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Agius JE, Johnson-Mackinnon JC, Fong W, Gall M, Lam C, Basile K, Kok J, Arnott A, Sintchenko V, Rockett RJ. SARS-CoV-2 Within-Host and in vitro Genomic Variability and Sub-Genomic RNA Levels Indicate Differences in Viral Expression Between Clinical Cohorts and in vitro Culture. Front Microbiol 2022; 13:824217. [PMID: 35663867 PMCID: PMC9161297 DOI: 10.3389/fmicb.2022.824217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/18/2022] [Indexed: 12/23/2022] Open
Abstract
Background Low frequency intrahost single nucleotide variants (iSNVs) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have been increasingly recognised as predictive indicators of positive selection. Particularly as growing numbers of SARS-CoV-2 variants of interest (VOI) and concern (VOC) emerge. However, the dynamics of subgenomic RNA (sgRNA) expression and its impact on genomic diversity and infection outcome remain poorly understood. This study aims to investigate and quantify iSNVs and sgRNA expression in single and longitudinally sampled cohorts over the course of mild and severe SARS-CoV-2 infection, benchmarked against an in vitro infection model. Methods Two clinical cohorts of SARS-CoV-2 positive cases in New South Wales, Australia collected between March 2020 and August 2021 were sequenced. Longitudinal samples from cases hospitalised due to SARS-CoV-2 infection (severe) (n = 16) were analysed and compared with cases that presented with SARS-CoV-2 symptoms but were not hospitalised (mild) (n = 23). SARS-CoV-2 genomic diversity profiles were also examined from daily sampling of culture experiments for three SARS-CoV-2 variants (Lineage A, B.1.351, and B.1.617.2) cultured in VeroE6 C1008 cells (n = 33). Results Intrahost single nucleotide variants were detected in 83% (19/23) of the mild cohort cases and 100% (16/16) of the severe cohort cases. SNP profiles remained relatively fixed over time, with an average of 1.66 SNPs gained or lost, and an average of 4.2 and 5.9 low frequency variants per patient were detected in severe and mild infection, respectively. sgRNA was detected in 100% (25/25) of the mild genomes and 92% (24/26) of the severe genomes. Total sgRNA expressed across all genes in the mild cohort was significantly higher than that of the severe cohort. Significantly higher expression levels were detected in the spike and the nucleocapsid genes. There was significantly less sgRNA detected in the culture dilutions than the clinical cohorts. Discussion and Conclusion The positions and frequencies of iSNVs in the severe and mild infection cohorts were dynamic overtime, highlighting the importance of continual monitoring, particularly during community outbreaks where multiple SARS-CoV-2 variants may co-circulate. sgRNA levels can vary across patients and the overall level of sgRNA reads compared to genomic RNA can be less than 1%. The relative contribution of sgRNA to the severity of illness warrants further investigation given the level of variation between genomes. Further monitoring of sgRNAs will improve the understanding of SARS-CoV-2 evolution and the effectiveness of therapeutic and public health containment measures during the pandemic.
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Affiliation(s)
- Jessica E. Agius
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Jessica C. Johnson-Mackinnon
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
- *Correspondence: Jessica C. Johnson-Mackinnon,
| | - Winkie Fong
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Mailie Gall
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Connie Lam
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Kerri Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Alicia Arnott
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
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Pang X, Li P, Zhang L, Que L, Dong M, Xie B, Wang Q, Wei Y, Xie X, Li L, Yin C, Wei L, Huang K, Hua Y, Zhou Q, Li Y, Yu L, Li W, Mo Z, Zhang M, Leng J, Hu Y. Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. Front Microbiol 2021; 12:753823. [PMID: 34733263 PMCID: PMC8558435 DOI: 10.3389/fmicb.2021.753823] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/20/2021] [Indexed: 12/28/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Understanding the influence of mutations in the SARS-CoV-2 gene on clinical outcomes is critical for treatment and prevention. Here, we analyzed all high-coverage complete SARS-CoV-2 sequences from GISAID database from January 1, 2020, to January 1, 2021, to mine the mutation hotspots associated with clinical outcome and developed a model to predict the clinical outcome in different epidemic strains. Exploring the cause of mutation based on RNA-dependent RNA polymerase (RdRp) and RNA-editing enzyme, mutation was more likely to occur in severe and mild cases than in asymptomatic cases, especially A > G, C > T, and G > A mutations. The mutations associated with asymptomatic outcome were mainly in open reading frame 1ab (ORF1ab) and N genes; especially R6997P and V30L mutations occurred together and were correlated with asymptomatic outcome with high prevalence. D614G, Q57H, and S194L mutations were correlated with mild and severe outcome with high prevalence. Interestingly, the single-nucleotide variant (SNV) frequency was higher with high percentage of nt14408 mutation in RdRp in severe cases. The expression of ADAR and APOBEC was associated with clinical outcome. The model has shown that the asymptomatic percentage has increased over time, while there is high symptomatic percentage in Alpha, Beta, and Gamma. These findings suggest that mutation in the SARS-CoV-2 genome may have a direct association with clinical outcomes and pandemic. Our result and model are helpful to predict the prevalence of epidemic strains and to further study the mechanism of mutation causing severe disease.
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Affiliation(s)
- Xianwu Pang
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Pu Li
- PFOMIC Bioinformatics Company, Nanning, China
| | - Lifeng Zhang
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases With Integrative Medicine, Guangxi University of Chinese Medicine, Nanning, China
| | - Lusheng Que
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Min Dong
- School of Pharmacy, Guangxi Medical University, Nanning, China
| | - Bo Xie
- School of Information and Management, Guangxi Medical University, Nanning, China
| | - Qihui Wang
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yinfeng Wei
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Xing Xie
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Lanxiang Li
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Chunyue Yin
- The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, China
| | - Liuchun Wei
- The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, China
| | - Kexin Huang
- School of Information and Management, Guangxi Medical University, Nanning, China
| | - Yiming Hua
- School of Information and Management, Guangxi Medical University, Nanning, China
| | - Qingniao Zhou
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yingfang Li
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Lei Yu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Weidong Li
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Maosheng Zhang
- School of Information and Management, Guangxi Medical University, Nanning, China
| | - Jing Leng
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases With Integrative Medicine, Guangxi University of Chinese Medicine, Nanning, China
| | - Yanling Hu
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
- School of Information and Management, Guangxi Medical University, Nanning, China
- Life Sciences Institute, Guangxi Medical University, Nanning, China
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
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3
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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: 92] [Impact Index Per Article: 30.7] [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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Holmes MV, Richardson TG, Ference BA, Davies NM, Davey Smith G. Integrating genomics with biomarkers and therapeutic targets to invigorate cardiovascular drug development. Nat Rev Cardiol 2021; 18:435-453. [PMID: 33707768 DOI: 10.1038/s41569-020-00493-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 01/30/2023]
Abstract
Drug development in cardiovascular disease is stagnating, with lack of efficacy and adverse effects being barriers to innovation. Human genetics can provide compelling evidence of causation through approaches such as Mendelian randomization, with genetic support for causation increasing the probability of a clinical trial succeeding. Mendelian randomization applied to quantitative traits can identify risk factors for disease that are both causal and amenable to therapeutic modification. However, important differences exist between genetic investigations of a biomarker (such as HDL cholesterol) and a drug target aimed at modifying the same biomarker of interest (such as cholesteryl ester transfer protein), with implications for the methodology, interpretation and application of Mendelian randomization to drug development. Differences include the comparative nature of the genetic architecture - that is, biomarkers are typically polygenic, whereas protein drug targets are influenced by either cis-acting or trans-acting genetic variants - and the potential for drug targets to show disease associations that might differ from those of the biomarker that they are intended to modify (target-mediated pleiotropy). In this Review, we compare and contrast the use of Mendelian randomization to evaluate potential drug targets versus quantitative traits. We explain how genetic epidemiological studies can be used to assess the aetiological roles of biomarkers in disease and to prioritize drug targets, including designing their evaluation in clinical trials.
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Affiliation(s)
- Michael V Holmes
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK.
| | - Tom G Richardson
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Brian A Ference
- Centre for Naturally Randomised Trials, University of Cambridge, Cambridge, UK
| | - Neil M Davies
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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5
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Armero A, Berthet N, Avarre JC. Intra-Host Diversity of SARS-Cov-2 Should Not Be Neglected: Case of the State of Victoria, Australia. Viruses 2021; 13:133. [PMID: 33477885 PMCID: PMC7833370 DOI: 10.3390/v13010133] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/05/2021] [Accepted: 01/14/2021] [Indexed: 12/14/2022] Open
Abstract
Since the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the etiological agent of the current COVID-19 pandemic, a rapid and massive effort has been made to obtain the genomic sequences of this virus to monitor (in near real time) the phylodynamic and diversity of this new pathogen. However, less attention has been given to the assessment of intra-host diversity. RNA viruses such as SARS-CoV-2 inhabit the host as a population of variants called quasispecies. We studied the quasispecies diversity in four of the main SARS-CoV-2 genes (ORF1a, ORF1b, S and N genes), using a dataset consisting of 210 next-generation sequencing (NGS) samples collected between January and early April of 2020 in the State of Victoria, Australia. We found evidence of quasispecies diversity in 68% of the samples, 76% of which was nonsynonymous variants with a higher density in the spike (S) glycoprotein and ORF1a genes. About one-third of the nonsynonymous intra-host variants were shared among the samples, suggesting host-to-host transmission. Quasispecies diversity changed over time. Phylogenetic analysis showed that some of the intra-host single-nucleotide variants (iSNVs) were restricted to specific lineages, highlighting their potential importance in the epidemiology of this virus. A greater effort must be made to determine the magnitude of the genetic bottleneck during transmission and the epidemiological and/or evolutionary factors that may play a role in the changes in the diversity of quasispecies over time.
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Affiliation(s)
- Alix Armero
- The Center for Microbes, Development and Health, Institut Pasteur of Shanghai—Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens, Shanghai 200000, China;
| | - Nicolas Berthet
- The Center for Microbes, Development and Health, Institut Pasteur of Shanghai—Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens, Shanghai 200000, China;
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6
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De Maio N, Walker CR, Turakhia Y, Lanfear R, Corbett-Detig R, Goldman N. Mutation rates and selection on synonymous mutations in SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.14.426705. [PMID: 33469589 PMCID: PMC7814826 DOI: 10.1101/2021.01.14.426705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The COVID-19 pandemic has seen an unprecedented response from the sequencing community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes, we study mutation rates and selective pressures affecting the virus. Understanding the processes and effects of mutation and selection has profound implications for the study of viral evolution, for vaccine design, and for the tracking of viral spread. We highlight and address some common genome sequence analysis pitfalls that can lead to inaccurate inference of mutation rates and selection, such as ignoring skews in the genetic code, not accounting for recurrent mutations, and assuming evolutionary equilibrium. We find that two particular mutation rates, G→U and C→U, are similarly elevated and considerably higher than all other mutation rates, causing the majority of mutations in the SARS-CoV-2 genome, and are possibly the result of APOBEC and ROS activity. These mutations also tend to occur many times at the same genome positions along the global SARS-CoV-2 phylogeny (i.e., they are very homoplasic). We observe an effect of genomic context on mutation rates, but the effect of the context is overall limited. While previous studies have suggested selection acting to decrease U content at synonymous sites, we bring forward evidence suggesting the opposite.
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Affiliation(s)
- Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Conor R Walker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Yatish Turakhia
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
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7
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Braun KM, Moreno GK, Halfmann PJ, Hodcroft EB, Baker DA, Boehm EC, Weiler AM, Haj AK, Hatta M, Chiba S, Maemura T, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.11.16.384917. [PMID: 33236011 PMCID: PMC7685321 DOI: 10.1101/2020.11.16.384917] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts and, potentially, undergo antigenic evolution depend on the ways genetic variation is generated and selected within and between individual hosts. Using domestic cats as a model, we show that SARS-CoV-2 consensus sequences remain largely unchanged over time within hosts, while dynamic sub-consensus diversity reveals processes of genetic drift and weak purifying selection. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. This variant arises rapidly and persists at intermediate frequencies in index cats. It also becomes fixed following transmission in two of three pairs. These dynamics suggest this site may be under positive selection in this system and illustrate how a variant can quickly arise and become fixed in parallel across multiple transmission pairs. Transmission of SARS-CoV-2 in cats involved a narrow bottleneck, with new infections founded by fewer than ten viruses. In RNA virus evolution, stochastic processes like narrow transmission bottlenecks and genetic drift typically act to constrain the overall pace of adaptive evolution. Our data suggest that here, positive selection in index cats followed by a narrow transmission bottleneck may have instead accelerated the fixation of S H655Y, a potentially beneficial SARS-CoV-2 variant. Overall, our study suggests species- and context-specific adaptations are likely to continue to emerge. This underscores the importance of continued genomic surveillance for new SARS-CoV-2 variants as well as heightened scrutiny for signatures of SARS-CoV-2 positive selection in humans and mammalian model systems.
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Affiliation(s)
- Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Emma B Hodcroft
- Institute of Social and Preventative Medicine, University of Bern, Bern, Switzerland
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Emma C Boehm
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Andrea M Weiler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Amelia K Haj
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Masato Hatta
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Shiho Chiba
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Tadashi Maemura
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Katia Koelle
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
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