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Wang X, Zhang J, Liu M, Guo Y, Guo P, Yang X, Shang B, Li M, Tian J, Zhang T, Wang X, Jin R, Zhou J, Gao GF, Liu J. Nonconserved epitopes dominate reverse preexisting T cell immunity in COVID-19 convalescents. Signal Transduct Target Ther 2024; 9:160. [PMID: 38866784 PMCID: PMC11169541 DOI: 10.1038/s41392-024-01876-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/30/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024] Open
Abstract
The herd immunity against SARS-CoV-2 is continuously consolidated across the world during the ongoing pandemic. However, the potential function of the nonconserved epitopes in the reverse preexisting cross-reactivity induced by SARS-CoV-2 to other human coronaviruses is not well explored. In our research, we assessed T cell responses to both conserved and nonconserved peptides shared by SARS-CoV-2 and SARS-CoV, identifying cross-reactive CD8+ T cell epitopes using enzyme-linked immunospot and intracellular cytokine staining assays. Then, in vitro refolding and circular dichroism were performed to evaluate the thermal stability of the HLA/peptide complexes. Lastly, single-cell T cell receptor reservoir was analyzed based on tetramer staining. Here, we discovered that cross-reactive T cells targeting SARS-CoV were present in individuals who had recovered from COVID-19, and identified SARS-CoV-2 CD8+ T cell epitopes spanning the major structural antigens. T cell responses induced by the nonconserved peptides between SARS-CoV-2 and SARS-CoV were higher and played a dominant role in the cross-reactivity in COVID-19 convalescents. Cross-T cell reactivity was also observed within the identified series of CD8+ T cell epitopes. For representative immunodominant peptide pairs, although the HLA binding capacities for peptides from SARS-CoV-2 and SARS-CoV were similar, the TCR repertoires recognizing these peptides were distinct. Our results could provide beneficial information for the development of peptide-based universal vaccines against coronaviruses.
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Affiliation(s)
- Xin Wang
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Jie Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Institute of Infectious Diseases, Beijing, 100015, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, P.R. China
| | - Maoshun Liu
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yuanyuan Guo
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Peipei Guo
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Xiaonan Yang
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Bingli Shang
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Min Li
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Jinmin Tian
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Ting Zhang
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Xi Wang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Institute of Infectious Diseases, Beijing, 100015, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, P.R. China
| | - Ronghua Jin
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Institute of Infectious Diseases, Beijing, 100015, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, P.R. China
| | - Jikun Zhou
- Shijiazhuang Fifth Hospital, Shijiazhuang, 050011, China.
| | - George F Gao
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jun Liu
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China.
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
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2
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Bae KH, Shunmuganathan B, Zhang L, Lim A, Gupta R, Wang Y, Chua BL, Wang Y, Gu Y, Qian X, Tan ISL, Purushotorman K, MacAry PA, White KP, Yang YY. Durable cross-protective neutralizing antibody responses elicited by lipid nanoparticle-formulated SARS-CoV-2 mRNA vaccines. NPJ Vaccines 2024; 9:43. [PMID: 38396073 PMCID: PMC10891077 DOI: 10.1038/s41541-024-00835-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
The advent of SARS-CoV-2 variants with defined mutations that augment pathogenicity and/or increase immune evasiveness continues to stimulate global efforts to improve vaccine formulation and efficacy. The extraordinary advantages of lipid nanoparticles (LNPs), including versatile design, scalability, and reproducibility, make them ideal candidates for developing next-generation mRNA vaccines against circulating SARS-CoV-2 variants. Here, we assess the efficacy of LNP-encapsulated mRNA booster vaccines encoding the spike protein of SARS-CoV-2 for variants of concern (Delta, Omicron) and using a predecessor (YN2016C isolated from bats) strain spike protein to elicit durable cross-protective neutralizing antibody responses. The mRNA-LNP vaccines have desirable physicochemical characteristics, such as small size (~78 nm), low polydispersity index (<0.13), and high encapsulation efficiency (>90%). We employ in vivo bioluminescence imaging to illustrate the capacity of our LNPs to induce robust mRNA expression in secondary lymphoid organs. In a BALB/c mouse model, a three-dose subcutaneous immunization of mRNA-LNPs vaccines achieved remarkably high levels of cross-neutralization against the Omicron B1.1.529 and BA.2 variants for extended periods of time (28 weeks) with good safety profiles for all constructs when used in a booster regime, including the YN2016C bat virus sequences. These findings have important implications for the design of mRNA-LNP vaccines that aim to trigger durable cross-protective immunity against the current and newly emerging variants.
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Affiliation(s)
- Ki Hyun Bae
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore
| | - Bhuvaneshwari Shunmuganathan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Republic of Singapore
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore
| | - Li Zhang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore
| | - Andrew Lim
- Provaxus, Inc, Dover, Delaware, 19901, USA
| | - Rashi Gupta
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Republic of Singapore
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore
| | - Yanming Wang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore
| | - Boon Lin Chua
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore
| | - Yang Wang
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis St, Singapore, 138672, Republic of Singapore
| | - Yue Gu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Republic of Singapore
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore
| | - Xinlei Qian
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore
| | - Isabelle Siang Ling Tan
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore
| | - Kiren Purushotorman
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Republic of Singapore
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore
| | - Paul A MacAry
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Republic of Singapore.
- NUS-Cambridge Immune Phenotyping Centre (NCIPC), Life Sciences Institute, National University of Singapore, Singapore, 117456, Republic of Singapore.
| | - Kevin P White
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis St, Singapore, 138672, Republic of Singapore.
- Department of Biochemistry and Precision Medicine Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Republic of Singapore.
| | - Yi Yan Yang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Republic of Singapore.
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3
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Zachariah A, Krishnankutty SP, Manazhi J, Omanakuttan V, Santosh S, Blanchard A, Tarlinton R. Lack of detection of SARS-CoV-2 in wildlife from Kerala, India in 2020-21. Access Microbiol 2024; 6:000686.v3. [PMID: 38361659 PMCID: PMC10866034 DOI: 10.1099/acmi.0.000686.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
Spillover of SARS-CoV-2 into a variety of wild and domestic animals has been an ongoing feature of the human pandemic. The establishment of a new reservoir in white-tailed deer in North America and increasing divergence of the viruses circulating in them from those circulating in the human population has highlighted the ongoing risk this poses for global health. Some parts of the world have seen more intensive monitoring of wildlife species for SARS-CoV-2 and related coronaviruses but there are still very large gaps in geographical and species-specific information. This paper reports negative results for SARS-CoV-2 PCR based testing using a pan coronavirus end point RDRP PCR and a Sarbecovirus specific E gene qPCR on lung and or gut tissue from wildlife from the Indian State of Kerala. These animals included: 121 Rhinolophus rouxii (Rufous Horsehoe Bat), six Rhinolophus bedommei (Lesser Woolly Horseshoe Bat), 15 Rossettus leschenaultii (Fulvous Fruit Bat), 47 Macaca radiata (Bonnet macaques), 35 Paradoxurus hermaphroditus (Common Palm Civet), five Viverricula indica (Small Indian Civet), four Herpestes edwardsii (Common Mongoose), ten Panthera tigris (Bengal Tiger), eight Panthera pardus fusca (Indian Leopard), four Prionailurus bengalensis (Leopard cats), two Felis chaus (Jungle cats), two Cuon alpinus (Wild dogs) and one Melursus ursinus (sloth bear).
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Affiliation(s)
| | | | | | | | | | - Adam Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Rachael Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
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4
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Zhao P, Shao N, Dong J, Su H, Sui H, Zhang T, Yang F. Genetic diversity and characterization of rhinoviruses from Chinese clinical samples with a global perspective. Microbiol Spectr 2023; 11:e0084023. [PMID: 37733296 PMCID: PMC10715137 DOI: 10.1128/spectrum.00840-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 08/03/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE Based on clinical samples collected in China, we detected and reported 22 types for the first time in China, as well as three types for the first time in Asia, and reported their genetic characteristics and diversity. We identified a novel type of Rhinovirus (RV), A110, highlighting its unique genetic features. We annotated the genomic structure and serotype of all the existing RV sequences in the database, and four novel RV types were identified and their genetic diversity reported. Combined with the sequence annotation, we constructed a complete VP1 data set of RV and conducted the first large-scale evolutionary dynamics analysis of RV. Based on a high-quality data set, we conducted a comprehensive analysis of the guanine-cytosine (GC) content variations among serotypes of RVs. This study provides crucial theoretical support and valuable data for understanding RV's genetic diversity and developing antiviral strategies.
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Affiliation(s)
- Peng Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Shao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haoxiang Su
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongtao Sui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
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5
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Liu B, Zhao P, Xu P, Han Y, Wang Y, Chen L, Wu Z, Yang J. A comprehensive dataset of animal-associated sarbecoviruses. Sci Data 2023; 10:681. [PMID: 37805633 PMCID: PMC10560225 DOI: 10.1038/s41597-023-02558-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/11/2023] [Indexed: 10/09/2023] Open
Abstract
Zoonotic spillover of sarbecoviruses (SarbeCoVs) from non-human animals to humans under natural conditions has led to two large-scale pandemics, the severe acute respiratory syndrome (SARS) pandemic in 2003 and the ongoing COVID-19 pandemic. Knowledge of the genetic diversity, geographical distribution, and host specificity of SarbeCoVs is therefore of interest for pandemic surveillance and origin tracing of SARS-CoV and SARS-CoV-2. This study presents a comprehensive repository of publicly available animal-associated SarbeCoVs, covering 1,535 viruses identified from 63 animal species distributed in 43 countries worldwide (as of February 14,2023). Relevant meta-information, such as host species, sampling time and location, was manually curated and included in the dataset to facilitate further research on the potential patterns of viral diversity and ecological characteristics. In addition, the dataset also provides well-annotated sequence sets of receptor-binding domains (RBDs) and receptor-binding motifs (RBMs) for the scientific community to highlight the potential determinants of successful cross-species transmission that could be aid in risk estimation and strategic design for future emerging infectious disease control and prevention.
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Affiliation(s)
- Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Peng Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Panpan Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Yelin Han
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Yuyang Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China.
| | - Zhiqiang Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China.
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 110730, China.
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6
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Temmam S, Tu TC, Regnault B, Bonomi M, Chrétien D, Vendramini L, Duong TN, Phong TV, Yen NT, Anh HN, Son TH, Anh PT, Amara F, Bigot T, Munier S, Thong VD, van der Werf S, Nam VS, Eloit M. Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence. Viruses 2023; 15:1897. [PMID: 37766303 PMCID: PMC10536463 DOI: 10.3390/v15091897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/11/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Bats are a major reservoir of zoonotic viruses, including coronaviruses. Since the emergence of SARS-CoV in 2002/2003 in Asia, important efforts have been made to describe the diversity of Coronaviridae circulating in bats worldwide, leading to the discovery of the precursors of epidemic and pandemic sarbecoviruses in horseshoe bats. We investigated the viral communities infecting horseshoe bats living in Northern Vietnam, and report here the first identification of sarbecoviruses in Rhinolophus thomasi and Rhinolophus siamensis bats. Phylogenetic characterization of seven strains of Vietnamese sarbecoviruses identified at least three clusters of viruses. Recombination and cross-species transmission between bats seemed to constitute major drivers of virus evolution. Vietnamese sarbecoviruses were mainly enteric, therefore constituting a risk of spillover for guano collectors or people visiting caves. To evaluate the zoonotic potential of these viruses, we analyzed in silico and in vitro the ability of their RBDs to bind to mammalian ACE2s and concluded that these viruses are likely restricted to their bat hosts. The workflow applied here to characterize the spillover potential of novel sarbecoviruses is of major interest for each time a new virus is discovered, in order to concentrate surveillance efforts on high-risk interfaces.
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Affiliation(s)
- Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
| | - Tran Cong Tu
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Béatrice Regnault
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
| | - Massimiliano Bonomi
- Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR3528, Université Paris Cité, 75015 Paris, France
| | - Delphine Chrétien
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
| | - Léa Vendramini
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
| | - Tran Nhu Duong
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Tran Vu Phong
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Nguyen Thi Yen
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Hoang Ngoc Anh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Tran Hai Son
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Pham Tuan Anh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Faustine Amara
- Institut Pasteur, G5 Evolutionary Genomics of RNA Viruses, Université Paris Cité, 75015 Paris, France
| | - Thomas Bigot
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université Paris Cité, 75015 Paris, France
| | - Sandie Munier
- Institut Pasteur, G5 Evolutionary Genomics of RNA Viruses, Université Paris Cité, 75015 Paris, France
| | - Vu Dinh Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology (VAST), Hanoi 70072, Vietnam
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses Unit, Institut Pasteur, CNRS UMR 3569, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, National Reference Center for Respiratory Viruses, Université Paris Cité, 75015 Paris, France
| | - Vu Sinh Nam
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Institut Pasteur, The OIE Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Université Paris Cité, 75015 Paris, France
- Ecole Nationale Vétérinaire d’Alfort, University of Paris-Est, 77420 Maisons-Alfort, France
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7
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Han Y, Xu P, Wang Y, Zhao W, Zhang J, Zhang S, Wang J, Jin Q, Wu Z. Panoramic analysis of coronaviruses carried by representative bat species in Southern China to better understand the coronavirus sphere. Nat Commun 2023; 14:5537. [PMID: 37684236 PMCID: PMC10491624 DOI: 10.1038/s41467-023-41264-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Bats, recognized as considerable reservoirs for coronaviruses (CoVs), serve as natural hosts for several highly pathogenic CoVs, including SARS-CoV and SARS-CoV-2. Investigating the bat CoV community provides insights into the origin for highly pathogenic CoVs and highlights bat CoVs with potential spillover risks. This study probes the evolution, recombination, host range, geographical distribution, and cross-species transmission characteristics of bat CoVs across China and its associated CoVs in other regions. Through detailed research on 13,064 bat samples from 14 provinces of China, 1141 CoV strains are found across 10 subgenera and one unclassified Alpha-CoV, generating 399 complete genome sequences. Within bat CoVs, 11 new CoV species are identified and 425 recombination events are detected. Bats in southern China, particularly in Yunnan province, exhibit a pronounced diversity of CoVs. Limited sampling and low detection rates exist for CoVs in Myotacovirus, Nyctacovirus, Hibecovirus, Nobecovirus in China. The genus Myotis is highlighted as a potential ancestral host for Alpha-CoV, with the genus Hipposideros suggested as a likely progenitor host for bat-associated Beta-CoV, indicating the complexity of cross-species transmission dynamics. Through the comprehensive analysis, this study enriches the understanding of bat CoVs and offers a valuable resource for future research.
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Affiliation(s)
- Yelin Han
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China
| | - Panpan Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuyang Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China
| | - Wenliang Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China
| | - Junpeng Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China.
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China.
| | - Zhiqiang Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China.
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences, Beijing, China.
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8
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Apaa T, Withers AJ, Staley C, Blanchard A, Bennett M, Bremner-Harrison S, Chadwick EA, Hailer F, Harrison SWR, Loose M, Mathews F, Tarlinton R. Sarbecoviruses of British horseshoe bats; sequence variation and epidemiology. J Gen Virol 2023; 104. [PMID: 37319000 DOI: 10.1099/jgv.0.001859] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
Horseshoe bats are the natural hosts of the Sarbecovirus subgenus that includes SARS-CoV and SARS-CoV- 2. Despite the devastating impact of the COVID-19 pandemic, there is still little known about the underlying epidemiology and virology of sarbecoviruses in their natural hosts, leaving large gaps in our pandemic preparedness. Here we describe the results of PCR testing for sarbecoviruses in the two horseshoe bat species (Rhinolophus hipposideros and R. ferrumequinum) present in Great Britain, collected in 2021-22 during the peak of COVID-19 pandemic. One hundred and ninety seven R. hipposideros samples from 33 roost sites and 277 R. ferrumequinum samples from 20 roost sites were tested. No coronaviruses were detected in any samples from R. ferrumequinum whereas 44 and 56 % of individual and pooled (respectively) faecal samples from R. hipposideros across multiple roost sites tested positive in a sarbecovirus-specific qPCR. Full genome sequences were generated from three of the positive samples (and partial genomes from two more) using Illumina RNAseq on unenriched samples. Phylogenetic analyses showed that the obtained sequences belong to the same monophyletic clade, with >95 % similarity to previously-reported European isolates from R. hipposideros. The sequences differed in the presence or absence of accessory genes ORF 7b, 9b and 10. All lacked the furin cleavage site of SARS-CoV-2 spike gene and are therefore unlikely to be infective for humans. These results demonstrate a lack, or at least low incidence, of SARS-CoV-2 spill over from humans to susceptible GB bats, and confirm that sarbecovirus infection is widespread in R. hipposideros. Despite frequently sharing roost sites with R. ferrumequinum, no evidence of cross-species transmission was found.
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Affiliation(s)
- Ternenge Apaa
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
- Animal and Plant Health Agency (APHA), Addlestone, UK
| | - Amy J Withers
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
- Animal and Plant Health Agency (APHA), Addlestone, UK
| | - Ceri Staley
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Adam Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Malcolm Bennett
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Samantha Bremner-Harrison
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, UK
- Vincent Wildlife Trust, Herefordshire, UK
| | - Elizabeth A Chadwick
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, UK
- Organisms and Environment, School of Biosciences, Cardiff University, UK
| | - Frank Hailer
- Organisms and Environment, School of Biosciences, Cardiff University, UK
| | - Stephen W R Harrison
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Southwell, UK
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Fiona Mathews
- School of Life sciences, University of Sussex, Brighton, UK
| | - Rachael Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
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9
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Cao Y, Chen L, Chen H, Cun Y, Dai X, Du H, Gao F, Guo F, Guo Y, Hao P, He S, He S, He X, Hu Z, Hoh BP, Jin X, Jiang Q, Jiang Q, Khan A, Kong HZ, Li J, Li SC, Li Y, Lin Q, Liu J, Liu Q, Lu J, Lu X, Luo S, Nie Q, Qiu Z, Shi T, Song X, Su J, Tao SC, Wang C, Wang CC, Wang GD, Wang J, Wu Q, Wu S, Xu S, Xue Y, Yang W, Yang Z, Ye K, Ye YN, Yu L, Zhao F, Zhao Y, Zhai W, Zhang D, Zhang L, Zheng H, Zhou Q, Zhu T, Zhang YP. Was Wuhan the early epicenter of the COVID-19 pandemic?-A critique. Natl Sci Rev 2023; 10:nwac287. [PMID: 37089192 PMCID: PMC10116607 DOI: 10.1093/nsr/nwac287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Yanan Cao
- Ruijin Hospital, Shanghai Jiao Tong University, China
| | - Lingling Chen
- College of Life Science and Technology, Guangxi University, China
| | - Hua Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, China
| | - Yupeng Cun
- Children's Hospital of Chongqing Medical University, China
| | - Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, China
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, China
| | - Fengbiao Guo
- School of Pharmaceutical Sciences, Wuhan University, China
| | - Yalong Guo
- Institute of Botany, Chinese Academy of Sciences, China
| | - Pei Hao
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, China
| | - Shunmin He
- Institute of Biophysics, Chinese Academy of Sciences, China
| | - Shunping He
- Institute of Hydrobiology, Chinese Academy of Sciences, China
| | - XiongLei He
- School of Life Sciences, Sun Yat-sen University, China
| | - Zheng Hu
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, China
| | - Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, University College Sedaya International, Malaysia
| | - Xin Jin
- School of Medicine, South China University of Technology, China
| | - Qian Jiang
- Department of Medical Genetics, Capital Institute of Pediatrics, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, China
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University, Pakistan
| | - Hong-Zhi Kong
- Institute of Botany, Chinese Academy of Sciences, China
| | - Jinchen Li
- Xiangya Hospital, Central South University, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, China
| | - Ying Li
- College of Life Science and Technology, Foshan University, China
| | - Qiang Lin
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | | | - Qi Liu
- School of Life Sciences and Technology, Tongji University, China
| | - Jian Lu
- School of Life Sciences, Peking University, China
| | - Xuemei Lu
- Kunming Institute of Zoology, Chinese Academy of Sciences, China
| | - Shujin Luo
- School of Life Sciences, Peking University, China
| | - Qinghua Nie
- College of Animal Science, South China Agricultural University, China
| | - Zilong Qiu
- Institute of Neuroscience, Chinese Academy of Sciences, China
| | - Tieliu Shi
- School of Life Sciences, East China Normal University, China
| | - Xiaofeng Song
- Nanjing University of Aeronautics and Astronautics, China
| | - Jianzhong Su
- Wenzhou Institute, University of Chinese Academy of Sciences, China
| | - Sheng-ce Tao
- Institute of Systems Biomedicine, Shanghai Jiao Tong University, China
| | - Chaolong Wang
- Tongji Medical College, Huazhong University of Science and Technology, China
| | | | - Guo-Dong Wang
- Kunming Institute of Zoology, Chinese Academy of Sciences, China
| | - Jiguang Wang
- Division of Life Science and Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, China
| | - Qi Wu
- Institute of Microbiology, Chinese Academy of Sciences, China
| | - Shaoyuan Wu
- School of Life Sciences, Jiangsu Normal University, China
| | - Shuhua Xu
- School of Life Sciences, Fudan University, China
| | - Yu Xue
- College of Life Science and Technology, Huazhong University of Science and Technology, China
| | - Wenjun Yang
- International Center for Aging and Cancer, Hainan Medical University, China
| | - Zhaohui Yang
- Academy of Medical Science, Zhengzhou University, China
| | - Kai Ye
- Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, China
| | - Yuan-Nong Ye
- Bioinformatics and BioMedical Bigdata Mining Laboratory, School of Big Health, Guizhou Medical University, China
| | - Li Yu
- School of Life Sciences, Yunnan University, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, China
| | - Yiqiang Zhao
- College of Biological Sciences, China Agricultural University, China
| | - Weiwei Zhai
- Institute of Zoology, Chinese Academy of Sciences, China
| | - Dandan Zhang
- Department of Pathology, and Department of Medical Oncology of the Second Affiliated Hospital, Zhejiang University School of Medicine, China
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, China
| | | | - Qi Zhou
- Life Sciences Institute, Zhejiang University, China
| | - Tianqi Zhu
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, China
| | - Ya-ping Zhang
- Kunming Institute of Zoology, Chinese Academy of Sciences, China
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10
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Ruan Y, Wen H, Hou M, Zhai W, Xu S, Lu X. On the epicenter of COVID-19 and the origin of the pandemic strain. Natl Sci Rev 2023; 10:nwac286. [PMID: 37089190 PMCID: PMC10115162 DOI: 10.1093/nsr/nwac286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, China
| | - Mei Hou
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, China
| | - Weiwei Zhai
- Institute of Zoology, Chinese Academy of Sciences, China
| | - Shuhua Xu
- School of Life Sciences, Fudan University, China
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution; Yunnan Key Laboratory of Biodiversity Information Kunming Institute of Zoology, Chinese Academy of Sciences, China
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11
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Discovery and characterization of novel paramyxoviruses from bat samples in China. Virol Sin 2023; 38:198-207. [PMID: 36649817 PMCID: PMC10176441 DOI: 10.1016/j.virs.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 11/14/2022] [Indexed: 01/15/2023] Open
Abstract
Many paramyxoviruses are responsible for a variety of mild to severe human and animal diseases. Based on the novel discoveries over the past several decades, the family Paramyxoviridae infecting various hosts across the world includes 4 subfamilies, 17 classified genera and 78 species now. However, no systematic surveys of bat paramyxoviruses are available from the Chinese mainland. In this study, 13,064 samples from 54 bat species were collected and a comprehensive paramyxovirus survey was conducted. We obtained 94 new genome sequences distributed across paramyxoviruses from 22 bat species in seven provinces. Bayesian phylodynamic and phylogenetic analyses showed that there were four different lineages in the Jeilongvirus genus. Based on available data, results of host and region switches showed that the bat colony was partial to interior, whereas the rodent colony was exported, and the felines and hedgehogs were most likely the intermediate hosts from Scotophilus spp. rather than rodents. Based on the evolutionary trend, genus Jeilongvirus may have originated from Mus spp. in Australia, then transmitted to bats and rodents in Africa, Asia and Europe, and finally to bats and rodents in America.
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12
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Dagotto G, Ventura JD, Martinez DR, Anioke T, Chung BS, Siamatu M, Barrett J, Miller J, Schäfer A, Yu J, Tostanoski LH, Wagh K, Baric RS, Korber B, Barouch DH. Immunogenicity and protective efficacy of a rhesus adenoviral vaccine targeting conserved COVID-19 replication transcription complex. NPJ Vaccines 2022; 7:125. [PMID: 36302778 PMCID: PMC9610341 DOI: 10.1038/s41541-022-00553-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 10/11/2022] [Indexed: 11/08/2022] Open
Abstract
The COVID-19 pandemic marks the third coronavirus pandemic this century (SARS-CoV-1, MERS, SARS-CoV-2), emphasizing the need to identify and evaluate conserved immunogens for a pan-sarbecovirus vaccine. Here we investigate the potential utility of a T-cell vaccine strategy targeting conserved regions of the sarbecovirus proteome. We identified the most conserved regions of the sarbecovirus proteome as portions of the RNA-dependent RNA polymerase (RdRp) and Helicase proteins, both of which are part of the coronavirus replication transcription complex (RTC). Fitness constraints suggest that as SARS-CoV-2 continues to evolve these regions may better preserve cross-reactive potential of T-cell responses than Spike, Nucleocapsid, or Membrane proteins. We sought to determine if vaccine-elicited T-cell responses to the highly conserved regions of the RTC would reduce viral loads following challenge with SARS-CoV-2 in mice using a rhesus adenovirus serotype 52 (RhAd52) vector. The RhAd52.CoV.Consv vaccine generated robust cellular immunity in mice and led to significant reductions in viral loads in the nasal turbinates following challenge with a mouse-adapted SARS-CoV-2. These data suggest the potential utility of T-cell targeting of conserved regions for a pan-sarbecovirus vaccine.
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Affiliation(s)
- Gabriel Dagotto
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - John D Ventura
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Benjamin S Chung
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Mazuba Siamatu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Julia Barrett
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jessica Miller
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Lisa H Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- The New Mexico Consortium, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- The New Mexico Consortium, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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