and bioinformaticsRNASARS-CoV-2TranscriptomicsViral infection
10.1038/S42003-021-02095-0
ISSN:2399-3642
Immunogenicity and safety of the CoronaVac inactivated vaccine in patients with autoimmune rheumatic diseases: a phase 4 trial
Medeiros-Ribeiro Ana C.•Aikawa Nadia E.•Saad Carla G. S.•Yuki Emily F. N.•Pedrosa Tatiana等 22 人
Nature Medicine
2021
•2021/7/30
•00 p.1-8
CoronaVac, an inactivated SARS-CoV-2 vaccine, has been approved for emergency use in several countries. However, its immunogenicity in immunocompromised individuals has not been well established. We initiated a prospective phase 4 controlled trial (no. NCT04754698, CoronavRheum) in 910 adults with a...
AntibodiesInactivated vaccinesRheumatic diseasesSARS-CoV-2Viral infection
10.1038/S41591-021-01469-5
ISSN:1078-8956
Preclinical development of kinetin as a safe error-prone SARS-CoV-2 antiviral able to attenuate virus-induced inflammation
Souza Thiago Moreno L.•Pinho Vagner D.•Setim Cristina F.•Sacramento Carolina Q.•Marcon Rodrigo等 35 人
Nature Communications
2023
•2023/1/13
•Vol.14 No.1 p.1-17
Orally available antivirals against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are necessary because of the continuous circulation of new variants that challenge immunized individuals. Because severe COVID-19 is a virus-triggered immune and inflammatory dysfunction, molecules endow...
AntiviralsPharmacodynamicsRNASARS-CoV-2
10.1038/S41467-023-35928-Z
ISSN:2041-1723
Characterization of ACTN4 as a novel antiviral target against SARS-CoV-2
Miao Zhu•Fang Huang•Huize Sun•Kunpeng Liu•Zhen Chen等 17 人
Signal Transduction And Targeted Therapy
2024
•2024/9/18
•Vol.9 No.1 p.1-14
The various mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pose a substantial challenge in mitigating the viral infectivity. The identification of novel host factors influencing SARS-CoV-2 replication holds potential for discovering new targets for broad-spectrum antiviral...
Cell biologyEpigeneticsSenescence
10.1038/S41392-024-01956-4
ISSN:2059-3635
A protein language model for exploring viral fitness landscapes
Jumpei Ito•Adam Strange•Wei Liu•Gustav Joas•Spyros Lytras等 6 人
Nature Communications
2025
•2025/5/13
•Vol.16 No.1 p.1-16
Successively emerging SARS-CoV-2 variants lead to repeated epidemic surges through escalated fitness (i.e., relative effective reproduction number between variants). Modeling the genotype–fitness relationship enables us to pinpoint the mutations boosting viral fitness and flag high-risk variants imm...
Machine learningSARS-CoV-2
10.1038/S41467-025-59422-W
ISSN:2041-1723
Poultry farm density and proximity drive highly pathogenic avian influenza spread
Claire Guinat•Cecilia Valenzuela Agüí•François-Xavier Briand•Debapriyo Chakraborty•Lisa Fourtune等 14 人
Communications Biology
2025
•2025/8/29
•Vol.8 No.1 p.1-8
The continuous spread of highly pathogenic avian influenza H5 viruses poses significant challenges, particularly in regions with high poultry farm densities where conventional control measures are less effective. Using phylogeographic and phylodynamic tools, we analysed virus spread in southwestern ...
Influenza virusMolecular evolutionRisk factors
10.1038/S42003-025-08687-4
ISSN:2399-3642
Evidence of monkeypox virus clade IIb lineage A.2.2 in the Republic of the Congo and co-circulation of clade Ia, Ib and clade IIb
Felix Koukouikila-Koussounda•Claude Kwe Yinda•Pembe Issamou Mayangue•Dachel Aymard Eyenet Boussam•Reiche Golmard Elenga等 17 人
Nature Medicine
2026
•2026/4/3
•00 p.1-5
In 2022, monkeypox virus (MPXV) clade IIb emerged resulting in a global epidemic driven by human-to-human transmission, mostly through sexual contact mainly among the population of men who have sex with men. To date, published data on the circulation of MPXV clade IIb in the central African region a...
Genetic testingPox virusViral infection
10.1038/S41591-026-04256-2
ISSN:1078-8956
Lineage-specific protection and immune imprinting shape the age distributions of influenza B cases
Marcos C. Vieira•Celeste M. Donato•Philip Arevalo•Guus F. Rimmelzwaan•Timothy Wood等 10 人
Nature Communications
2021
•2021/7/14
•Vol.12 No.1 p.1-14
How a history of influenza virus infections contributes to protection is not fully understood, but such protection might explain the contrasting age distributions of cases of the two lineages of influenza B, B/Victoria and B/Yamagata. Fitting a statistical model to those distributions using surveill...
Computational modelsEcological epidemiologyEpidemiologyInfluenza virus
10.1038/S41467-021-24566-Y
ISSN:2041-1723
International importance and spread of SARS-CoV-2 variants Alpha, Delta, and Omicron BA.1 into Spain
Pilar Gallego-García•Samuel L. Hong•Nena Bollen•Simon Dellicour•Guy Baele等 8 人
Communications Medicine
2025
•2025/5/30
•Vol.5 No.1 p.1-8
The spread of SARS-CoV-2 has been influenced by multiple factors, from the inherent transmission capabilities of the different variants to the control measurements put in place. Understanding how new variants enter a country is essential for managing future outbreaks. This study investigates how thr...
EpidemiologyEvolutionViral infection
10.1038/S43856-025-00912-9
ISSN:2730-664X
Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks
Fatemeh Mohebbi•Alex Zelikovsky•Serghei Mangul•Gerardo Chowell•Pavel Skums
Nature Communications
2024
•2024/4/2
•Vol.15 No.1 p.1-16
The emergence of viral variants with altered phenotypes is a public health challenge underscoring the need for advanced evolutionary forecasting methods. Given extensive epistatic interactions within viral genomes and known viral evolutionary history, efficient genomic surveillance necessitates earl...
Genome evolutionMolecular evolutionNetwork topologyViral geneticsViral infection
10.1038/S41467-024-47304-6
ISSN:2041-1723
A broadly protective human monoclonal antibody targeting the sialidase activity of influenza A and B virus neuraminidases
Yasuhara Atsuhiro•Yamayoshi Seiya•Kiso Maki•Sakai-Tagawa Yuko•Okuda Moe等 6 人
Nature Communications
2022
•2022/11/3
•Vol.13 No.1 p.1-11
Improved vaccines and antiviral agents that provide better, broader protection against seasonal and emerging influenza viruses are needed. The viral surface glycoprotein hemagglutinin (HA) is a primary target for the development of universal influenza vaccines and therapeutic antibodies. The other m...
AntibodiesInfluenza virus
10.1038/S41467-022-34521-0
ISSN:2041-1723
Genetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021
Morang’a Collins M.•Ngoi Joyce M.•Gyamfi Jones•Amuzu Dominic S. Y.•Nuertey Benjamin D.等 56 人
Nature Communications
2022
•2022/5/6
•Vol.13 No.1 p.1-11
The COVID-19 pandemic is one of the fastest evolving pandemics in recent history. As such, the SARS-CoV-2 viral evolution needs to be continuously tracked. This study sequenced 1123 SARS-CoV-2 genomes from patient isolates (121 from arriving travellers and 1002 from communities) to track the molecul...
EpidemiologyMolecular evolutionPhylogeneticsSARS-CoV-2Viral infection
10.1038/S41467-022-30219-5
ISSN:2041-1723
SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal
Borges Vítor•Isidro Joana•Trovão Nídia Sequeira•Duarte Sílvia•Cortes-Martins Helena等 11 人
Communications Medicine
2022
•2022/1/28
•Vol.2 No.1 p.1-11
Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. By applying recent phylodynamic models that allow integration of individual...
SARS-CoV-2Viral infection
10.1038/S43856-022-00072-0
ISSN:2730-664X
Evolving spike mutations in SARS-CoV-2 Omicron variants facilitate evasion from breakthrough infection-acquired antibodies
Shiqi Chen•Zehong Huang•Yue Guo•Huilin Guo•Lijuan Jian等 15 人
Cell Discovery
2023
•2023/8/18
•Vol.9 No.1 p.1-5
ImmunologyMolecular biology
10.1038/S41421-023-00584-6
ISSN:2056-5968
Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater
Nicolae Sapoval•Yunxi Liu•Esther G. Lou•Loren Hopkins•Katherine B. Ensor等 8 人
Nature Communications
2023
•2023/5/17
•Vol.14 No.1 p.1-7
As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant of concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection based on quasi-unique mutations. The benefits of QuaID are thre...
Computational modelsMicrobiomeSoftware
10.1038/S41467-023-38184-3
ISSN:2041-1723
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda
Daniel Lule Bugembe•My V. T. Phan•Isaac Ssewanyana•Patrick Semanda•Hellen Nansumba等 11 人
Nature Microbiology
2021
•2021/6/23
•00 p.1-8
Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with a population of approximately 40 million people. We report 322 full SARS-CoV-2 genomes from 39,424 reported SARS-CoV-2 infections, thus representing 0.8% of the report...
SARS-CoV-2Viral infection
10.1038/S41564-021-00933-9
ISSN:2058-5276
Accurately clustering biological sequences in linear time by relatedness sorting
Erik Wright
Nature Communications
2024
•2024/4/8
•Vol.15 No.1 p.1-13
Clustering biological sequences into similar groups is an increasingly important task as the number of available sequences continues to grow exponentially. Search-based approaches to clustering scale super-linearly with the number of input sequences, making it impractical to cluster very large sets ...
Functional clusteringProteome informaticsSoftware
10.1038/S41467-024-47371-9
ISSN:2041-1723
Viral and host factors related to the clinical outcome of COVID-19
Xiaonan Zhang•Yun Tan•Yun Ling•Gang Lu•Feng Liu等 25 人
Nature
2020
•2020/5/20
•Vol.583 No.7816 p.437-440
In December 2019, coronavirus disease 2019 (COVID-19), which is caused by the new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified in Wuhan (Hubei province, China)1; it soon spread across the world. In this ongoing pandemic, public health concerns and the urge...
RespirationSARS-CoV-2Viral infection
10.1038/S41586-020-2355-0
ISSN:0028-0836
COVIDep: a web-based platform for real-time reporting of vaccine target recommendations for SARS-CoV-2
Syed Faraz Ahmed•Ahmed A. Quadeer•Matthew R. McKay
Nature Protocols
2020
•2020/6/17
•Vol.15 No.7 p.2141-2142
Software
10.1038/S41596-020-0358-9
ISSN:1754-2189
Unraveling the mechanism behind the probable extinction of the B/Yamagata lineage of influenza B viruses
Wenjie Han•Jinfeng Zeng•Jiayi Shi•Jingru Feng•Yilin Chen等 21 人
Nature Communications
2025
•2025/11/25
•Vol.16 No.1 p.104400
The COVID-19 pandemic caused an unprecedented disruption to the global circulation of influenza viruses. Among the most notable outcomes was the probable extinction of the B/Yamagata lineage of influenza B viruses, which has been rarely detected since March 2020. However, the underlying mechanism of...
Computational modelsEpidemiologyInfluenza virusMolecular evolutionViral infection
10.1038/S41467-025-65396-6
ISSN:2041-1723
Lung tropism in hospitalized patients following infection with SARS-CoV-2 variants from D614G to Omicron BA.2
Hirotsu Yosuke•Kakizaki Yumiko•Saito Akitoshi•Tsutsui Toshiharu•Hanawa Syunya等 11 人
Communications Medicine
2023
•2023/2/25
•Vol.3 No.1 p.1-10
The genetic and pathogenic characteristics of SARS-CoV-2 have evolved from the original isolated strains; however, the changes in viral virulence have not been fully defined. In this study, we analyzed the association between the severity of the pathogenesis of pneumonia in humans and SARS-CoV-2 var...
RadiographyViral infection
10.1038/S43856-023-00261-5
ISSN:2730-664X
Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2
Philippe Lemey•Samuel L. Hong•Verity Hill•Guy Baele•Chiara Poletto等 13 人
Nature Communications
2020
•2020/10/9
•Vol.11 No.1 p.1-14
Spatiotemporal bias in genome sampling can severely confound discrete trait phylogeographic inference. This has impeded our ability to accurately track the spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, despite the availability of unprecedented numbers of SARS-CoV-2 genomes. ...
Ecological epidemiologyPhylogeneticsPhylogenomicsSARS-CoV-2
10.1038/S41467-020-18877-9
ISSN:2041-1723
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Tegally Houriiyah•Moir Monika•Everatt Josie•Giovanetti Marta•Scheepers Cathrine等 56 人
Nature Medicine
2022
•2022/6/27
•Vol.28 No.9 p.1785-1790
Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa’s fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave...
EpidemiologyPhylogeny
10.1038/S41591-022-01911-2
ISSN:1078-8956
Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions
Dudas Gytis•Hong Samuel L.•Potter Barney I.•Calvignac-Spencer Sébastien•Niatou-Singa Frédéric S.等 70 人
Nature Communications
2021
•2021/10/1
•Vol.12 No.1 p.1-12
Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations...
Molecular evolutionPathogensPhylogeneticsViral infection
10.1038/S41467-021-26055-8
ISSN:2041-1723
Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024
Benjamin Sobkowiak•Amy Langdon•Pedro E. Romero•Gabriel Carrasco-Escobar•Diego Villa等 36 人
Communications Medicine
2026
•2026/1/9
•Vol.6 No.1 p.220
Peru recorded one of the world’s highest COVID-19 mortality rates, with nearly 4.5 million reported cases and 220,000 deaths by March 2024. Understanding the emergence and spread of SARS-CoV-2 variants in this context is key to informing effective public health responses. This study describes the ge...
Computational biology and bioinformaticsEpidemiologySARS-CoV-2
10.1038/S43856-025-01273-Z
ISSN:2730-664X
Optimizing a human monoclonal antibody for better neutralization of SARS-CoV-2
Qian Wang•Yicheng Guo•Ryan G. Casner•Jian Yu•Manoj S. Nair等 15 人
Nature Communications
2025
•2025/7/4
•Vol.16 No.1 p.1-14
SARS-CoV-2 has largely evolved to resist antibody pressure, with each successive viral variant becoming more and more resistant to serum antibodies in the population. This evolution renders all previously authorized anti-spike therapeutic monoclonal antibodies inactive, and it threatens the remainin...
AntibodiesCryoelectron microscopySARS-CoV-2Viral immune evasionViral infection
10.1038/S41467-025-61472-Z
ISSN:2041-1723
Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins
Tommy Tsan-Yuk Lam•Na Jia•Ya-Wei Zhang•Marcus Ho-Hin Shum•Jia-Fu Jiang等 29 人
Nature
2020
•2020/3/26
•Vol.583 No.7815 p.282-285
The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-21. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection2. Although bats are pro...
Evolutionary geneticsSARS-CoV-2Viral infectionViral reservoirs
10.1038/S41586-020-2169-0
ISSN:0028-0836
A single mutation may contribute to accelerated evolution of SARS-CoV-2 toward Omicron
Xiaoyuan Lin•Zhou Sha•Chunlin Zhang•Julia M. Adler•Ricardo Martin Vidal等 22 人
Nature Communications
2025
•2025/7/29
•Vol.16 No.1 p.1-18
How SARS-CoV-2 Omicron evolved remains obscure. T492I, an Omicron-specific mutation encountered in SARS-CoV-2 nonstructural protein 4 (NSP4), enhances viral replication and alters nonstructural protein cleavage, inferring potentials to drive evolution. Through evolve-and-resequence experiments of SA...
Evolutionary biologySARS-CoV-2Viral evolution
10.1038/S41467-025-62300-0
ISSN:2041-1723
Analysis of well-annotated next-generation sequencing data reveals increasing cases of SARS-CoV-2 reinfection with Omicron
Burkholz Scott•Rubsamen Michael•Blankenberg Luke•Carback Richard T.•Mochly-Rosen Daria等 6 人
Communications Biology
2023
•2023/3/18
•Vol.6 No.1 p.1-6
SARS-CoV-2 has extensively mutated creating variants of concern (VOC) resulting in global infection surges. The Omicron VOC reinfects individuals exposed to earlier variants of SARS-CoV-2 at a higher frequency than previously seen for non-Omicron VOC. An analysis of the sub-lineages associated with ...
Genetic databasesViral infection
10.1038/S42003-023-04687-4
ISSN:2399-3642
Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel
Danielle Miller•Michael A. Martin•Noam Harel•Omer Tirosh•Talia Kustin等 19 人
Nature Communications
2020
•2020/11/2
•Vol.11 No.1 p.1-10
Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that trav...
EpidemiologyPhylogeneticsSARS-CoV-2
10.1038/S41467-020-19248-0
ISSN:2041-1723
Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale
Amman Fabian•Markt Rudolf•Endler Lukas•Hupfauf Sebastian•Agerer Benedikt等 39 人
Nature Biotechnology
2022
•2022/7/18
•Vol.40 No.12 p.1814-1822
SARS-CoV-2 surveillance by wastewater-based epidemiology is poised to provide a complementary approach to sequencing individual cases. However, robust quantification of variants and de novo detection of emerging variants remains challenging for existing strategies. We deep sequenced 3,413 wastewater...
EpidemiologyPhylogenySARS-CoV-2Viral infection
10.1038/S41587-022-01387-Y
ISSN:1087-0156
Global solidarity in genomic surveillance improves early detection of acute respiratory virus threats
Simon P. J. de Jong•Brooke E. Nichols•Anniek de Ruijter•Edyth Parker•Vera Mitesser等 9 人
Nature Communications
2026
•2026/1/13
•Vol.17 No.1 p.7650
As genomic surveillance is key to detecting novel respiratory viruses or variants, the highly unequal global distribution of respiratory virus sequencing infrastructure raises concerns about preparedness for future threats. Using mathematical models and global epidemic simulations, we demonstrate th...
Health policyInfectious diseasesPolicy and public health in microbiologyPublic health
10.1038/S41467-025-67442-9
ISSN:2041-1723
Characterization of two non-competing antibodies to influenza H3N2 hemagglutinin stem reveals its evolving antigenicity
Akshita B. Gopal•Huibin Lv•Tossapol Pholcharee•Wenhao O. Ouyang•Qi Wen Teo等 10 人
Nature Communications
2025
•2025/11/26
•Vol.16 No.1 p.105570
The conserved stem domain of influenza hemagglutinin (HA), which is classified into group 1 and group 2, is a target of broadly neutralizing antibodies. While many group 1 HA stem antibodies have been described, much less is known about group 2 HA stem antibodies. This study structurally characteriz...
AntibodiesCryoelectron microscopyInfluenza virus
10.1038/S41467-025-65595-1
ISSN:2041-1723
MAIVeSS: streamlined selection of antigenically matched, high-yield viruses for seasonal influenza vaccine production
Cheng Gao•Feng Wen•Minhui Guan•Bijaya Hatuwal•Lei Li等 13 人
Nature Communications
2024
•2024/2/6
•Vol.15 No.1 p.1-15
Vaccines are the main pharmaceutical intervention used against the global public health threat posed by influenza viruses. Timely selection of optimal seed viruses with matched antigenicity between vaccine antigen and circulating viruses and with high yield underscore vaccine efficacy and supply, re...
Computational modelsInfluenza virusMachine learningProtein designVaccines
10.1038/S41467-024-45145-X
ISSN:2041-1723
Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions
Manon Ragonnet-Cronin•Olivia Boyd•Lily Geidelberg•David Jorgensen•Fabricia F. Nascimento等 16 人
Nature Communications
2021
•2021/4/12
•Vol.12 No.1 p.1-7
Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. We carried out a phylogenetic analysis of more than 29,000 publicly availabl...
EpidemiologyPhylogenyPopulation geneticsSARS-CoV-2
10.1038/S41467-021-22366-Y
ISSN:2041-1723
A third vaccination with a single T cell epitope confers protection in a murine model of SARS-CoV-2 infection
Pardieck Iris N.•van der Sluis Tetje C.•van der Gracht Esmé T. I.•Veerkamp Dominique M. B.•Behr Felix M.等 26 人
Nature Communications
2022
•2022/7/8
•Vol.13 No.1 p.1-11
Understanding the mechanisms and impact of booster vaccinations are essential in the design and delivery of vaccination programs. Here we show that a three dose regimen of a synthetic peptide vaccine elicits an accruing CD8+ T cell response against one SARS-CoV-2 Spike epitope. We see prot...
CD8-positive T cellsInfectionPeptide vaccinesSARS-CoV-2
10.1038/S41467-022-31721-6
ISSN:2041-1723
SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings
Ramuta Mitchell D.•Newman Christina M.•Brakefield Savannah F.•Stauss Miranda R.•Wiseman Roger W.等 28 人
Nature Communications
2022
•2022/8/11
•Vol.13 No.1 p.1-14
Two years after the emergence of SARS-CoV-2, there is still a need for better ways to assess the risk of transmission in congregate spaces. We deployed active air samplers to monitor the presence of SARS-CoV-2 in real-world settings across communities in the Upper Midwestern states of Wisconsin and ...
Air microbiologyEpidemiologyPathogensPolicy and public health in microbiologySARS-CoV-2
10.1038/S41467-022-32406-W
ISSN:2041-1723
COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance
Michele Simonetti•Ning Zhang•Luuk Harbers•Maria Grazia Milia•Silvia Brossa等 13 人
Nature Communications
2021
•2021/6/23
•Vol.12 No.1 p.1-10
While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow—COVseq—which can be us...
DNA sequencingGenomic analysisSARS-CoV-2
10.1038/S41467-021-24078-9
ISSN:2041-1723
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland
Ana da Silva Filipe•James G. Shepherd•Thomas Williams•Joseph Hughes•Elihu Aranday-Cortes等 48 人
Nature Microbiology
2020
•2020/12/21
•Vol.6 No.1 p.112-122
Coronavirus disease 2019 (COVID-19) was first diagnosed in Scotland on 1 March 2020. During the first month of the outbreak, 2,641 cases of COVID-19 led to 1,832 hospital admissions, 207 intensive care admissions and 126 deaths. We aimed to identify the source and number of introductions of severe a...
SARS-CoV-2Viral epidemiology
10.1038/S41564-020-00838-Z
ISSN:2058-5276
Genetic diversity of H9N2 avian influenza viruses in poultry across China and implications for zoonotic transmission
Jing Yang•Juan Li•Ju Sun•Jiaming Li•Guanghua Fu等 28 人
Nature Microbiology
2025
•2025/6/3
•Vol.10 No.6 p.1378-1392
Nationwide surveillance of avian influenza viruses (AIVs) in live poultry markets across China has occurred since 2014, providing a resource for AIV prevalence and genetic diversity studies. Here we report that 3,237 of 18,425 samples from poultry were AIV positive (17.57%) between 2019 and 2023, wi...
Influenza virus
10.1038/S41564-025-02002-X
ISSN:2058-5276
Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data
Brian Lee•Ahmed Abdul Quadeer•Muhammad Saqib Sohail•Elizabeth Finney•Syed Faraz Ahmed等 7 人
Nature Communications
2025
•2025/1/7
•Vol.16 No.1 p.1-13
New and more transmissible variants of SARS-CoV-2 have arisen multiple times over the course of the pandemic. Rapidly identifying mutations that affect transmission could improve our understanding of viral biology and highlight new variants that warrant further study. Here we develop a generic, anal...
Biological physicsEvolutionary theorySARS-CoV-2Statistical methodsStatistical physics
10.1038/S41467-024-55593-0
ISSN:2041-1723
HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2
Chiara Matteo•Horner David S.•Ferrandi Erika•Gissi Carmela•Pesole Graziano
Communications Biology
2023
•2023/4/22
•Vol.6 No.1 p.1-15
Accurate and timely monitoring of the evolution of SARS-CoV-2 is crucial for identifying and tracking potentially more transmissible/virulent viral variants, and implement mitigation strategies to limit their spread. Here we introduce HaploCoV, a novel software framework that enables the exploration...
Comparative genomicsComputational biology and bioinformaticsPathogens
10.1038/S42003-023-04784-4
ISSN:2399-3642
Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies
Delphine Planas•Timothée Bruel•Ludivine Grzelak•Florence Guivel-Benhassine•Isabelle Staropoli等 33 人
Nature Medicine
2021
•2021/3/26
•00 p.1-8
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.7 and B.1.351 variants were first identified in the United Kingdom and South Africa, respectively, and have since spread to many countries. These variants harboring diverse mutations in the gene encoding the spike protein raise impor...
AntibodiesImmune evasionSARS-CoV-2
10.1038/S41591-021-01318-5
ISSN:1078-8956
Sixteen novel lineages of SARS-CoV-2 in South Africa
Houriiyah Tegally•Eduan Wilkinson•Richard J. Lessells•Jennifer Giandhari•Sureshnee Pillay等 31 人
Nature Medicine
2021
•2021/2/2
•Vol.27 No.3 p.440-446
The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. Despite the early response, by November 2020, over 785,000 people in South Africa were i...
Genetics researchPhylogenetics
10.1038/S41591-021-01255-3
ISSN:1078-8956
Detection of a SARS-CoV-2 variant of concern in South Africa
Houriiyah Tegally•Eduan Wilkinson•Marta Giovanetti•Arash Iranzadeh•Vagner Fonseca等 47 人
Nature
2021
•2021/3/9
•00 p.1-6
Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the...
EpidemiologyMolecular evolutionSARS-CoV-2
10.1038/S41586-021-03402-9
ISSN:0028-0836
Influenza vaccine strain selection with an AI-based evolutionary and antigenicity model
Wenxian Shi•Jeremy Wohlwend•Menghua Wu•Regina Barzilay
Nature Medicine
2025
•2025/8/28
•00 p.1-9
Current vaccines provide limited protection against rapidly evolving viruses. For example, Centers for Disease Control and Prevention estimates show that the overall influenza vaccine effectiveness against outpatient illness in the United States averaged below 40% between 2012 and 2021. Moreover, th...
EpidemiologyMachine learningVaccines
10.1038/S41591-025-03917-Y
ISSN:1078-8956
Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant
Jumpei Ito•Rigel Suzuki•Keiya Uriu•Yukari Itakura•Jiri Zahradnik等 39 人
Nature Communications
2023
•2023/5/11
•Vol.14 No.1 p.1-20
In late 2022, various Omicron subvariants emerged and cocirculated worldwide. These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. Here, we characterize the convergent evolution of Omicron subvar...
SARS-CoV-2Virus–host interactions
10.1038/S41467-023-38188-Z
ISSN:2041-1723
Serological evidence of clade Ib Mpox transmission by sex workers and within household in South Kivu, DRC
Leandre Murhula Masirika•Luca M. Zaeck•Pacifique Ndishimye•Jean Claude Udahemuka•Saria Otani等 18 人
Nature Communications
2025
•2025/8/1
•Vol.16 No.1 p.1-8
Understanding secondary attack rates is a key knowledge gap in the ongoing clade Ib mpox virus (MPXV) outbreak in the Democratic Republic of the Congo. Here, we report the first cross-sectional serological study to investigate local MPXV clade Ib transmission in South Kivu, DRC. Seropositivity was d...
AntibodiesDNA sequencingPolicy and public health in microbiologyViral infection
10.1038/S41467-025-62064-7
ISSN:2041-1723
Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling
Rebecca J. Rockett•Alicia Arnott•Connie Lam•Rosemarie Sadsad•Verlaine Timms等 24 人
Nature Medicine
2020
•2020/7/9
•Vol.26 No.9 p.1398-1404
In January 2020, a novel betacoronavirus (family Coronaviridae), named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of a cluster of pneumonia cases occurring in Wuhan City, Hubei Province, China1,2. The disease arising from SARS-CoV-2 infectio...
EpidemiologyGenetic testingSARS-CoV-2Viral geneticsViral infection
10.1038/S41591-020-1000-7
ISSN:1078-8956
BNT162b2 vaccination enhances interferon-JAK-STAT-regulated antiviral programs in COVID-19 patients infected with the SARS-CoV-2 Beta variant
Knabl Ludwig•Lee Hye Kyung•Wieser Manuel•Mur Anna•Zabernigg August等 12 人
Communications Medicine
2022
•2022/2/22
•Vol.2 No.1 p.1-10
SARS-CoV-2 infection activates interferon-controlled signaling pathways and elicits a wide spectrum of immune responses and clinical manifestations in human patients. Here, we investigate the impact of prior vaccination on the innate immune response of hospitalized COVID-19 patients infected with th...
High-throughput screeningViral infection
10.1038/S43856-022-00083-X
ISSN:2730-664X
De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report
Gandhi Shiv•Klein Jonathan•Robertson Alexander J.•Peña-Hernández Mario A.•Lin Michelle J.等 23 人
Nature Communications
2022
•2022/3/17
•Vol.13 No.1 p.1-8
SARS-CoV-2 remdesivir resistance mutations have been generated in vitro but have not been reported in patients receiving treatment with the antiviral agent. We present a case of an immunocompromised patient with acquired B-cell deficiency who developed an indolent, protracted course of SARS-CoV-2 in...
Antiviral agentsSARS-CoV-2Viral evolutionViral infection
10.1038/S41467-022-29104-Y
ISSN:2041-1723
Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread
Gage K. Moreno•Katarina M. Braun•Kasen K. Riemersma•Michael A. Martin•Peter J. Halfmann等 24 人
Nature Communications
2020
•2020/11/3
•Vol.11 No.1 p.1-13
Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities...
EpidemiologyPhylogeneticsSARS-CoV-2Viral infection
10.1038/S41467-020-19346-Z
ISSN:2041-1723
Learning from prepandemic data to forecast viral escape
Nicole N. Thadani•Sarah Gurev•Pascal Notin•Noor Youssef•Nathan J. Rollins等 9 人
Nature
2023
•2023/10/11
•00 p.1-8
Effective pandemic preparedness relies on anticipating viral mutations that are able to evade host immune responses to facilitate vaccine and therapeutic design. However, current strategies for viral evolution prediction are not available early in a pandemic—experimental approaches require host poly...
Computational modelsImmune evasion
10.1038/S41586-023-06617-0
ISSN:0028-0836
A non-spike nucleocapsid R204P mutation in SARS-CoV-2 Omicron XEC enhances inflammation and pathogenicity
Shuhei Tsujino•Masumi Tsuda•Sayaka Deguchi•Jumpei Ito•Taha Y. Taha等 18 人
Nature Communications
2025
•2025/12/14
0The global circulation of SARS-CoV-2 in human populations has driven the emergence of Omicron subvariants, which have become highly diversified through recombination. In late 2024, SARS-CoV-2 Omicron XEC variant emerged from the recombination of two JN.1 progeny, KS.1.1 and KP.3.3, and became predom...
InfectionPathogensSARS-CoV-2
10.1038/S41467-025-67455-4
ISSN:2041-1723
GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein
Ming Zhao•Yu Yu•Li-Ming Sun•Jia-Qing Xing•Tingting Li等 21 人
Nature Communications
2021
•2021/4/9
•Vol.12 No.1 p.1-14
Lack of detailed knowledge of SARS-CoV-2 infection has been hampering the development of treatments for coronavirus disease 2019 (COVID-19). Here, we report that RNA triggers the liquid–liquid phase separation (LLPS) of the SARS-CoV-2 nucleocapsid protein, N. By analyzing all 29 proteins of SARS-CoV...
Protein aggregationSARS-CoV-2
10.1038/S41467-021-22297-8
ISSN:2041-1723
A novel SARS-CoV-2 related coronavirus in bats from Cambodia
Delaune Deborah•Hul Vibol•Karlsson Erik A.•Hassanin Alexandre•Ou Tey Putita等 18 人
Nature Communications
2021
•2021/11/9
•Vol.12 No.1 p.1-7
Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 re...
EpidemiologyMetagenomicsMolecular evolutionSARS-CoV-2
10.1038/S41467-021-26809-4
ISSN:2041-1723
No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2
Lucy van Dorp•Damien Richard•Cedric C. S. Tan•Liam P. Shaw•Mislav Acman等 6 人
Nature Communications
2020
•2020/11/25
•Vol.11 No.1 p.1-8
COVID-19 is caused by the coronavirus SARS-CoV-2, which jumped into the human population in late 2019 from a currently uncharacterised animal reservoir. Due to this recent association with humans, SARS-CoV-2 may not yet be fully adapted to its human host. This has led to speculations that SARS-CoV-2...
Genome informaticsPhylogeneticsSARS-CoV-2Viral genetics
10.1038/S41467-020-19818-2
ISSN:2041-1723
A phase 2 single center open label randomised control trial for convalescent plasma therapy in patients with severe COVID-19
Ray Yogiraj•Paul Shekhar Ranjan•Bandopadhyay Purbita•D’Rozario Ranit•Sarif Jafar等 38 人
Nature Communications
2022
•2022/1/19
•Vol.13 No.1 p.1-9
A single center open label phase 2 randomised control trial (Clinical Trial Registry of India No. CTRI/2020/05/025209) was done to assess clinical and immunological benefits of passive immunization using convalescent plasma therapy. At the Infectious Diseases and Beleghata General Hospital in Kolkat...
Outcomes researchViral infection
10.1038/S41467-022-28064-7
ISSN:2041-1723
Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020
Smith Maureen Rebecca•Trofimova Maria•Weber Ariane•Duport Yannick•Kühnert Denise等 6 人
Nature Communications
2021
•2021/10/14
•Vol.12 No.1 p.1-13
By October 2021, 230 million SARS-CoV-2 diagnoses have been reported. Yet, a considerable proportion of cases remains undetected. Here, we propose GInPipe, a method that rapidly reconstructs SARS-CoV-2 incidence profiles solely from publicly available, time-stamped viral genomes. We validate GInPipe...
Data processingEpidemiologyPhylogenyPopulation geneticsStochastic modelling
10.1038/S41467-021-26267-Y
ISSN:2041-1723
Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission
Pickering Bradley•Lung Oliver•Maguire Finlay•Kruczkiewicz Peter•Kotwa Jonathon D.等 40 人
Nature Microbiology
2022
•2022/11/10
•Vol.7 No.12 p.2011-2024
Wildlife reservoirs of broad-host-range viruses have the potential to enable evolution of viral variants that can emerge to infect humans. In North America, there is phylogenomic evidence of continual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to white-t...
EvolutionSARS-CoV-2
10.1038/S41564-022-01268-9
ISSN:2058-5276
Model-directed generation of artificial CRISPR–Cas13a guide RNA sequences improves nucleic acid detection
Sreekar Mantena•Priya P. Pillai•Brittany A. Petros•Nicole L. Welch•Cameron Myhrvold等 7 人
Nature Biotechnology
2024
•2024/10/11
•00 p.1-8
CRISPR guide RNA sequences deriving exactly from natural sequences may not perform optimally in every application. Here we implement and evaluate algorithms for designing maximally fit, artificial CRISPR–Cas13a guides with multiple mismatches to natural sequences that are tailored for diagnostic app...
Infectious-disease diagnosticsMachine learning
10.1038/S41587-024-02422-W
ISSN:1087-0156
Molecular determinants and mechanism for antibody cocktail preventing SARS-CoV-2 escape
Zhiqiang Ku•Xuping Xie•Edgar Davidson•Xiaohua Ye•Hang Su等 21 人
Nature Communications
2021
•2021/1/20
•Vol.12 No.1 p.1-13
Antibody cocktails represent a promising approach to prevent SARS-CoV-2 escape. The determinants for selecting antibody combinations and the mechanism that antibody cocktails prevent viral escape remain unclear. We compared the critical residues in the receptor-binding domain (RBD) used by multiple ...
AntibodiesSARS-CoV-2
10.1038/S41467-020-20789-7
ISSN:2041-1723
Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru
Santiago Justo Arevalo•Carmen Sofia Uribe Calampa•Cinthy Jimenez Silva•Mauro Quiñones Aguilar•Remco Bouckaert等 6 人
Nature Communications
2023
•2023/6/15
•Vol.14 No.1 p.1-13
At over 0.6% of the population, Peru has one of the highest SARS-CoV-2 mortality rate in the world. Much effort to sequence genomes has been done in this country since mid-2020. However, an adequate analysis of the dynamics of the variants of concern and interest (VOCIs) is missing. We investigated ...
PhylogeneticsPhylogenomicsSARS-CoV-2
10.1038/S41467-023-39216-8
ISSN:2041-1723
Immunization with V987H-stabilized Spike glycoprotein protects K18-hACE2 mice and golden Syrian hamsters upon SARS-CoV-2 infection
Carlos Ávila-Nieto•Júlia Vergara-Alert•Pep Amengual-Rigo•Erola Ainsua-Enrich•Marco Brustolin等 33 人
Nature Communications
2024
•2024/3/21
•Vol.15 No.1 p.1-18
Safe and effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are crucial to fight against the coronavirus disease 2019 pandemic. Most vaccines are based on a mutated version of the Spike glycoprotein [K986P/V987P (S-2P)] with improved stability, yield and immunogenicity. ...
Protein vaccinesViral infection
10.1038/S41467-024-46714-W
ISSN:2041-1723
SARS-CoV-2 evolution on a dynamic immune landscape
N. Alexia Raharinirina•Nils Gubela•Daniela Börnigen•Maureen Rebecca Smith•Djin-Ye Oh等 14 人
Nature
2025
•2025/1/29
•Vol.639 No.8053 p.196-204
Since the onset of the pandemic, many SARS-CoV-2 variants have emerged, exhibiting substantial evolution in the virus’ spike protein1, the main target of neutralizing antibodies2. A plausible hypothesis proposes that the virus evolves to evade antibody-mediated neutralization (vaccine- or infection-...
Data integrationEpidemiologyViral infection
10.1038/S41586-024-08477-8
ISSN:0028-0836
Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity
Butera Yvan•Mukantwari Enatha•Artesi Maria•Umuringa Jeanne d’arc•O’Toole Áine Niamh等 36 人
Nature Communications
2021
•2021/9/29
•Vol.12 No.1 p.1-11
COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging ...
EpidemiologyGenetics researchPhylogenomicsSARS-CoV-2
10.1038/S41467-021-25985-7
ISSN:2041-1723
Global landscape of SARS-CoV-2 genomic surveillance and data sharing
Chen Zhiyuan•Azman Andrew S.•Chen Xinhua•Zou Junyi•Tian Yuyang等 15 人
Nature Genetics
2022
•2022/3/28
•00 p.1-9
Genomic surveillance has shaped our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. We performed a global landscape analysis on SARS-CoV-2 genomic surveillance and genomic data using a collection of country-specific data. Here, we characterize increasing circu...
EpidemiologyInfectious diseases
10.1038/S41588-022-01033-Y
ISSN:1061-4036
Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations
Jingzhi Lou•Weiwen Liang•Lirong Cao•Inchi Hu•Shi Zhao等 18 人
Nature Communications
2024
•2024/3/21
•Vol.15 No.1 p.1-11
Influenza virus continuously evolves to escape human adaptive immunity and generates seasonal epidemics. Therefore, influenza vaccine strains need to be updated annually for the upcoming flu season to ensure vaccine effectiveness. We develop a computational approach, beth-1, to forecast virus evolut...
EpidemiologyInfluenza virusMolecular evolutionVaccines
10.1038/S41467-024-46918-0
ISSN:2041-1723
Dual receptor-binding, infectivity, and transmissibility of an emerging H2N2 low pathogenicity avian influenza virus
Ju Sun•Tianyi Zheng•Mingjun Jia•Yanjun Wang•Jingru Yang等 20 人
Nature Communications
2024
•2024/11/19
•Vol.15 No.1 p.1-16
The 1957 H2N2 influenza pandemic virus [A(H2N2)pdm1957] has disappeared from humans since 1968, while H2N2 avian influenza viruses (AIVs) are still circulating in birds. It is necessary to reveal the recurrence risk and potential cross-species infection of these AIVs from avian to mammals. We find t...
Influenza virusViral pathogenesisViral transmission
10.1038/S41467-024-54374-Z
ISSN:2041-1723
Early detection of emerging SARS-CoV-2 Variants from wastewater through genome sequencing and machine learning
Xiaowei Zhuang•Van Vo•Michael A. Moshi•Ketan Dhede•Nabih Ghani等 18 人
Nature Communications
2025
•2025/7/8
•Vol.16 No.1 p.1-12
Genome sequencing from wastewater enables accurate and cost-effective identification of SARS-CoV-2 variants. However, existing computational pipelines have limitations in detecting emerging variants not yet characterized in humans. Here, we present an unsupervised learning approach that clusters co-...
Environmental social sciencesInfectious diseases
10.1038/S41467-025-61280-5
ISSN:2041-1723
Household transmission of SARS-CoV-2 Omicron variant of concern subvariants BA.1 and BA.2 in Denmark
Lyngse Frederik Plesner•Kirkeby Carsten Thure•Denwood Matthew•Christiansen Lasse Engbo•Mølbak Kåre等 19 人
Nature Communications
2022
•2022/9/30
•Vol.13 No.1 p.1-7
SARS coronavirus 2 (SARS-CoV-2) continues to evolve and new variants emerge. Using nationwide Danish data, we estimate the transmission dynamics of SARS-CoV-2 Omicron subvariants BA.1 and BA.2 within households. Among 22,678 primary cases, we identified 17,319 secondary infections among 50,588 house...
EpidemiologySARS-CoV-2Viral infection
10.1038/S41467-022-33498-0
ISSN:2041-1723
Omicron subvariant BA.5 efficiently infects lung cells
Markus Hoffmann•Lok-Yin Roy Wong•Prerna Arora•Lu Zhang•Cheila Rocha等 17 人
Nature Communications
2023
•2023/6/13
•Vol.14 No.1 p.1-11
The SARS-CoV-2 Omicron subvariants BA.1 and BA.2 exhibit reduced lung cell infection relative to previously circulating SARS-CoV-2 variants, which may account for their reduced pathogenicity. However, it is unclear whether lung cell infection by BA.5, which displaced these variants, remains attenuat...
SARS-CoV-2Virus–host interactions
10.1038/S41467-023-39147-4
ISSN:2041-1723
Multivalent S2 subunit vaccines provide broad protection against Clade 1 sarbecoviruses in female mice
Peter J. Halfmann•Raj S. Patel•Kathryn Loeffler•Atsuhiro Yasuhara•Lee-Ann Van De Velde等 15 人
Nature Communications
2025
•2025/1/7
•Vol.16 No.1 p.1-17
The continuing emergence of immune evasive SARS-CoV-2 variants and the previous SARS-CoV-1 outbreak collectively underscore the need for broadly protective sarbecovirus vaccines. Targeting the conserved S2 subunit of SARS-CoV-2 is a particularly promising approach to elicit broad protection. Here, w...
Protein vaccinesSARS-CoV-2Viral infection
10.1038/S41467-025-55824-Y
ISSN:2041-1723
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Gangavarapu Karthik•Latif Alaa Abdel•Mullen Julia L.•Alkuzweny Manar•Hufbauer Emory等 24 人
Nature Methods
2023
•2023/2/23
•00 p.1-11
In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution...
Genetic variationHardware and infrastructureSARS-CoV-2Software
10.1038/S41592-023-01769-3
ISSN:1548-7091
Organ-specific genome diversity of replication-competent SARS-CoV-2
Van Cleemput Jolien•van Snippenberg Willem•Lambrechts Laurens•Dendooven Amélie•D’Onofrio Valentino等 23 人
Nature Communications
2021
•2021/11/16
•Vol.12 No.1 p.1-11
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is not always confined to the respiratory system, as it impacts people on a broad clinical spectrum from asymptomatic to severe systemic manifestations resulting in death. Further, accumulation of intra-host single nucleotide var...
Clinical microbiologySARS-CoV-2Viral pathogenesis
10.1038/S41467-021-26884-7
ISSN:2041-1723
A mosaic influenza virus-like particles vaccine provides broad humoral and cellular immune responses against influenza A viruses
Xuejie Liu•Tianyi Zhao•Liangliang Wang•Zhuolin Yang•Chuming Luo等 10 人
Npj Vaccines
2023
•2023/9/7
•Vol.8 No.1 p.1-14
The development of a universal influenza vaccine to elicit broad immune responses is essential in reducing disease burden and pandemic impact. In this study, the mosaic vaccine design strategy and genetic algorithms were utilized to optimize the seasonal influenza A virus (H1N1, H3N2) hemagglutinin ...
Influenza virusVaccines
10.1038/S41541-023-00728-5
ISSN:2059-0105
Using multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data
Inward Rhys P. D.•Parag Kris V.•Faria Nuno R.
Nature Communications
2022
•2022/9/23
•Vol.13 No.1 p.1-14
The choice of viral sequences used in genetic and epidemiological analysis is important as it can induce biases that detract from the value of these rich datasets. This raises questions about how a set of sequences should be chosen for analysis. We provide insights on these largely understudied prob...
Computational modelsEpidemiologyPhylogeneticsSARS-CoV-2
10.1038/S41467-022-32812-0
ISSN:2041-1723
Structural insights into tecovirimat antiviral activity and poxvirus resistance
Riccardo Vernuccio•Alejandro Martínez León•Chetan S. Poojari•Julian Buchrieser•Christopher N. Selverian等 18 人
Nature Microbiology
2025
•2025/2/12
•Vol.10 No.3 p.734-748
Mpox is a zoonotic disease endemic to Central and West Africa. Since 2022, two human-adapted monkeypox virus (MPXV) strains have caused large outbreaks outside these regions. Tecovirimat is the most widely used drug to treat mpox. It blocks viral egress by targeting the viral phospholipase F13; howe...
Pox virusTarget validationX-ray crystallography
10.1038/S41564-025-01936-6
ISSN:2058-5276
Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies
Allison J. Greaney•Tyler N. Starr•Christopher O. Barnes•Yiska Weisblum•Fabian Schmidt等 19 人
Nature Communications
2021
•2021/7/7
•Vol.12 No.1 p.1-14
Monoclonal antibodies targeting a variety of epitopes have been isolated from individuals previously infected with SARS-CoV-2, but the relative contributions of these different antibody classes to the polyclonal response remains unclear. Here we use a yeast-display system to map all mutations to the...
SARS-CoV-2Viral evolutionViral infection
10.1038/S41467-021-24435-8
ISSN:2041-1723
Molecular basis of potent antiviral HLA-C-restricted CD8+ T cell response to an immunodominant SARS-CoV-2 nucleocapsid epitope
Yoshihiko Goto•You Min Ahn•Mako Toyoda•Hiroshi Hamana•Yan Jin等 27 人
Nature Communications
2025
•2025/8/28
•Vol.16 No.1 p.1-18
The emergence of SARS-CoV-2 Variants of Concern (VOC) is a major clinical threat; however, VOC remain susceptible to cytotoxic T lymphocyte (CTL) recognition. Therefore, it is crucial to identify potent CTL responses targeting conserved epitopes across VOCs. Here, we demonstrate that the nucleocapsi...
Cytotoxic T cellsImmunological memorySARS-CoV-2Viral infection
10.1038/S41467-025-63288-3
ISSN:2041-1723
Antibody evasion by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4 and BA.5
Wang Qian•Guo Yicheng•Iketani Sho•Nair Manoj S.•Li Zhiteng等 20 人
Nature
2022
•2022/7/5
•Vol.608 No.7923 p.603-608
SARS-CoV-2 Omicron subvariants BA.2.12.1 and BA.4/5 have surged notably to become dominant in the United States and South Africa, respectively1,2. These new subvariants carrying further mutations in their spike proteins raise concerns that they may further evade neutralizing antibodies, thereby furt...
SARS-CoV-2Viral evolutionViral host responseViral immune evasion
10.1038/S41586-022-05053-W
ISSN:0028-0836
Spatiotemporal evolution and transmission dynamics of Alpha and Delta SARS-CoV-2 variants contributing to sequential outbreaks in Cambodia during 2021
Yvonne C. F. Su•Michael A. Zeller•Tey Putita Ou•Jordan Ma•Leakhena Pum等 43 人
Communications Medicine
2024
•2024/11/28
•Vol.4 No.1 p.1-14
Tracking the emergence, introduction and spread of SARS-CoV-2 variants of concern are essential for informing public health strategies. In 2021, Cambodia faced two major epidemic waves of SARS-CoV-2 triggered by the successive rise of the Alpha and Delta variants. Phylodynamic analysis of 1,163 comp...
EpidemiologySARS-CoV-2Viral epidemiology
10.1038/S43856-024-00685-7
ISSN:2730-664X
Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant
Tomokazu Tamura•Takashi Irie•Sayaka Deguchi•Hisano Yajima•Masumi Tsuda等 38 人
Nature Communications
2024
•2024/2/8
•Vol.15 No.1 p.1-17
Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the S486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays...
Cryoelectron microscopySARS-CoV-2Virus–host interactions
10.1038/S41467-024-45274-3
ISSN:2041-1723
SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication
Soren Alexandersen•Anthony Chamings•Tarka Raj Bhatta
Nature Communications
2020
•2020/11/27
•Vol.11 No.1 p.1-13
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first detected in late December 2019 and has spread worldwide. Coronaviruses are enveloped, positive sense, single-stranded RNA viruses and employ a complicated pattern of virus genome length RNA replication as well as transcription of...
SARS-CoV-2Virus–host interactions
10.1038/S41467-020-19883-7
ISSN:2041-1723
Phase 1 randomized trial of a plant-derived virus-like particle vaccine for COVID-19
Brian J. Ward•Philipe Gobeil•Annie Séguin•Judith Atkins•Iohann Boulay等 19 人
Nature Medicine
2021
•2021/5/18
•00 p.1-8
Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are being deployed, but the global need greatly exceeds the supply, and different formulations might be required for specific populations. Here we report Day 42 interim safety and immunogenicity data from an observer-blind...
Drug developmentTranslational research
10.1038/S41591-021-01370-1
ISSN:1078-8956
Potent efficacy of an NA-targeting antibody against a broad spectrum of H5N1 influenza viruses
Saya Moriyama•Julia di Iulio•Fabrizia Zatta•Kevin Hauser•Hideki Asanuma等 25 人
Nature Communications
2026
•2026/3/2
•Vol.17 No.1 p.33510
For nearly 30 years, Goose/Guangdong-derived highly pathogenic avian influenza H5N1 viruses have posed significant risks to economic stability, food security, and public health. Virus evolution has resulted in various clades, including the panzootic subclade 2.3.4.4b, recognized for its pandemic pot...
Antiviral agentsCryoelectron microscopyInfluenza virus
10.1038/S41467-026-70036-8
ISSN:2041-1723
COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence
Felipe Gomes Naveca•Valdinete Nascimento•Victor Costa de Souza•André de Lima Corado•Fernanda Nascimento等 29 人
Nature Medicine
2021
•2021/5/25
•00 p.1-9
The northern state of Amazonas is among the regions in Brazil most heavily affected by the COVID-19 epidemic and has experienced two exponentially growing waves, in early and late 2020. Through a genomic epidemiology study based on 250 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) gen...
SARS-CoV-2Virology
10.1038/S41591-021-01378-7
ISSN:1078-8956
Ablation of CD8+ T cell recognition of an immunodominant epitope in SARS-CoV-2 Omicron variants BA.1, BA.2 and BA.3
Swaminathan Srividhya•Lineburg Katie E.•Panikkar Archana•Raju Jyothy•Murdolo Lawton D.等 17 人
Nature Communications
2022
•2022/10/27
•Vol.13 No.1 p.1-6
The emergence of the SARS-CoV-2 Omicron variant has raised concerns of escape from vaccine-induced immunity. A number of studies have demonstrated a reduction in antibody-mediated neutralization of the Omicron variant in vaccinated individuals. Preliminary observations have suggested that T cells ar...
Cellular immunityCytotoxic T cellsImmunological memoryMHC class ISARS-CoV-2
10.1038/S41467-022-34180-1
ISSN:2041-1723
Safety and immunogenicity of an AS03-adjuvanted plant-based SARS-CoV-2 vaccine in Adults with and without Comorbidities
Charland Nathalie•Gobeil Philipe•Pillet Stéphane•Boulay Iohann•Séguin Annie等 30 人
Npj Vaccines
2022
•2022/11/9
•Vol.7 No.1 p.1-13
The rapid spread of SARS-CoV-2 continues to impact humanity on a global scale with rising total morbidity and mortality. Despite the development of several effective vaccines, new products are needed to supply ongoing demand and to fight variants. We report herein a pre-specified interim analysis of...
AdjuvantsProtein vaccinesRecombinant vaccineSARS-CoV-2Viral infection
10.1038/S41541-022-00561-2
ISSN:2059-0105
Antibodies targeting the neuraminidase active site inhibit influenza H3N2 viruses with an S245N glycosylation site
Stadlbauer Daniel•McMahon Meagan•Turner Hannah L.•Zhu Xueyong•Wan Hongquan等 16 人
Nature Communications
2022
•2022/12/21
•Vol.13 No.1 p.1-8
Contemporary influenza A H3N2 viruses circulating since 2016 have acquired a glycosylation site in the neuraminidase in close proximity to the enzymatic active site. Here, we investigate if this S245N glycosylation site, as a result of antigenic evolution, can impact binding and function of human mo...
AntibodiesInfluenza virus
10.1038/S41467-022-35586-7
ISSN:2041-1723
Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1
Hisano Yajima•Yuki Anraku•Yu Kaku•Kanako Terakado Kimura•Arnon Plianchaisuk等 18 人
Nature Communications
2024
•2024/10/7
•Vol.15 No.1 p.1-14
Since 2019, SARS-CoV-2 has undergone mutations, resulting in pandemic and epidemic waves. The SARS-CoV-2 spike protein, crucial for cellular entry, binds to the ACE2 receptor exclusively when its receptor-binding domain (RBD) adopts the up-conformation. However, whether ACE2 also interacts with the ...
Cryoelectron microscopySARS-CoV-2Virus structures
10.1038/S41467-024-52808-2
ISSN:2041-1723
Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa
Graeme Dor•Eduan Wilkinson•Darren P. Martin•Monika Moir•Derek Tshiabuila等 32 人
Nature Communications
2025
•2025/5/28
•Vol.16 No.1 p.1-10
Since November 2021, five genetically distinct SARS-CoV-2 Omicron lineages (BA.1–BA.5) are believed to have emerged in southern Africa, with four (BA.1, BA.2, BA.4, and BA.5) spreading globally and collectively dominating SARS-CoV-2 diversity. In 2023, BA.2.86, a highly divergent BA.2 lineage that r...
EpidemiologyPhylogenySARS-CoV-2Viral infection
10.1038/S41467-025-60081-0
ISSN:2041-1723
The SARS-CoV-2 Omicron BA.1 spike G446S mutation potentiates antiviral T-cell recognition
Motozono Chihiro•Toyoda Mako•Tan Toong Seng•Hamana Hiroshi•Goto Yoshihiko等 14 人
Nature Communications
2022
•2022/9/21
•Vol.13 No.1 p.1-11
Although the Omicron variant of the SARS-CoV-2 virus shows resistance to neutralizing antibody, it retains susceptibility to the cellular immune response. Here we characterize vaccine-induced T cells specific for various SARS-CoV-2 variants and identified HLA-A*24:02-restricted CD8+ T cells that str...
InfectionSARS-CoV-2T cellsViral infection
10.1038/S41467-022-33068-4
ISSN:2041-1723
Surveillance of avian influenza through bird guano in remote regions of the global south to uncover transmission dynamics
Dhammika Leshan Wannigama•Mohan Amarasiri•Phatthranit Phattharapornjaroen•Cameron Hurst•Charin Modchang等 44 人
Nature Communications
2025
•2025/5/27
•Vol.16 No.1 p.1-10
Avian influenza viruses (AIVs) pose a growing global health threat, particularly in low- and middle-income countries (LMICs), where limited surveillance capacity and under-resourced healthcare systems hinder timely detection and response. Migratory birds play a significant role in the transboundary ...
Animal migrationEpidemiologyInfluenza virusMicrobial ecologyViral infection
10.1038/S41467-025-59322-Z
ISSN:2041-1723
Clinical and virologic characteristics of the first 12 patients with coronavirus disease 2019 (COVID-19) in the United States
Nature Medicine
2020
•2020/4/23
•Vol.26 No.6 p.861-868
Data on the detailed clinical progression of COVID-19 in conjunction with epidemiological and virological characteristics are limited. In this case series, we describe the first 12 US patients confirmed to have COVID-19 from 20 January to 5 February 2020, including 4 patients described previously1–3...
Infectious diseasesRespiratory tract diseasesVirology
10.1038/S41591-020-0877-5
ISSN:1078-8956
Multiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria
Ozer Egon A.•Simons Lacy M.•Adewumi Olubusuyi M.•Fowotade Adeola A.•Omoruyi Ewean C.等 20 人
Nature Communications
2022
•2022/2/3
•Vol.13 No.1 p.1-13
Disparities in SARS-CoV-2 genomic surveillance have limited our understanding of the viral population dynamics and may delay identification of globally important variants. Despite being the most populated country in Africa, Nigeria has remained critically under sampled. Here, we report sequences fro...
EpidemiologyPhylogenomicsSARS-CoV-2Viral infection
10.1038/S41467-022-28317-5
ISSN:2041-1723
A pneumonia outbreak associated with a new coronavirus of probable bat origin
Peng Zhou•Xing-Lou Yang•Xian-Guang Wang•Ben Hu•Lei Zhang等 29 人
Nature
2020
•2020/2/3
•Vol.579 No.7798 p.270-273
Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats1–4. Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans5–7. Here we r...
PathogensSARS-CoV-2Virology
10.1038/S41586-020-2012-7
ISSN:0028-0836
The phylodynamics of SARS-CoV-2 during 2020 in Finland
Truong Nguyen Phuoc•Kant Ravi•Van den Broeck Frederik•Suvanto Maija T.•Alburkat Hussein等 27 人
Communications Medicine
2022
•2022/6/10
•Vol.2 No.1 p.1-9
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of infections and fatalities globally since its emergence in late 2019. The virus was first detected in Finland in January 2020, after which it rapidly spread among the populace in spring. However, compared to other Eur...
SARS-CoV-2Viral epidemiology
10.1038/S43856-022-00130-7
ISSN:2730-664X
Rapid evaluation of COVID-19 vaccine effectiveness against symptomatic infection with SARS-CoV-2 variants by analysis of genetic distance
Cao Lirong•Lou Jingzhi•Chan See Yeung•Zheng Hong•Liu Caiqi等 17 人
Nature Medicine
2022
•2022/6/16
•00 p.1-8
Timely evaluation of the protective effects of Coronavirus Disease 2019 (COVID-19) vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is urgently needed to inform pandemic control planning. Based on 78 vaccine efficacy or effectiveness (VE) data from 49...
Computational modelsInfectious diseases
10.1038/S41591-022-01877-1
ISSN:1078-8956
Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2
Jingsong Zhang•Yang Zhang•Jun-Yan Kang•Shuiye Chen•Yongqun He等 11 人
Cell Discovery
2021
•2021/6/15
•Vol.7 No.1 p.1-10
The presence of SARS-CoV-2 mutants, including the emerging variant B.1.1.7, has raised great concerns in terms of pathogenesis, transmission, and immune escape. Characterizing SARS-CoV-2 mutations, evolution, and effects on infectivity and pathogenicity is crucial to the design of antibody therapies...
BioinformaticsGenomic analysis
10.1038/S41421-021-00282-1
ISSN:2056-5968
Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants
Rui Wang•Jiahui Chen•Kaifu Gao•Yuta Hozumi•Changchuan Yin等 6 人
Communications Biology
2021
•2021/2/15
•Vol.4 No.1 p.1-14
SARS-CoV-2 has been mutating since it was first sequenced in early January 2020. Here, we analyze 45,494 complete SARS-CoV-2 geneome sequences in the world to understand their mutations. Among them, 12,754 sequences are from the United States. Our analysis suggests the presence of four substrains an...
Genome informaticsSARS-CoV-2Viral infection
10.1038/S42003-021-01754-6
ISSN:2399-3642
High-throughput, targeted MHC class I immunopeptidomics using a functional genetics screening platform
Bruno Peter M.•Timms Richard T.•Abdelfattah Nouran S.•Leng Yumei•Lelis Felipe J. N.等 8 人
Nature Biotechnology
2023
•2023/1/2
•00 p.1-13
Identification of CD8+ T cell epitopes is critical for the development of immunotherapeutics. Existing methods for major histocompatibility complex class I (MHC class I) ligand discovery are time intensive, specialized and unable to interrogate specific proteins on a large scale. Here, we present Ep...
Antigen processing and presentationApplied immunology
10.1038/S41587-022-01566-X
ISSN:1087-0156
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
Dami A. Collier•Anna De Marco•Isabella A. T. M. Ferreira•Bo Meng•Rawlings P. Datir等 39 人
Nature
2021
•2021/3/11
•00 p.1-10
Transmission of SARS-CoV-2 is uncontrolled in many parts of the world; control is compounded in some areas by the higher transmission potential of the B.1.1.7 variant1, which has now been reported in 94 countries. It is unclear whether the response of the virus to vaccines against SARS-CoV-2 on the ...
SARS-CoV-2VaccinesVirology
10.1038/S41586-021-03412-7
ISSN:0028-0836
SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses
Mukhlid Yousif•Said Rachida•Setshaba Taukobong•Nkosenhle Ndlovu•Chinwe Iwu-Jaja等 19 人
Nature Communications
2023
•2023/10/10
•Vol.14 No.1 p.1-9
As global SARS-CoV-2 burden and testing frequency have decreased, wastewater surveillance has emerged as a key tool to support clinical surveillance efforts. The aims of this study were to identify and characterize SARS-CoV-2 variants in wastewater samples collected from urban centers across South A...
EpidemiologyGenomicsSARS-CoV-2
10.1038/S41467-023-41369-5
ISSN:2041-1723
Low neutralization of SARS-CoV-2 Omicron BA.2.75.2, BQ.1.1 and XBB.1 by parental mRNA vaccine or a BA.5 bivalent booster
Kurhade Chaitanya•Zou Jing•Xia Hongjie•Liu Mingru•Chang Hope C.等 8 人
Nature Medicine
2022
•2022/12/6
•Vol.29 No.2 p.344-347
The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages, including the BA.2-derived BA.2.75.2 and the BA.5-derived BQ.1.1 and XBB.1, have accumulated additional spike mutations that may affect vaccine effectiveness. Here we report neutralizing activities of...
RNA vaccinesSARS-CoV-2
10.1038/S41591-022-02162-X
ISSN:1078-8956
Dominant subtype switch in avian influenza viruses during 2016–2019 in China
Yuhai Bi•Juan Li•Shanqin Li•Guanghua Fu•Tao Jin等 42 人
Nature Communications
2020
•2020/11/20
•Vol.11 No.1 p.1-12
We have surveyed avian influenza virus (AIV) genomes from live poultry markets within China since 2014. Here we present a total of 16,091 samples that were collected from May 2016 to February 2019 in 23 provinces and municipalities in China. We identify 2048 AIV-positive samples and perform next gen...
EpidemiologyGenomeInfluenza virusPhylogenetics
10.1038/S41467-020-19671-3
ISSN:2041-1723
Disruption of seasonal influenza circulation and evolution during the 2009 H1N1 and COVID-19 pandemics in Southeastern Asia
Zhiyuan Chen•Joseph L.-H. Tsui•Jun Cai•Shuo Su•Cécile Viboud等 9 人
Nature Communications
2025
•2025/1/8
•Vol.16 No.1 p.1-14
East, South, and Southeast Asia (together referred to as Southeastern Asia hereafter) have been recognized as critical areas fuelling the global circulation of seasonal influenza. However, the seasonal influenza migration network within Southeastern Asia remains unclear, including how pandemic-relat...
Influenza virusPhylogenetics
10.1038/S41467-025-55840-Y
ISSN:2041-1723
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Andrew Rambaut•Edward C. Holmes•Áine O’Toole•Verity Hill•John T. McCrone等 8 人
Nature Microbiology
2020
•2020/7/15
•Vol.5 No.11 p.1403-1407
The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor acce...
Classification and taxonomyPhylogeneticsPhylogenySARS-CoV-2Viral evolution
10.1038/S41564-020-0770-5
ISSN:2058-5276
Systematic review and integrated data analysis reveal diverse pangolin-associated microbes with infection potential
Run-Ze Ye•Xiao-Yang Wang•Yu-Yu Li•Bao-Yu Wang•Ke Song等 21 人
Nature Communications
2023
•2023/10/25
•Vol.14 No.1 p.1-10
There has been increasing global concern about the spillover transmission of pangolin-associated microbes. To assess the risk of these microbes for emergence as human pathogens, we integrated data from multiple sources to describe the distribution and spectrum of microbes harbored by pangolins. Wild...
Genome informaticsPathogensPhylogenyVirology
10.1038/S41467-023-42592-W
ISSN:2041-1723
Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events
Ou Junxian•Lan Wendong•Wu Xiaowei•Zhao Tie•Duan Biyan等 14 人
Signal Transduction And Targeted Therapy
2022
•2022/4/26
•Vol.7 No.1 p.1-9
The current pandemic of COVID-19 is fueled by more infectious emergent Omicron variants. Ongoing concerns of emergent variants include possible recombinants, as genome recombination is an important evolutionary mechanism for the emergence and re-emergence of human viral pathogens. In this study, we ...
Infectious diseasesMicrobiology
10.1038/S41392-022-00992-2
ISSN:2059-3635
Genomic surveillance of COVID-19 cases in Beijing
Pengcheng Du•Nan Ding•Jiarui Li•Fujie Zhang•Qi Wang等 28 人
Nature Communications
2020
•2020/10/30
•Vol.11 No.1 p.1-9
The spread of SARS-CoV-2 in Beijing before May, 2020 resulted from transmission following both domestic and global importation of cases. Here we present genomic surveillance data on 102 imported cases, which account for 17.2% of the total cases in Beijing. Our data suggest that all of the cases in B...
PhylogeneticsSARS-CoV-2Viral infection
10.1038/S41467-020-19345-0
ISSN:2041-1723
Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders
Qiqi Yang•Ben Wang•Phillipe Lemey•Lu Dong•Tong Mu等 20 人
Nature Communications
2024
•2024/2/6
•Vol.15 No.1 p.1-13
Highly pathogenic avian influenza virus (HPAIV) A H5, particularly clade 2.3.4.4, has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migration is currently acknowledged as an important ecolo...
Ecological epidemiologyInfluenza virusPhylogenomics
10.1038/S41467-024-45462-1
ISSN:2041-1723
A deep mutational scanning-informed protein language model predicts SARS-CoV-2 evolution dynamics with spatiotemporal resolution
Sijie Yang•Xiaowei Luo•Jiejian Luo•Fanchong Jian•Yunlong Cao
Nature Microbiology
2026
•2026/5/27
•00 p.1-14
Early identification of emerging dominant variants of pathogens such as SARS-CoV-2 is important for effective public health responses, yet existing approaches are not feasible for real-time surveillance. Here we introduce DeepCoV (DMS-Empowered Evolution Prediction of CoronaVirus), a deep-learning f...
SARS-CoV-2Viral evolutionViral infection
10.1038/S41564-026-02377-5
ISSN:2058-5276
Characterizing spatial epidemiology in a heterogeneous transmission landscape using the spatial transmission count statistic
Leke Lyu•Gabriella Veytsel•Guppy Stott•Spencer Fox•Cody Dailey等 12 人
Communications Medicine
2025
•2025/5/9
•Vol.5 No.1 p.1-9
Viral genomes contain records of geographic movements and cross-scale transmission dynamics. However, the impact of regional heterogeneity, particularly among rural and urban centers, on viral spread and epidemic trajectory has been less explored due to limited data availability. Intensive and wides...
Viral epidemiologyViral transmission
10.1038/S43856-025-00888-6
ISSN:2730-664X
Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants
Tomokazu Tamura•Jumpei Ito•Keiya Uriu•Jiri Zahradnik•Izumi Kida等 44 人
Nature Communications
2023
•2023/5/16
•Vol.14 No.1 p.1-20
In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged through the recombination of two cocirculating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer o...
SARS-CoV-2Viral evolutionVirus–host interactions
10.1038/S41467-023-38435-3
ISSN:2041-1723
Increased transmissibility of SARS-CoV-2 lineage B.1.1.7 by age and viral load
Lyngse Frederik Plesner•Mølbak Kåre•Skov Robert Leo•Christiansen Lasse Engbo•Mortensen Laust Hvas等 14 人
Nature Communications
2021
•2021/12/13
•Vol.12 No.1 p.1-8
New lineages of SARS-CoV-2 are of potential concern due to higher transmissibility, risk of severe outcomes, and/or escape from neutralizing antibodies. Lineage B.1.1.7 (the Alpha variant) became dominant in early 2021, but the association between transmissibility and risk factors, such as age of pr...
EpidemiologySARS-CoV-2Viral infection
10.1038/S41467-021-27202-X
ISSN:2041-1723
Impact of SARS-CoV-2 Gamma lineage introduction and COVID-19 vaccination on the epidemiological landscape of a Brazilian city
Banho Cecília Artico•Sacchetto Lívia•Campos Guilherme Rodrigues Fernandes•Bittar Cíntia•Possebon Fábio Sossai等 35 人
Communications Medicine
2022
•2022/4/13
•Vol.2 No.1 p.1-11
The emergence of the Brazilian variant of concern, Gamma lineage (P.1), impacted the epidemiological profile of COVID-19 cases due to its higher transmissibility rate and immune evasion ability. We sequenced 305 SARS-CoV-2 whole-genomes and performed phylogenetic analyses to identify introduction ev...
EpidemiologyViral infection
10.1038/S43856-022-00108-5
ISSN:2730-664X
Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza
Alice Fusaro•Bianca Zecchin•Bram Vrancken•Celia Abolnik•Rose Ademun等 27 人
Nature Communications
2019
•2019/11/22
•Vol.10 No.1 p.1-13
The role of Africa in the dynamics of the global spread of a zoonotic and economically-important virus, such as the highly pathogenic avian influenza (HPAI) H5Nx of the Gs/GD lineage, remains unexplored. Here we characterise the spatiotemporal patterns of virus diffusion during three HPAI H5Nx inter...
Influenza virusPhylogeneticsViral epidemiologyViral transmission
10.1038/S41467-019-13287-Y
ISSN:2041-1723
Natural evidence of coronaviral 2′-O-methyltransferase activity affecting viral pathogenesis via improved substrate RNA binding
Jikai Deng•Shimin Yang•Yingjian Li•Xue Tan•Jiejie Liu等 15 人
Signal Transduction And Targeted Therapy
2024
•2024/5/29
•Vol.9 No.1 p.1-16
Previous studies through targeted mutagenesis of K-D-K-E motif have demonstrated that 2′-O-MTase activity is essential for efficient viral replication and immune evasion. However, the K-D-K-E catalytic motif of 2′-O-MTase is highly conserved across numerous viruses, including flaviviruses, vaccinia ...
InflammationMicrobiology
10.1038/S41392-024-01860-X
ISSN:2059-3635
MHC class II proteins mediate sialic acid independent entry of human and avian H2N2 influenza A viruses
Umut Karakus•Milagros Sempere Borau•Patricia Martínez-Barragán•Josephine von Kempis•Soner Yildiz等 12 人
Nature Microbiology
2024
•2024/7/15
•00 p.1-16
Influenza A viruses (IAV) pose substantial burden on human and animal health. Avian, swine and human IAV bind sialic acid on host glycans as receptor, whereas some bat IAV require MHC class II complexes for cell entry. It is unknown how this difference evolved and whether dual receptor specificity i...
Influenza virusVirus–host interactions
10.1038/S41564-024-01771-1
ISSN:2058-5276
Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean
Tiago Gräf•Alexander A. Martinez•Gonzalo Bello•Simon Dellicour•Philippe Lemey等 21 人
Nature Communications
2024
•2024/2/28
•Vol.15 No.1 p.1-11
Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV...
EpidemiologyPhylogeneticsSARS-CoV-2
10.1038/S41467-024-46143-9
ISSN:2041-1723
A single-dose live-attenuated YF17D-vectored SARS-CoV-2 vaccine candidate
Lorena Sanchez-Felipe•Thomas Vercruysse•Sapna Sharma•Ji Ma•Viktor Lemmens等 48 人
Nature
2020
•2020/12/1
•Vol.590 No.7845 p.320-325
The expanding pandemic of coronavirus disease 2019 (COVID-19) requires the development of safe, efficacious and fast-acting vaccines. Several vaccine platforms are being leveraged for a rapid emergency response1. Here we describe the development of a candidate vaccine (YF-S0) for severe acute respir...
Live attenuated vaccinesSARS-CoV-2Viral infection
10.1038/S41586-020-3035-9
ISSN:0028-0836
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes
Irwin Jungreis•Rachel Sealfon•Manolis Kellis
Nature Communications
2021
•2021/5/11
•Vol.12 No.1 p.1-20
Despite its clinical importance, the SARS-CoV-2 gene set remains unresolved, hindering dissection of COVID-19 biology. We use comparative genomics to provide a high-confidence protein-coding gene set, characterize evolutionary constraint, and prioritize functional mutations. We select 44 Sarbecoviru...
Comparative genomicsMolecular evolutionSARS-CoV-2Sequence annotation
10.1038/S41467-021-22905-7
ISSN:2041-1723
SARS-CoV-2 infection dynamics in a MHCI-mismatched lung transplant recipient
Jonas Fuchs•Vivien Karl•Ina Hettich•Jaime Alvarado•Daniel Eckert等 34 人
Nature Communications
2025
•2025/9/16
•Vol.16 No.1 p.1-13
A 48-year-old patient underwent lung transplantation because of severe COVID-19, which aggravated his underlying interstitial lung disease, despite the presence of detectable SARS-CoV-2. Subsequently, the graft is re-infected early in the post-procedural phase, leading to viral persistence for more ...
Immunological memoryMHC class IMolecular medicineTranslational researchViral infection
10.1038/S41467-025-63681-Y
ISSN:2041-1723
Maximum likelihood pandemic-scale phylogenetics
De Maio Nicola•Kalaghatgi Prabhav•Turakhia Yatish•Corbett-Detig Russell•Minh Bui Quang等 6 人
Nature Genetics
2023
•2023/4/10
•00 p.1-7
Phylogenetics has a crucial role in genomic epidemiology. Enabled by unparalleled volumes of genome sequence data generated to study and help contain the COVID-19 pandemic, phylogenetic analyses of SARS-CoV-2 genomes have shed light on the virus’s origins, spread, and the emergence and reproductive ...
Genome informaticsGenomicsMicrobial geneticsMolecular biologySoftware
10.1038/S41588-023-01368-0
ISSN:1061-4036
STAT2 signaling restricts viral dissemination but drives severe pneumonia in SARS-CoV-2 infected hamsters
Robbert Boudewijns•Hendrik Jan Thibaut•Suzanne J. F. Kaptein•Rong Li•Valentijn Vergote等 51 人
Nature Communications
2020
•2020/11/17
•Vol.11 No.1 p.1-10
Emergence of SARS-CoV-2 causing COVID-19 has resulted in hundreds of thousands of deaths. In search for key targets of effective therapeutics, robust animal models mimicking COVID-19 in humans are urgently needed. Here, we show that Syrian hamsters, in contrast to mice, are highly permissive to SARS...
InfectionPathogensSARS-CoV-2Viral infection
10.1038/S41467-020-19684-Y
ISSN:2041-1723
Temporal lineage replacements and dominance of imported variants of concern during the COVID-19 pandemic in Kenya
Kimita Gathii•Nyataya Josphat•Omuseni Esther•Sigei Faith•Lemtudo Alan等 16 人
Communications Medicine
2022
•2022/8/17
•Vol.2 No.1 p.1-13
Kenya’s COVID-19 epidemic was seeded early in March 2020 and did not peak until early August 2020 (wave 1), late-November 2020 (wave 2), mid-April 2021 (wave 3), late August 2021 (wave 4), and mid-January 2022 (wave 5). Here, we present SARS-CoV-2 lineages associated with the five waves through anal...
Respiratory distress syndromeViral infection
10.1038/S43856-022-00167-8
ISSN:2730-664X
Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance
Rockett Rebecca J.•Draper Jenny•Gall Mailie•Sim Eby M.•Arnott Alicia等 25 人
Nature Communications
2022
•2022/5/18
•Vol.13 No.1 p.1-7
Co-infections with different variants of SARS-CoV-2 are a key precursor to recombination events that are likely to drive SARS-CoV-2 evolution. Rapid identification of such co-infections is required to determine their frequency in the community, particularly in populations at-risk of severe COVID-19,...
EpidemiologyInfectious-disease diagnosticsMicrobial genetics
10.1038/S41467-022-30518-X
ISSN:2041-1723
Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic
Yatish Turakhia•Bryan Thornlow•Angie S. Hinrichs•Nicola De Maio•Landen Gozashti等 8 人
Nature Genetics
2021
•2021/5/10
•Vol.53 No.6 p.809-816
As the SARS-CoV-2 virus spreads through human populations, the unprecedented accumulation of viral genome sequences is ushering in a new era of ‘genomic contact tracing’—that is, using viral genomes to trace local transmission dynamics. However, because the viral phylogeny is already so large—and wi...
Data processingEpidemiology
10.1038/S41588-021-00862-7
ISSN:1061-4036
Genomic features associated with sustained mammalian transmission of avian influenza A viruses
Yongtao Ye•Huiping Shuai•Yi Song•Marcus Ho-Hin Shum•David K. Smith等 15 人
Nature Microbiology
2026
•2026/1/27
•Vol.11 No.3 p.802-814
Comparably few lineages of influenza A virus (IAV) have evolved long-term sustained transmission in mammals. The reasons remain largely unknown, and the possibility of avian IAVs evolving sustained mammalian transmission is an ongoing concern. Here we measured the GC content and frequency of GC dinu...
Evolutionary geneticsInfluenza virusRisk factors
10.1038/S41564-025-02257-4
ISSN:2058-5276
COVID-19 vaccine BNT162b1 elicits human antibody and T H 1 T cell responses
Ugur Sahin•Alexander Muik•Evelyna Derhovanessian•Isabel Vogler•Lena M. Kranz等 42 人
Nature
2020
•2020/9/30
•Vol.586 No.7830 p.594-599
An effective vaccine is needed to halt the spread of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic. Recently, we reported safety, tolerability and antibody response data from an ongoing placebo-controlled, observer-blinded phase I/II coronavirus disease 2019 (COVID-19) va...
BiomarkersBiotechnologyDiseasesImmunologyMedical researchSARS-CoV-2
10.1038/S41586-020-2814-7
ISSN:0028-0836
Transmission of SARS-CoV-2 from humans to animals and potential host adaptation
Tan Cedric C. S.•Lam Su Datt•Richard Damien•Owen Christopher J.•Berchtold Dorothea等 11 人
Nature Communications
2022
•2022/5/27
•Vol.13 No.1 p.1-13
SARS-CoV-2, the causative agent of the COVID-19 pandemic, can infect a wide range of mammals. Since its spread in humans, secondary host jumps of SARS-CoV-2 from humans to multiple domestic and wild populations of mammals have been documented. Understanding the extent of adaptation to these animal h...
Molecular evolutionSARS-CoV-2Viral epidemiologyViral transmission
10.1038/S41467-022-30698-6
ISSN:2041-1723
Pathogenesis and transmission of SARS-CoV-2 in golden hamsters
Sin Fun Sia•Li-Meng Yan•Alex W. H. Chin•Kevin Fung•Ka-Tim Choy等 12 人
Nature
2020
•2020/5/14
•Vol.583 No.7818 p.834-838
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus with high nucleotide identity to SARS-CoV and to SARS-related coronaviruses that have been detected in horseshoe bats, has spread across the world and had a global effect on healthcare systems and economies1,2. A suita...
SARS-CoV-2Viral pathogenesisViral transmission
10.1038/S41586-020-2342-5
ISSN:0028-0836
Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage
Scheepers Cathrine•Everatt Josie•Amoako Daniel G.•Tegally Houriiyah•Wibmer Constantinos Kurt等 45 人
Nature Communications
2022
•2022/4/8
•Vol.13 No.1 p.1-9
Global genomic surveillance of SARS-CoV-2 has identified variants associated with increased transmissibility, neutralization resistance and disease severity. Here we report the emergence of the PANGO lineage C.1.2, detected at low prevalence in South Africa and eleven other countries. The initial C....
EpidemiologySARS-CoV-2Viral infection
10.1038/S41467-022-29579-9
ISSN:2041-1723