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Odigie AE, Capozza P, Tempesta M, Decaro N, Pratelli A. Epidemiological investigation of enteric canine coronaviruses in domestic dogs: A systematic review and meta-analysis. Res Vet Sci 2024; 174:105289. [PMID: 38749265 DOI: 10.1016/j.rvsc.2024.105289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 06/11/2024]
Abstract
Canine enteric coronavirus (CeCoV) is a globally distributed enteric pathogen that causes significant harm to canines. The objective of this systematic review was to examine the global dissemination of CeCoV and assess the potential for infected canines to be exposed to various CeCoV genotypes and subtypes. With an aggregated prevalence of 18.8%, the study predicted regional variations, indicating that CeCoV is an exceptionally prevalent disease. The increased likelihood that infected canines will be asymptomatic is a significant cause for concern, as undetected cases of CeCoV infection could persist and spread the disease. This underscores the significance of ongoing surveillance of CeCoV in order to avert its transmission. Nevertheless, further investigation is necessary in order to ascertain the moderators that significantly impact the prevalence and distribution of distinct subtypes and genotypes of CeCoV. Hence, it is imperative to undertake randomized clinical trials in order to acquire a more accurate understanding of the variables that influence the prevalence of CeCoV. By conducting ongoing surveillance, regional variations in the prevalence of CeCoV in canines can be accounted for, thereby enhancing our comprehension of the illness and ultimately impeding its transmission.
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Affiliation(s)
| | - Paolo Capozza
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Maria Tempesta
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Annamaria Pratelli
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy.
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2
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Tolentino JE, Lytras S, Ito J, Sato K. Recombination analysis on the receptor switching event of MERS-CoV and its close relatives: implications for the emergence of MERS-CoV. Virol J 2024; 21:84. [PMID: 38600521 PMCID: PMC11008012 DOI: 10.1186/s12985-024-02358-2] [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: 11/21/2023] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND PlMERS-CoV is a coronavirus known to cause severe disease in humans, taxonomically classified under the subgenus Merbecovirus. Recent findings showed that the close relatives of MERS-CoV infecting vespertillionid bats (family Vespertillionidae), named NeoCoV and PDF-2180, use their hosts' ACE2 as their entry receptor, unlike the DPP4 receptor usage of MERS-CoV. Previous research suggests that this difference in receptor usage between these related viruses is a result of recombination. However, the precise location of the recombination breakpoints and the details of the recombination event leading to the change of receptor usage remain unclear. METHODS We used maximum likelihood-based phylogenetics and genetic similarity comparisons to characterise the evolutionary history of all complete Merbecovirus genome sequences. Recombination events were detected by multiple computational methods implemented in the recombination detection program. To verify the influence of recombination, we inferred the phylogenetic relation of the merbecovirus genomes excluding recombinant segments and that of the viruses' receptor binding domains and examined the level of congruency between the phylogenies. Finally, the geographic distribution of the genomes was inspected to identify the possible location where the recombination event occurred. RESULTS Similarity plot analysis and the recombination-partitioned phylogenetic inference showed that MERS-CoV is highly similar to NeoCoV (and PDF-2180) across its whole genome except for the spike-encoding region. This is confirmed to be due to recombination by confidently detecting a recombination event between the proximal ancestor of MERS-CoV and a currently unsampled merbecovirus clade. Notably, the upstream recombination breakpoint was detected in the N-terminal domain and the downstream breakpoint at the S2 subunit of spike, indicating that the acquired recombined fragment includes the receptor-binding domain. A tanglegram comparison further confirmed that the receptor binding domain-encoding region of MERS-CoV was acquired via recombination. Geographic mapping analysis on sampling sites suggests the possibility that the recombination event occurred in Africa. CONCLUSION Together, our results suggest that recombination can lead to receptor switching of merbecoviruses during circulation in bats. These results are useful for future epidemiological assessments and surveillance to understand the spillover risk of bat coronaviruses to the human population.
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Affiliation(s)
- Jarel Elgin Tolentino
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Spyros Lytras
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
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3
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Xiong Q, Ma C, Liu C, Tong F, Huang M, Yan H. ACE2-using merbecoviruses: Further evidence of convergent evolution of ACE2 recognition by NeoCoV and other MERS-CoV related viruses. CELL INSIGHT 2024; 3:100145. [PMID: 38476250 PMCID: PMC10928290 DOI: 10.1016/j.cellin.2023.100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 03/14/2024]
Abstract
Angiotensin-converting enzyme 2 (ACE2) was recognized as an entry receptor shared by coronaviruses from Sarbecovirus and Setracovirus subgenera, including three human coronaviruses: SARS-CoV, SARS-CoV-2, and NL63. We recently disclosed that NeoCoV and three other merbecoviruses (PDF-2180, MOW15-22, PnNL 2018B), which are MERS-CoV relatives found in African and European bats, also utilize ACE2 as their functional receptors through unique receptor binding mechanisms. This unexpected receptor usage assumes significance, particularly in light of the prior recognition of Dipeptidyl peptidase-4 (DPP4) as the only known protein receptor for merbecoviruses. In contrast to other ACE2-using coronaviruses, NeoCoV and PDF-2180 engage a distinct and relatively compact binding surface on ACE2, facilitated by protein-glycan interactions, which is demonstrated by the Cryo-EM structures of the receptor binding domains (RBDs) of these viruses in complex with a bat ACE2 orthologue. These findings further support the hypothesis that phylogenetically distant coronaviruses, characterized by distinct RBD structures, can independently evolve to acquire ACE2 affinity during inter-species transmission and adaptive evolution. To date, these viruses have exhibited limited efficiency in entering human cells, although single mutations like T510F in NeoCoV can overcome the incompatibility with human ACE2. In this review, we present a comprehensive overview of ACE2-using merbecoviruses, summarize our current knowledge regarding receptor usage and host tropism determination, and deliberate on potential strategies for prevention and intervention, with the goal of mitigating potential future outbreaks caused by spillover of these viruses.
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Affiliation(s)
- Qing Xiong
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Chengbao Ma
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Chen Liu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Fei Tong
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Meiling Huang
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Huan Yan
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430072, China
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4
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Wells HL, Bonavita CM, Navarrete-Macias I, Vilchez B, Rasmussen AL, Anthony SJ. The coronavirus recombination pathway. Cell Host Microbe 2023; 31:874-889. [PMID: 37321171 PMCID: PMC10265781 DOI: 10.1016/j.chom.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Recombination is thought to be a mechanism that facilitates cross-species transmission in coronaviruses, thus acting as a driver of coronavirus spillover and emergence. Despite its significance, the mechanism of recombination is poorly understood, limiting our potential to estimate the risk of novel recombinant coronaviruses emerging in the future. As a tool for understanding recombination, here, we outline a framework of the recombination pathway for coronaviruses. We review existing literature on coronavirus recombination, including comparisons of naturally observed recombinant genomes as well as in vitro experiments, and place the findings into the recombination pathway framework. We highlight gaps in our understanding of coronavirus recombination illustrated by the framework and outline how further experimental research is critical for disentangling the molecular mechanism of recombination from external environmental pressures. Finally, we describe how an increased understanding of the mechanism of recombination can inform pandemic predictive intelligence, with a retrospective emphasis on SARS-CoV-2.
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Affiliation(s)
- Heather L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA; Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
| | - Cassandra M Bonavita
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Isamara Navarrete-Macias
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Blake Vilchez
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
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5
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Intragenomic rearrangements involving 5'-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses. Virol J 2023; 20:36. [PMID: 36829234 PMCID: PMC9957694 DOI: 10.1186/s12985-023-01998-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses that was first documented in an infectious isolate of the betacoronavirus SARS-CoV-2, obtained from 3 patients in Hong Kong that had a 5'-untranslated region segment at the end of the ORF6 gene that in its new location translated into an ORF6 protein with a predicted modified carboxyl terminus. While comparing the amino acid sequences of translated ORF8 genes in the GenBank database, we found a subsegment of the same 5'-UTR-derived amino acid sequence modifying the distal end of ORF8 of an isolate from the United States and decided to carry out a systematic search. METHODS Using the nucleotide and in the case of SARS-CoV-2 also the translated amino acid sequence in three reading frames of the genomic termini of coronaviruses as query sequences, we searched for 5'-UTR sequences in regions other than the 5'-UTR in SARS-CoV-2 and reference strains of alpha-, beta-, gamma-, and delta-coronaviruses. RESULTS We here report numerous genomic insertions of 5'-untranslated region sequences into coding regions of SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses, but not delta- or gammacoronaviruses. To our knowledge this is the first systematic description of such insertions. In many cases, these insertions would change viral protein sequences and further foster genomic flexibility and viral adaptability through insertion of transcription regulatory sequences in novel positions within the genome. Among human Embecorivus betacoronaviruses, for instance, from 65% to all of the surveyed sequences in publicly available databases contain inserted 5'-UTR sequences. CONCLUSION The intragenomic rearrangements involving 5'-untranslated region sequences described here, which in several cases affect highly conserved genes with a low propensity for recombination, may underlie the generation of variants homotypic with those of concern or interest and with potentially differing pathogenic profiles. Intragenomic rearrangements thus add to our appreciation of how variants of SARS-CoV-2 and other beta- and alphacoronaviruses may arise.
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6
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Influence of viral genome properties on polymerase fidelity. Trends Genet 2023; 39:9-14. [PMID: 36402624 DOI: 10.1016/j.tig.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/27/2022] [Accepted: 10/30/2022] [Indexed: 11/17/2022]
Abstract
The first step of viral evolution takes place during genome replication via the error-prone viral polymerase. Among the mutants that arise through this process, only a few well-adapted variants will be selected by natural selection, renewing the viral genome population. Viral polymerase-mediated errors are thought to occur stochastically. However, accumulating evidence suggests that viral polymerase-mediated mutations are heterogeneously distributed throughout the viral genome. Here, we review work that supports this concept and provides mechanistic insights into how specific features of the viral genome could modulate viral polymerase-mediated errors. A predisposition to accumulate viral polymerase-mediated errors at specific loci in the viral genome may guide evolution to specific pathways, thus opening new directions of research to better understand viral evolutionary dynamics.
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7
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Rojas-Cruz AF, Gallego-Gómez JC, Bermúdez-Santana CI. RNA structure-altering mutations underlying positive selection on Spike protein reveal novel putative signatures to trace crossing host-species barriers in Betacoronavirus. RNA Biol 2022; 19:1019-1044. [PMID: 36102368 PMCID: PMC9481089 DOI: 10.1080/15476286.2022.2115750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Similar to other RNA viruses, the emergence of Betacoronavirus relies on cross-species viral transmission, which requires careful health surveillance monitoring of protein-coding information as well as genome-wide analysis. Although the evolutionary jump from natural reservoirs to humans may be mainly traced-back by studying the effect that hotspot mutations have on viral proteins, it is largely unexplored if other impacts might emerge on the structured RNA genome of Betacoronavirus. In this survey, the protein-coding and viral genome architecture were simultaneously studied to uncover novel insights into cross-species horizontal transmission events. We analysed 1,252,952 viral genomes of SARS-CoV, MERS-CoV, and SARS-CoV-2 distributed across the world in bats, intermediate animals, and humans to build a new landscape of changes in the RNA viral genome. Phylogenetic analyses suggest that bat viruses are the most closely related to the time of most recent common ancestor of Betacoronavirus, and missense mutations in viral proteins, mainly in the S protein S1 subunit: SARS-CoV (G > T; A577S); MERS-CoV (C > T; S746R and C > T; N762A); and SARS-CoV-2 (A > G; D614G) appear to have driven viral diversification. We also found that codon sites under positive selection on S protein overlap with non-compensatory mutations that disrupt secondary RNA structures in the RNA genome complement. These findings provide pivotal factors that might be underlying the eventual jumping the species barrier from bats to intermediate hosts. Lastly, we discovered that nearly half of the Betacoronavirus genomes carry highly conserved RNA structures, and more than 90% of these RNA structures show negative selection signals, suggesting essential functions in the biology of Betacoronavirus that have not been investigated to date. Further research is needed on negatively selected RNA structures to scan for emerging functions like the potential of coding virus-derived small RNAs and to develop new candidate antiviral therapeutic strategies.
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Affiliation(s)
- Alexis Felipe Rojas-Cruz
- Theoretical and Computational RNomics Group, Department of Biology, Faculty of Sciences, National University of Colombia, Bogota Colombia
| | - Juan Carlos Gallego-Gómez
- Molecular and Translational Medicine Group, Faculty of Medicine, University of Antioquia, Medellin Colombia
| | - Clara Isabel Bermúdez-Santana
- Theoretical and Computational RNomics Group, Department of Biology, Faculty of Sciences, National University of Colombia, Bogota Colombia
- Center of Excellence in Scientific Computing, National University of Colombia, Bogota Colombia
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8
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Ku X, Zhang C, Li P, Yu X, Sun Q, Xu F, Qian P, He Q. Epidemiological and genetic characteristics of porcine circovirus 3 in 15 provinces and municipalities of China between 2016 and 2020. Virol J 2022; 19:187. [PMID: 36376944 PMCID: PMC9661739 DOI: 10.1186/s12985-022-01893-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Porcine circovirus 3 (PCV3) is a newly emerging virus and has been found associated with porcine dermatitis and nephropathy syndrome in pigs. Compared with PCV2, research into PCV3 cap gene sequencing is deficient. To investigate the prevalence and genotype distribution of PCV3, we collected 1291 samples from 211 pig farms throughout 15 provinces and municipalities. 312 out of 1291 samples were tested positive by PCR. We further sequenced and analyzed 164 PCR-positive samples. The majority (61.8%) of isolates we sequenced belong to genotype PCV3c. PCV3c is also the dominant genotype in Hubei, Hunan, Hebei province and Chongqing city. We found 3 sites under positive selection and located in predicted epitope peptide, revealing that the pig’s immunity may be a reason those sites are undergoing highly positive selection.
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Turakhia Y, Thornlow B, Hinrichs A, McBroome J, Ayala N, Ye C, Smith K, De Maio N, Haussler D, Lanfear R, Corbett-Detig R. Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape. Nature 2022; 609:994-997. [PMID: 35952714 PMCID: PMC9519458 DOI: 10.1038/s41586-022-05189-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
Accurate and timely detection of recombinant lineages is crucial for interpreting genetic variation, reconstructing epidemic spread, identifying selection and variants of interest, and accurately performing phylogenetic analyses1-4. During the SARS-CoV-2 pandemic, genomic data generation has exceeded the capacities of existing analysis platforms, thereby crippling real-time analysis of viral evolution5. Here, we use a new phylogenomic method to search a nearly comprehensive SARS-CoV-2 phylogeny for recombinant lineages. In a 1.6 million sample tree from May 2021, we identify 589 recombination events, which indicate that around 2.7% of sequenced SARS-CoV-2 genomes have detectable recombinant ancestry. Recombination breakpoints are inferred to occur disproportionately in the 3' portion of the genome that contains the spike protein. Our results highlight the need for timely analyses of recombination for pinpointing the emergence of recombinant lineages with the potential to increase transmissibility or virulence of the virus. We anticipate that this approach will empower comprehensive real-time tracking of viral recombination during the SARS-CoV-2 pandemic and beyond.
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Affiliation(s)
- Yatish Turakhia
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, USA.
| | - Bryan Thornlow
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Angie Hinrichs
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jakob McBroome
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Nicolas Ayala
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Cheng Ye
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, USA
| | - Kyle Smith
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - David Haussler
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
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Forni D, Cagliani R, Pozzoli U, Mozzi A, Arrigoni F, De Gioia L, Clerici M, Sironi M. Dating the Emergence of Human Endemic Coronaviruses. Viruses 2022; 14:v14051095. [PMID: 35632836 PMCID: PMC9148137 DOI: 10.3390/v14051095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 01/09/2023] Open
Abstract
Four endemic coronaviruses infect humans and cause mild symptoms. Because previous analyses were based on a limited number of sequences and did not control for effects that affect molecular dating, we re-assessed the timing of endemic coronavirus emergence. After controlling for recombination, selective pressure, and molecular clock model, we obtained similar tMRCA (time to the most recent common ancestor) estimates for the four coronaviruses, ranging from 72 (HCoV-229E) to 54 (HCoV-NL63) years ago. The split times of HCoV-229E and HCoV-OC43 from camel alphacoronavirus and bovine coronavirus were dated ~268 and ~99 years ago. The split times of HCoV-HKU1 and HCoV-NL63 could not be calculated, as their zoonoticic sources are unknown. To compare the timing of coronavirus emergence to that of another respiratory virus, we recorded the occurrence of influenza pandemics since 1500. Although there is no clear relationship between pandemic occurrence and human population size, the frequency of influenza pandemics seems to intensify starting around 1700, which corresponds with the initial phase of exponential increase of human population and to the emergence of HCoV-229E. The frequency of flu pandemics in the 19th century also suggests that the concurrence of HCoV-OC43 emergence and the Russian flu pandemic may be due to chance.
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Affiliation(s)
- Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
- Correspondence:
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
| | - Uberto Pozzoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
| | - Alessandra Mozzi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy; (F.A.); (L.D.G.)
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy; (F.A.); (L.D.G.)
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, 20122 Milan, Italy;
- Don Carlo Gnocchi Foundation ONLUS, IRCCS, 20148 Milan, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (R.C.); (U.P.); (A.M.); (M.S.)
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11
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Holding M, Otter AD, Dowall S, Takumi K, Hicks B, Coleman T, Hemingway G, Royds M, Findlay-Wilson S, Curran-French M, Vipond R, Sprong H, Hewson R. Screening of wild deer populations for exposure to SARS-CoV-2 in the United Kingdom, 2020-2021. Transbound Emerg Dis 2022; 69:e3244-e3249. [PMID: 35338581 PMCID: PMC9115462 DOI: 10.1111/tbed.14534] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/07/2022] [Accepted: 03/21/2022] [Indexed: 11/30/2022]
Abstract
Following findings in Northern America of SARS‐CoV‐2 infections in white‐tailed deer, there is concern of similar infections in European deer and their potential as reservoirs of SARS‐CoV‐2 including opportunities for the emergence of new variants. UK deer sera were collected in 2020–2021 from 6 species and a hybrid with 1748 tested using anti‐spike and anti‐nucleocapsid serology assays. No samples were positive on both assays nor by surrogate neutralization testing. There is no evidence that spill‐over infections of SARS‐CoV‐2 occurred from the human population to UK deer or that SARS‐CoV‐2 has been circulating in UK deer (over the study period). Although it cannot be ruled out, study results indicate that spill‐over infections followed by circulation of SARS‐CoV‐2 to the most common European deer species is small.
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Affiliation(s)
- Maya Holding
- Virology and Pathogenesis group, UK Health Security Agency, Porton Down, United Kingdom.,National Institute for HealthS Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Ashley David Otter
- SARS-CoV-2 Serosurveillance laboratory, UK Health Security Agency, Porton Down, United Kingdom
| | - Stuart Dowall
- Virology and Pathogenesis group, UK Health Security Agency, Porton Down, United Kingdom
| | - Katsuhisa Takumi
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Bethany Hicks
- SARS-CoV-2 Serosurveillance laboratory, UK Health Security Agency, Porton Down, United Kingdom
| | - Tom Coleman
- SARS-CoV-2 Serosurveillance laboratory, UK Health Security Agency, Porton Down, United Kingdom
| | - Georgia Hemingway
- SARS-CoV-2 Serosurveillance laboratory, UK Health Security Agency, Porton Down, United Kingdom
| | - Matthew Royds
- SARS-CoV-2 Serosurveillance laboratory, UK Health Security Agency, Porton Down, United Kingdom
| | | | - Mollie Curran-French
- Virology and Pathogenesis group, UK Health Security Agency, Porton Down, United Kingdom
| | - Richard Vipond
- Virology and Pathogenesis group, UK Health Security Agency, Porton Down, United Kingdom.,National Institute for HealthS Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Hein Sprong
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Roger Hewson
- Virology and Pathogenesis group, UK Health Security Agency, Porton Down, United Kingdom.,National Institute for HealthS Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,London School of Hygiene and Tropical Medicine, Faculty of Infectious and Tropical Diseases, Keppel Street, London, WC1E 7HT, United Kingdom
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12
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Hassanin A, Rambaud O, Klein D. Genomic Bootstrap Barcodes and Their Application to Study the Evolution of Sarbecoviruses. Viruses 2022; 14:v14020440. [PMID: 35216033 PMCID: PMC8879460 DOI: 10.3390/v14020440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/07/2022] [Accepted: 02/18/2022] [Indexed: 01/22/2023] Open
Abstract
Recombination creates mosaic genomes containing regions with mixed ancestry, and the accumulation of such events over time can complicate greatly many aspects of evolutionary inference. Here, we developed a sliding window bootstrap (SWB) method to generate genomic bootstrap (GB) barcodes to highlight the regions supporting phylogenetic relationships. The method was applied to an alignment of 56 sarbecoviruses, including SARS-CoV and SARS-CoV-2, responsible for the SARS epidemic and COVID-19 pandemic, respectively. The SWB analyses were also used to construct a consensus tree showing the most reliable relationships and better interpret hidden phylogenetic signals. Our results revealed that most relationships were supported by just a few genomic regions and confirmed that three divergent lineages could be found in bats from Yunnan: SCoVrC, which groups SARS-CoV related coronaviruses from China; SCoV2rC, which includes SARS-CoV-2 related coronaviruses from Southeast Asia and Yunnan; and YunSar, which contains a few highly divergent viruses recently described in Yunnan. The GB barcodes showed evidence for ancient recombination between SCoV2rC and YunSar genomes, as well as more recent recombination events between SCoVrC and SCoV2rC genomes. The recombination and phylogeographic patterns suggest a strong host-dependent selection of the viral RNA-dependent RNA polymerase. In addition, SARS-CoV-2 appears as a mosaic genome composed of regions sharing recent ancestry with three bat SCoV2rCs from Yunnan (RmYN02, RpYN06, and RaTG13) or related to more ancient ancestors in bats from Yunnan and Southeast Asia. Finally, our results suggest that viral circular RNAs may be key molecules for the mechanism of recombination.
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13
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Kettenburg G, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, DeRisi JL, Gentles A, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, Dussart P, Heraud JM, Brook CE. Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade. Front Public Health 2022; 10:786060. [PMID: 35223729 PMCID: PMC8873168 DOI: 10.3389/fpubh.2022.786060] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Bats are natural reservoirs for both Alpha- and Betacoronaviruses and the hypothesized original hosts of five of seven known zoonotic coronaviruses. To date, the vast majority of bat coronavirus research has been concentrated in Asia, though coronaviruses are globally distributed; indeed, SARS-CoV and SARS-CoV-2-related Betacoronaviruses in the subgenus Sarbecovirus have been identified circulating in Rhinolophid bats in both Africa and Europe, despite the relative dearth of surveillance in these regions. As part of a long-term study examining the dynamics of potentially zoonotic viruses in three species of endemic Madagascar fruit bat (Pteropus rufus, Eidolon dupreanum, Rousettus madagascariensis), we carried out metagenomic Next Generation Sequencing (mNGS) on urine, throat, and fecal samples obtained from wild-caught individuals. We report detection of RNA derived from Betacoronavirus subgenus Nobecovirus in fecal samples from all three species and describe full genome sequences of novel Nobecoviruses in P. rufus and R. madagascariensis. Phylogenetic analysis indicates the existence of five distinct Nobecovirus clades, one of which is defined by the highly divergent ancestral sequence reported here from P. rufus bats. Madagascar Nobecoviruses derived from P. rufus and R. madagascariensis demonstrate, respectively, Asian and African phylogeographic origins, mirroring those of their fruit bat hosts. Bootscan recombination analysis indicates significant selection has taken place in the spike, nucleocapsid, and NS7 accessory protein regions of the genome for viruses derived from both bat hosts. Madagascar offers a unique phylogeographic nexus of bats and viruses with both Asian and African phylogeographic origins, providing opportunities for unprecedented mixing of viral groups and, potentially, recombination. As fruit bats are handled and consumed widely across Madagascar for subsistence, understanding the landscape of potentially zoonotic coronavirus circulation is essential for mitigation of future zoonotic threats.
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Affiliation(s)
- Gwenddolen Kettenburg
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Hafaliana Christian Ranaivoson
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Angelo Andrianiaina
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Santino Andry
- Department of Entomology, University of Antananarivo, Antananarivo, Madagascar
| | | | - Anecia Gentles
- Odum School of Ecology, University of Georgia, Athens, GA, United States
| | | | | | | | | | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jean-Michel Heraud
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cara E. Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
- *Correspondence: Cara E. Brook
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14
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Abstract
Hedgehogs are common in the majority of European countries and are known to host various pathogens, including viruses. The recent discovery of MERS-related coronaviruses (CoVs) in hedgehogs from Germany, France, the UK, China, and Italy suggests that hedgehogs may represent a wild reservoir of betacoronaviruses. This study reports the first detection and characterization of novel betacoronovirus, subgenus Merbecovirus in wild hedgehogs in Poland. The CoV RNA was detected in 10 out of 40 hedgehogs' rectal swabs and in 1 out of 18 samples of the lung. No viral RNA was identified in the duodenum and kidney. There was no significant relationship between clinical status, gender, hedgehogs' age, and coronaviral RNA detection. Phylogenetic analysis showed that CoVs detected in our study grouped together with other representatives of Hedgehog coronavirus 1 species identified in Western Europe. Our findings provide further evidence that hedgehogs are a natural reservoir of Merbecovirus. Considering the high mutation rate of CoVs and their potential for crossing interspecies barriers, the proper management of hedgehogs admitted to wildlife rehabilitation centres is needed. It cannot be excluded that merbecovirus strains detected in hedgehogs may recombine with other CoVs leading to new viruses with potential for interspecies transmission.
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15
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Amoutzias GD, Nikolaidis M, Tryfonopoulou E, Chlichlia K, Markoulatos P, Oliver SG. The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2. Viruses 2022; 14:78. [PMID: 35062282 PMCID: PMC8778387 DOI: 10.3390/v14010078] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/22/2021] [Accepted: 12/31/2021] [Indexed: 12/13/2022] Open
Abstract
Coronaviruses (CoVs) constitute a large and diverse subfamily of positive-sense single-stranded RNA viruses. They are found in many mammals and birds and have great importance for the health of humans and farm animals. The current SARS-CoV-2 pandemic, as well as many previous epidemics in humans that were of zoonotic origin, highlights the importance of studying the evolution of the entire CoV subfamily in order to understand how novel strains emerge and which molecular processes affect their adaptation, transmissibility, host/tissue tropism, and patho non-homologous genicity. In this review, we focus on studies over the last two years that reveal the impact of point mutations, insertions/deletions, and intratypic/intertypic homologous and non-homologous recombination events on the evolution of CoVs. We discuss whether the next generations of CoV vaccines should be directed against other CoV proteins in addition to or instead of spike. Based on the observed patterns of molecular evolution for the entire subfamily, we discuss five scenarios for the future evolutionary path of SARS-CoV-2 and the COVID-19 pandemic. Finally, within this evolutionary context, we discuss the recently emerged Omicron (B.1.1.529) VoC.
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Affiliation(s)
- Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Eleni Tryfonopoulou
- Laboratory of Molecular Immunology, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus-Dragana, 68100 Alexandroupolis, Greece; (E.T.); (K.C.)
| | - Katerina Chlichlia
- Laboratory of Molecular Immunology, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus-Dragana, 68100 Alexandroupolis, Greece; (E.T.); (K.C.)
| | - Panayotis Markoulatos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Stephen G. Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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16
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de Klerk A, Swanepoel P, Lourens R, Zondo M, Abodunran I, Lytras S, MacLean OA, Robertson D, Kosakovsky Pond SL, Zehr JD, Kumar V, Stanhope MJ, Harkins G, Murrell B, Martin DP. Conserved recombination patterns across coronavirus subgenera. Virus Evol 2022; 8:veac054. [PMID: 35814334 PMCID: PMC9261289 DOI: 10.1093/ve/veac054] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/03/2022] [Accepted: 06/10/2022] [Indexed: 11/12/2022] Open
Abstract
Recombination contributes to the genetic diversity found in coronaviruses and is known to be a prominent mechanism whereby they evolve. It is apparent, both from controlled experiments and in genome sequences sampled from nature, that patterns of recombination in coronaviruses are non-random and that this is likely attributable to a combination of sequence features that favour the occurrence of recombination break points at specific genomic sites, and selection disfavouring the survival of recombinants within which favourable intra-genome interactions have been disrupted. Here we leverage available whole-genome sequence data for six coronavirus subgenera to identify specific patterns of recombination that are conserved between multiple subgenera and then identify the likely factors that underlie these conserved patterns. Specifically, we confirm the non-randomness of recombination break points across all six tested coronavirus subgenera, locate conserved recombination hot- and cold-spots, and determine that the locations of transcriptional regulatory sequences are likely major determinants of conserved recombination break-point hotspot locations. We find that while the locations of recombination break points are not uniformly associated with degrees of nucleotide sequence conservation, they display significant tendencies in multiple coronavirus subgenera to occur in low guanine-cytosine content genome regions, in non-coding regions, at the edges of genes, and at sites within the Spike gene that are predicted to be minimally disruptive of Spike protein folding. While it is apparent that sequence features such as transcriptional regulatory sequences are likely major determinants of where the template-switching events that yield recombination break points most commonly occur, it is evident that selection against misfolded recombinant proteins also strongly impacts observable recombination break-point distributions in coronavirus genomes sampled from nature.
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Affiliation(s)
- Arné de Klerk
- Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa
| | - Phillip Swanepoel
- Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa
| | - Rentia Lourens
- Division of Neurosurgery, Neuroscience Institute, Department of Surgery, University of Cape Town, Cape Town, 7701, South Africa
| | - Mpumelelo Zondo
- Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa
| | - Isaac Abodunran
- Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Oscar A MacLean
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - David Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Sergei L Kosakovsky Pond
- Department of Biology, Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, PA 19122, USA
| | - Jordan D Zehr
- Department of Biology, Temple University, Institute for Genomics and Evolutionary Medicine, Philadelphia, PA 19122, USA
| | - Venkatesh Kumar
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 14186, Sweden
| | - Michael J Stanhope
- Department of Population and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gordon Harkins
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, 7535, South Africa
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 14186, Sweden
| | - Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa
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17
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Evolution of the SARS-CoV-2 genome and emergence of variants of concern. Arch Virol 2021; 167:293-305. [PMID: 34846601 PMCID: PMC8629736 DOI: 10.1007/s00705-021-05295-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/22/2021] [Indexed: 01/08/2023]
Abstract
The high transmission and mortality rates associated with SARS-CoV-2 have led to tragic consequences worldwide. Large-scale whole-genome sequencing of the SARS-CoV-2 genome since its identification in late 2019 has identified many sequence changes and the emergence of novel strains, each described by co-segregation of a particular set of sequence variations. Variants designated G, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2) are important lineages that emerged sequentially and are considered variants of concern. A notable feature of the last four, each of which ultimately evolved from clade G, is the large number (≥ 20) of co-segregating sequence variations associated with them. Several variations are in the spike gene, and some variations are shared among or between strains. Meanwhile, observation of recurrent infections with the same or different SARS-CoV-2 lineages has raised concerns about the duration of the immune responses induced by the initial infection or the vaccine that was administered. While the alpha strain is sensitive to immune responses induced by earlier strains, the beta, gamma, and delta strains can escape antibody neutralization. Apart from random replication errors, intra-host RNA editing, chronic infections, and recombination are processes that may promote the accumulation of sequence changes in the SARS-CoV-2 genome. The known contribution of recombination to coronavirus evolution and recent data pertaining to SARS-CoV-2 suggest that recombination may be particularly important. Continued surveillance of the SARS-CoV-2 genome is imperative.
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