1
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Sinclair P, Zhao L, Beggs CB, Illingworth CJR. The airborne transmission of viruses causes tight transmission bottlenecks. Nat Commun 2024; 15:3540. [PMID: 38670957 PMCID: PMC11053022 DOI: 10.1038/s41467-024-47923-z] [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: 04/14/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The transmission bottleneck describes the number of viral particles that initiate an infection in a new host. Previous studies have used genome sequence data to suggest that transmission bottlenecks for influenza and SARS-CoV-2 involve few viral particles, but the general principles of virus transmission are not fully understood. Here we show that, across a broad range of circumstances, tight transmission bottlenecks are a simple consequence of the physical process of airborne viral transmission. We use mathematical modelling to describe the physical process of the emission and inhalation of infectious particles, deriving the result that that the great majority of transmission bottlenecks involve few viral particles. While exceptions to this rule exist, the circumstances needed to create these exceptions are likely very rare. We thus provide a physical explanation for previous inferences of bottleneck size, while predicting that tight transmission bottlenecks prevail more generally in respiratory virus transmission.
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Affiliation(s)
- Patrick Sinclair
- MRC University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Lei Zhao
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Clive B Beggs
- Carnegie School of Sport, Leeds Beckett University, Leeds, UK
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2
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Raglow Z, Surie D, Chappell JD, Zhu Y, Martin ET, Kwon JH, Frosch AE, Mohamed A, Gilbert J, Bendall EE, Bahr A, Halasa N, Talbot HK, Grijalva CG, Baughman A, Womack KN, Johnson C, Swan SA, Koumans E, McMorrow ML, Harcourt JL, Atherton LJ, Burroughs A, Thornburg NJ, Self WH, Lauring AS. SARS-CoV-2 shedding and evolution in immunocompromised hosts during the Omicron period: a multicenter prospective analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.22.23294416. [PMID: 37662226 PMCID: PMC10473782 DOI: 10.1101/2023.08.22.23294416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background Prolonged SARS-CoV-2 infections in immunocompromised hosts may predict or source the emergence of highly mutated variants. The types of immunosuppression placing patients at highest risk for prolonged infection and associated intrahost viral evolution remain unclear. Methods Adults aged ≥18 years were enrolled at 5 hospitals and followed from 4/11/2022 - 2/1/2023. Eligible patients were SARS-CoV-2-positive in the previous 14 days and had a moderate or severely immunocompromising condition or treatment. Nasal specimens were tested by rRT-PCR every 2-4 weeks until negative in consecutive specimens. Positive specimens underwent viral culture and whole genome sequencing. A Cox proportional hazards model was used to assess factors associated with duration of infection. Results We enrolled 150 patients with: B cell malignancy or anti-B cell therapy (n=18), solid organ or hematopoietic stem cell transplant (SOT/HSCT) (n=59), AIDS (n=5), non-B cell malignancy (n=23), and autoimmune/autoinflammatory conditions (n=45). Thirty-eight (25%) were rRT-PCR-positive and 12 (8%) were culture-positive ≥21 days after initial SARS-CoV-2 detection or illness onset. Patients with B cell dysfunction had longer duration of rRT-PCR-positivity compared to those with autoimmune/autoinflammatory conditions (aHR 0.32, 95% CI 0.15-0.64). Consensus (>50% frequency) spike mutations were identified in 5 individuals who were rRT-PCR-positive >56 days; 61% were in the receptor-binding domain (RBD). Mutations shared by multiple individuals were rare (<5%) in global circulation. Conclusions In this cohort, prolonged replication-competent Omicron SARS-CoV-2 infections were uncommon. Within-host evolutionary rates were similar across patients, but individuals with infections lasting >56 days accumulated spike mutations, which were distinct from those seen globally.
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Affiliation(s)
- Zoe Raglow
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Diya Surie
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Emily T Martin
- School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Jennie H Kwon
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Anne E Frosch
- Department of Medicine, Hennepin County Medical Center, Minneapolis, Minnesota
| | - Amira Mohamed
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Julie Gilbert
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Emily E Bendall
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Auden Bahr
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - H Keipp Talbot
- Departments of Medicine and Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adrienne Baughman
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kelsey N Womack
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cassandra Johnson
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sydney A Swan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Emilia Koumans
- Division of STD Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Meredith L McMorrow
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Jennifer L Harcourt
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Lydia J Atherton
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Ashley Burroughs
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Natalie J Thornburg
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Wesley H Self
- Vanderbilt Institute for Clinical and Translational Research and Department of Emergency Medicine and, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adam S Lauring
- Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
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3
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Roder AE, Johnson KEE, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lassig M, Łuksza M, Das S, Gresham D, Ghedin E. Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.05.05.442873. [PMID: 36656775 PMCID: PMC9836620 DOI: 10.1101/2021.05.05.442873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller, and use of replicate sequencing have the most significant impact on single nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false negative rates. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intrahost viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intrahost variation, viral diversity, and viral evolution. IMPORTANCE When viruses replicate inside a host, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus, nor strongly beneficial, can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in inclusion of false positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant calling tools. We used simulated and synthetic data to test their performance against a true set of variants, and then used these studies to inform variant identification in data from clinical SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.
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4
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Li B, Deng A, Li K, Hu Y, Li Z, Shi Y, Xiong Q, Liu Z, Guo Q, Zou L, Zhang H, Zhang M, Ouyang F, Su J, Su W, Xu J, Lin H, Sun J, Peng J, Jiang H, Zhou P, Hu T, Luo M, Zhang Y, Zheng H, Xiao J, Liu T, Tan M, Che R, Zeng H, Zheng Z, Huang Y, Yu J, Yi L, Wu J, Chen J, Zhong H, Deng X, Kang M, Pybus OG, Hall M, Lythgoe KA, Li Y, Yuan J, He J, Lu J. Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant. Nat Commun 2022; 13:460. [PMID: 35075154 PMCID: PMC8786931 DOI: 10.1038/s41467-022-28089-y] [Citation(s) in RCA: 184] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/04/2022] [Indexed: 12/30/2022] Open
Abstract
The SARS-CoV-2 Delta variant has spread rapidly worldwide. To provide data on its virological profile, we here report the first local transmission of Delta in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of quarantined individuals indicated that the viral loads of Delta infections, when they first become PCR-positive, were on average ~1000 times greater compared to lineage A/B infections during the first epidemic wave in China in early 2020, suggesting potentially faster viral replication and greater infectiousness of Delta during early infection. The estimated transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in 29 donor-recipient transmission pairs. However, the transmission of minor iSNVs resulted in at least 3 of the 34 substitutions that were identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.
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Affiliation(s)
- Baisheng Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Aiping Deng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Kuibiao Li
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Yao Hu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhencui Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yaling Shi
- Guangzhou 8th People's Hospital, Guangzhou, Guangdong, China
| | - Qianling Xiong
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Zhe Liu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Qianfang Guo
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lirong Zou
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huan Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Meng Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Fangzhu Ouyang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Juan Su
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Wenzhe Su
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Jing Xu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huifang Lin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jing Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jinju Peng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Huiming Jiang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Pingping Zhou
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Ting Hu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Min Luo
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yingtao Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huanying Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jianpeng Xiao
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Tao Liu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Mingkai Tan
- Guangzhou 8th People's Hospital, Guangzhou, Guangdong, China
| | - Rongfei Che
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Hanri Zeng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhonghua Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yushi Huang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jianxiang Yu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lina Yi
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jie Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jingdiao Chen
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Haojie Zhong
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaoling Deng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Min Kang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Katrina A Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Yan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China. .,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
| | - Jun Yuan
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
| | - Jianfeng He
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China. .,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
| | - Jing Lu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China. .,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China. .,Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China.
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5
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Li B, Deng A, Li K, Hu Y, Li Z, Shi Y, Xiong Q, Liu Z, Guo Q, Zou L, Zhang H, Zhang M, Ouyang F, Su J, Su W, Xu J, Lin H, Sun J, Peng J, Jiang H, Zhou P, Hu T, Luo M, Zhang Y, Zheng H, Xiao J, Liu T, Tan M, Che R, Zeng H, Zheng Z, Huang Y, Yu J, Yi L, Wu J, Chen J, Zhong H, Deng X, Kang M, Pybus OG, Hall M, Lythgoe KA, Li Y, Yuan J, He J, Lu J. Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant. Nat Commun 2022. [PMID: 35075154 DOI: 10.1101/2021.07.07.21260122] [Citation(s) in RCA: 100] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
The SARS-CoV-2 Delta variant has spread rapidly worldwide. To provide data on its virological profile, we here report the first local transmission of Delta in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of quarantined individuals indicated that the viral loads of Delta infections, when they first become PCR-positive, were on average ~1000 times greater compared to lineage A/B infections during the first epidemic wave in China in early 2020, suggesting potentially faster viral replication and greater infectiousness of Delta during early infection. The estimated transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in 29 donor-recipient transmission pairs. However, the transmission of minor iSNVs resulted in at least 3 of the 34 substitutions that were identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.
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Affiliation(s)
- Baisheng Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Aiping Deng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Kuibiao Li
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Yao Hu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhencui Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yaling Shi
- Guangzhou 8th People's Hospital, Guangzhou, Guangdong, China
| | - Qianling Xiong
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Zhe Liu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Qianfang Guo
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lirong Zou
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huan Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Meng Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Fangzhu Ouyang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Juan Su
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Wenzhe Su
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Jing Xu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huifang Lin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jing Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jinju Peng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Huiming Jiang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Pingping Zhou
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Ting Hu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Min Luo
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yingtao Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huanying Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jianpeng Xiao
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Tao Liu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Mingkai Tan
- Guangzhou 8th People's Hospital, Guangzhou, Guangdong, China
| | - Rongfei Che
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Hanri Zeng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhonghua Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yushi Huang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jianxiang Yu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lina Yi
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jie Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jingdiao Chen
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Haojie Zhong
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaoling Deng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Min Kang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Katrina A Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Yan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
| | - Jun Yuan
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
| | - Jianfeng He
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
| | - Jing Lu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China.
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6
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Li B, Deng A, Li K, Hu Y, Li Z, Shi Y, Xiong Q, Liu Z, Guo Q, Zou L, Zhang H, Zhang M, Ouyang F, Su J, Su W, Xu J, Lin H, Sun J, Peng J, Jiang H, Zhou P, Hu T, Luo M, Zhang Y, Zheng H, Xiao J, Liu T, Tan M, Che R, Zeng H, Zheng Z, Huang Y, Yu J, Yi L, Wu J, Chen J, Zhong H, Deng X, Kang M, Pybus OG, Hall M, Lythgoe KA, Li Y, Yuan J, He J, Lu J. Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant. Nat Commun 2022; 13:460. [PMID: 35075154 DOI: 10.21203/rs.3.rs-738164/v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/04/2022] [Indexed: 05/18/2023] Open
Abstract
The SARS-CoV-2 Delta variant has spread rapidly worldwide. To provide data on its virological profile, we here report the first local transmission of Delta in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of quarantined individuals indicated that the viral loads of Delta infections, when they first become PCR-positive, were on average ~1000 times greater compared to lineage A/B infections during the first epidemic wave in China in early 2020, suggesting potentially faster viral replication and greater infectiousness of Delta during early infection. The estimated transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in 29 donor-recipient transmission pairs. However, the transmission of minor iSNVs resulted in at least 3 of the 34 substitutions that were identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.
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Affiliation(s)
- Baisheng Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Aiping Deng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Kuibiao Li
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Yao Hu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhencui Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yaling Shi
- Guangzhou 8th People's Hospital, Guangzhou, Guangdong, China
| | - Qianling Xiong
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Zhe Liu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Qianfang Guo
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lirong Zou
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huan Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Meng Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Fangzhu Ouyang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Juan Su
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Wenzhe Su
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Jing Xu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huifang Lin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jing Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jinju Peng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Huiming Jiang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Pingping Zhou
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Ting Hu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Min Luo
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yingtao Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huanying Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jianpeng Xiao
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Tao Liu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Mingkai Tan
- Guangzhou 8th People's Hospital, Guangzhou, Guangdong, China
| | - Rongfei Che
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Hanri Zeng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhonghua Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yushi Huang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jianxiang Yu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lina Yi
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jie Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jingdiao Chen
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Haojie Zhong
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaoling Deng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Min Kang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Katrina A Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Yan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
| | - Jun Yuan
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
| | - Jianfeng He
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
| | - Jing Lu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China.
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7
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Li B, Deng A, Li K, Hu Y, Li Z, Shi Y, Xiong Q, Liu Z, Guo Q, Zou L, Zhang H, Zhang M, Ouyang F, Su J, Su W, Xu J, Lin H, Sun J, Peng J, Jiang H, Zhou P, Hu T, Luo M, Zhang Y, Zheng H, Xiao J, Liu T, Tan M, Che R, Zeng H, Zheng Z, Huang Y, Yu J, Yi L, Wu J, Chen J, Zhong H, Deng X, Kang M, Pybus OG, Hall M, Lythgoe KA, Li Y, Yuan J, He J, Lu J. Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant. Nat Commun 2022; 13:460. [PMID: 35075154 DOI: 10.1101/2021.1107.1107.21260122v21260122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/04/2022] [Indexed: 05/23/2023] Open
Abstract
The SARS-CoV-2 Delta variant has spread rapidly worldwide. To provide data on its virological profile, we here report the first local transmission of Delta in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of quarantined individuals indicated that the viral loads of Delta infections, when they first become PCR-positive, were on average ~1000 times greater compared to lineage A/B infections during the first epidemic wave in China in early 2020, suggesting potentially faster viral replication and greater infectiousness of Delta during early infection. The estimated transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in 29 donor-recipient transmission pairs. However, the transmission of minor iSNVs resulted in at least 3 of the 34 substitutions that were identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.
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Affiliation(s)
- Baisheng Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Aiping Deng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Kuibiao Li
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Yao Hu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhencui Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yaling Shi
- Guangzhou 8th People's Hospital, Guangzhou, Guangdong, China
| | - Qianling Xiong
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Zhe Liu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Qianfang Guo
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lirong Zou
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huan Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Meng Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Fangzhu Ouyang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Juan Su
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Wenzhe Su
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | - Jing Xu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huifang Lin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jing Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jinju Peng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Huiming Jiang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Pingping Zhou
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Ting Hu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Min Luo
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yingtao Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huanying Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jianpeng Xiao
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Tao Liu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Mingkai Tan
- Guangzhou 8th People's Hospital, Guangzhou, Guangdong, China
| | - Rongfei Che
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Hanri Zeng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhonghua Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yushi Huang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jianxiang Yu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lina Yi
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China
| | - Jie Wu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jingdiao Chen
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Haojie Zhong
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaoling Deng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Min Kang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Katrina A Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Yan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
| | - Jun Yuan
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
| | - Jianfeng He
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
| | - Jing Lu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China.
- Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, Guangdong, China.
- Guangdong Provincial Institution of Public Health, Guangzhou, Guangdong, China.
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8
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Abstract
The success of many viruses depends upon cooperative interactions between viral genomes. However, whenever cooperation occurs, there is the potential for 'cheats' to exploit that cooperation. We suggest that: (1) the biology of viruses makes viral cooperation particularly susceptible to cheating; (2) cheats are common across a wide range of viruses, including viral entities that are already well studied, such as defective interfering genomes, and satellite viruses. Consequently, the evolutionary theory of cheating could help us understand and manipulate viral dynamics, while viruses also offer new opportunities to study the evolution of cheating.
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Affiliation(s)
- Asher Leeks
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Melanie Ghoul
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
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9
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Hofstätter N, Hofer S, Duschl A, Himly M. Children's Privilege in COVID-19: The Protective Role of the Juvenile Lung Morphometry and Ventilatory Pattern on Airborne SARS-CoV-2 Transmission to Respiratory Epithelial Barriers and Disease Severity. Biomedicines 2021; 9:1414. [PMID: 34680531 PMCID: PMC8533273 DOI: 10.3390/biomedicines9101414] [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: 08/30/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 11/17/2022] Open
Abstract
The incidence of severe COVID-19 in children is low, and underlying mechanisms for lower SARS-CoV-2 susceptibility and self-limiting disease severity are poorly understood. Severe clinical manifestations in adults require SARS-CoV-2 inoculation in the lower respiratory tract, establishing a pulmonary disease phase. This may be either accomplished by direct inoculation of the thoracic region upon exposure to virion-laden aerosols, or by infection of the upper respiratory system and aspiration of virion-laden aerosols originating right there into the lower respiratory tract. The particularities of epithelial barriers as the anatomical site of first viral deposition specifically determine the initial characteristics of an innate immune response, emerging respiratory tissue damage and dysfunctionality, and hence, severity of clinical symptoms. We, thus, investigated by in silico modeling whether the combined effect of juvenile lung morphometry, children's ventilatory pattern and the peculiarities of the virion-laden aerosols' properties, render children more resilient to aerosol deposition in the lower respiratory tract. Our study presents evidence for major age-dependent differences of the regional virion-laden aerosol deposition. We identified deposition hotspots in the alveolar-interstitial region of the young adult. Our data reveal that children are void of corresponding hotspots. The inoculum quantum in the alveolar-interstitial region hotspots is found to be considerably related to age. Our results suggest that children are intrinsically protected against SARS-CoV-2 inoculation in the lower respiratory tract, which may help to explain the lower risk of severe clinical manifestations associated with a pulmonary phase.
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Affiliation(s)
| | | | | | - Martin Himly
- Department of Biosciences, Paris Lodron University of Salzburg (PLUS), 5020 Salzburg, Austria; (N.H.); (S.H.); (A.D.)
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10
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Tonkin-Hill G, Martincorena I, Amato R, Lawson ARJ, Gerstung M, Johnston I, Jackson DK, Park N, Lensing SV, Quail MA, Gonçalves S, Ariani C, Spencer Chapman M, Hamilton WL, Meredith LW, Hall G, Jahun AS, Chaudhry Y, Hosmillo M, Pinckert ML, Georgana I, Yakovleva A, Caller LG, Caddy SL, Feltwell T, Khokhar FA, Houldcroft CJ, Curran MD, Parmar S, Alderton A, Nelson R, Harrison EM, Sillitoe J, Bentley SD, Barrett JC, Torok ME, Goodfellow IG, Langford C, Kwiatkowski D. Patterns of within-host genetic diversity in SARS-CoV-2. eLife 2021; 10:e66857. [PMID: 34387545 PMCID: PMC8363274 DOI: 10.7554/elife.66857] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.
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Affiliation(s)
| | | | | | | | | | | | | | - Naomi Park
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | | | | | | | | | | | | | - Luke W Meredith
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Grant Hall
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Aminu S Jahun
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Myra Hosmillo
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Malte L Pinckert
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Iliana Georgana
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Anna Yakovleva
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Laura G Caller
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Sarah L Caddy
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Theresa Feltwell
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Fahad A Khokhar
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of CambridgeCambridgeUnited Kingdom
| | | | | | | | | | | | | | - Ewan M Harrison
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- European Bioinformatics InstituteHinxtonUnited Kingdom
| | | | | | | | - M Estee Torok
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Ian G Goodfellow
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | | | - Dominic Kwiatkowski
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
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11
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Gu H, Xie R, Adam DC, Tsui JLH, Chu DK, Chang LD, Cheuk SS, Gurung S, Krishnan P, Ng DY, Liu GY, Wan CK, Edwards KM, Leung KS, Wu JT, Tsang DN, Leung GM, Cowling BJ, Peiris M, Lam TT, Dhanasekaran V, Poon LL. SARS-CoV-2 under an elimination strategy in Hong Kong. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.06.19.21259169. [PMID: 34189537 PMCID: PMC8240692 DOI: 10.1101/2021.06.19.21259169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Hong Kong utilized an elimination strategy with intermittent use of public health and social measures and increasingly stringent travel regulations to control SARS-CoV-2 transmission. By analyzing >1700 genome sequences representing 17% of confirmed cases from 23-January-2020 to 26-January-2021, we reveal the effects of fluctuating control measures on the evolution and epidemiology of SARS-CoV-2 lineages in Hong Kong. Despite numerous importations, only three introductions were responsible for 90% of locally-acquired cases, two of which circulated cryptically for weeks while less stringent measures were in place. We found that SARS-CoV-2 within-host diversity was most similar among transmission pairs and epidemiological clusters due to a strong transmission bottleneck through which similar genetic background generates similar within-host diversity. ONE SENTENCE SUMMARY Out of the 170 detected introductions of SARS-CoV-2 in Hong Kong during 2020, three introductions caused 90% of community cases.
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Affiliation(s)
- Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ruopeng Xie
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Dillon C. Adam
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Joseph L.-H. Tsui
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Daniel K. Chu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lydia D.J. Chang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Sammi S.Y. Cheuk
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Shreya Gurung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Daisy Y.M. Ng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Gigi Y.Z. Liu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Carrie K.C. Wan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kimberly M. Edwards
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kathy S.M. Leung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong, China
| | - Joseph T. Wu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong, China
| | - Dominic N.C. Tsang
- Centre for Health Protection, Department of Health, The Government of Hong Kong Special Administrative Region, Hong Kong, China
| | - Gabriel M. Leung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong, China
| | - Benjamin J. Cowling
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong, China
| | - Tommy T.Y. Lam
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong, China
| | - Vijaykrishna Dhanasekaran
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Leo L.M. Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong, China
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12
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Sender R, Bar-On YM, Gleizer S, Bernshtein B, Flamholz A, Phillips R, Milo R. The total number and mass of SARS-CoV-2 virions. Proc Natl Acad Sci U S A 2021; 118:e2024815118. [PMID: 34083352 PMCID: PMC8237675 DOI: 10.1073/pnas.2024815118] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Quantitatively describing the time course of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection within an infected individual is important for understanding the current global pandemic and possible ways to combat it. Here we integrate the best current knowledge about the typical viral load of SARS-CoV-2 in bodily fluids and host tissues to estimate the total number and mass of SARS-CoV-2 virions in an infected person. We estimate that each infected person carries 109 to 1011 virions during peak infection, with a total mass in the range of 1 μg to 100 μg, which curiously implies that all SARS-CoV-2 virions currently circulating within human hosts have a collective mass of only 0.1 kg to 10 kg. We combine our estimates with the available literature on host immune response and viral mutation rates to demonstrate how antibodies markedly outnumber the spike proteins, and the genetic diversity of virions in an infected host covers all possible single nucleotide substitutions.
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Affiliation(s)
- Ron Sender
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yinon M Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Biana Bernshtein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Avi Flamholz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Department of Physics, California Institute of Technology, Pasadena, CA 91125
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel;
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13
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Cobey S, Larremore DB, Grad YH, Lipsitch M. Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination. Nat Rev Immunol 2021; 21:330-335. [PMID: 33795856 PMCID: PMC8014893 DOI: 10.1038/s41577-021-00544-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2021] [Indexed: 12/18/2022]
Abstract
When vaccines are in limited supply, expanding the number of people who receive some vaccine, such as by halving doses or increasing the interval between doses, can reduce disease and mortality compared with concentrating available vaccine doses in a subset of the population. A corollary of such dose-sparing strategies is that the vaccinated individuals may have less protective immunity. Concerns have been raised that expanding the fraction of the population with partial immunity to SARS-CoV-2 could increase selection for vaccine-escape variants, ultimately undermining vaccine effectiveness. We argue that, although this is possible, preliminary evidence instead suggests such strategies should slow the rate of viral escape from vaccine or naturally induced immunity. As long as vaccination provides some protection against escape variants, the corresponding reduction in prevalence and incidence should reduce the rate at which new variants are generated and the speed of adaptation. Because there is little evidence of efficient immune selection of SARS-CoV-2 during typical infections, these population-level effects are likely to dominate vaccine-induced evolution.
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Affiliation(s)
- Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
| | - Daniel B Larremore
- Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Marc Lipsitch
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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14
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Lythgoe KA, Hall M, Ferretti L, de Cesare M, MacIntyre-Cockett G, Trebes A, Andersson M, Otecko N, Wise EL, Moore N, Lynch J, Kidd S, Cortes N, Mori M, Williams R, Vernet G, Justice A, Green A, Nicholls SM, Ansari MA, Abeler-Dörner L, Moore CE, Peto TEA, Eyre DW, Shaw R, Simmonds P, Buck D, Todd JA, Connor TR, Ashraf S, da Silva Filipe A, Shepherd J, Thomson EC, Bonsall D, Fraser C, Golubchik T. SARS-CoV-2 within-host diversity and transmission. Science 2021; 372:eabg0821. [PMID: 33688063 PMCID: PMC8128293 DOI: 10.1126/science.abg0821] [Citation(s) in RCA: 224] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/03/2021] [Indexed: 12/14/2022]
Abstract
Extensive global sampling and sequencing of the pandemic virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have enabled researchers to monitor its spread and to identify concerning new variants. Two important determinants of variant spread are how frequently they arise within individuals and how likely they are to be transmitted. To characterize within-host diversity and transmission, we deep-sequenced 1313 clinical samples from the United Kingdom. SARS-CoV-2 infections are characterized by low levels of within-host diversity when viral loads are high and by a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with minimal persistence of shared diversity, patterns that are readily observable on the phylogenetic tree. Our results suggest that transmission-enhancing and/or immune-escape SARS-CoV-2 variants are likely to arise infrequently but could spread rapidly if successfully transmitted.
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Affiliation(s)
- Katrina A Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.
| | - Luca Ferretti
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Mariateresa de Cesare
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Amy Trebes
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Monique Andersson
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
- Division of Medical Virology, Stellenbosch University, Stellenbosch, South Africa
| | - Newton Otecko
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Emma L Wise
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Nathan Moore
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
| | - Jessica Lynch
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
| | - Stephen Kidd
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
| | - Nicholas Cortes
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
- Gibraltar Health Authority, Gibraltar, UK
| | - Matilde Mori
- School of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Rebecca Williams
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
| | - Gabrielle Vernet
- Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK
| | - Anita Justice
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
| | - Angie Green
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Samuel M Nicholls
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - M Azim Ansari
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Lucie Abeler-Dörner
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Catrin E Moore
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Timothy E A Peto
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
| | - David W Eyre
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
- Big Data Institute, Nuffield Department of Public Health, University of Oxford, Old Road Campus, Oxford OX3 7FL, UK
| | - Robert Shaw
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
| | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - David Buck
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - John A Todd
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff CF10 4BZ, UK
- Cardiff University School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Shirin Ashraf
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | | | - James Shepherd
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - David Bonsall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
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15
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Sender R, Bar-On YM, Gleizer S, Bernsthein B, Flamholz A, Phillips R, Milo R. The total number and mass of SARS-CoV-2 virions. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.11.16.20232009. [PMID: 33236021 PMCID: PMC7685332 DOI: 10.1101/2020.11.16.20232009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Quantitatively describing the time course of the SARS-CoV-2 infection within an infected individual is important for understanding the current global pandemic and possible ways to combat it. Here we integrate the best current knowledge about the typical viral load of SARS-CoV-2 in bodily fluids and host tissues to estimate the total number and mass of SARS-CoV-2 virions in an infected person. We estimate that each infected person carries 109-1011 virions during peak infection, with a total mass in the range of 1-100 μg, which curiously implies that all SARS-CoV-2 virions currently circulating within human hosts have a collective mass of only 0.1-10 kg. We combine our estimates with the available literature on host immune response and viral mutation rates to demonstrate how antibodies markedly outnumber the spike proteins and the genetic diversity of virions in an infected host covers all possible single nucleotide substitutions.
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Affiliation(s)
- Ron Sender
- Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | | | - Biana Bernsthein
- Weizmann Institute of Science, Rehovot 7610001, Israel
- Present address: Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02138, USA
| | - Avi Flamholz
- California Institute of Technology, Pasadena, CA 91125, USA
| | - Rob Phillips
- California Institute of Technology, Pasadena, CA 91125, USA
- Chan Zuckerberg Biohub, 499 Illinois Street, SF CA 94158, USA
| | - Ron Milo
- Weizmann Institute of Science, Rehovot 7610001, Israel
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