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Liu C, Huang W, He X, Feng Z, Chen Q. Research Advances on Swine Acute Diarrhea Syndrome Coronavirus. Animals (Basel) 2024; 14:448. [PMID: 38338091 PMCID: PMC10854734 DOI: 10.3390/ani14030448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a virulent pathogen that causes acute diarrhea in piglets. The virus was first discovered in Guangdong Province, China, in 2017 and has since emerged in Jiangxi, Fujian, and Guangxi Provinces. The outbreak exhibited a localized and sporadic pattern, with no discernable temporal continuity. The virus can infect human progenitor cells and demonstrates considerable potential for cross-species transmission, representing a potential risk for zoonotic transmission. Therefore, continuous surveillance of and comprehensive research on SADS-CoV are imperative. This review provides an overview of the temporal and evolutionary features of SADS-CoV outbreaks, focusing on the structural characteristics of the virus, which serve as the basis for discussing its potential for interspecies transmission. Additionally, the review summarizes virus-host interactions, including the effects on host cells, as well as apoptotic and autophagic behaviors, and discusses prevention and treatment modalities for this viral infection.
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Affiliation(s)
- Chuancheng Liu
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Weili Huang
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Xinyan He
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Zhihua Feng
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Qi Chen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
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2
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Šimičić P, Židovec-Lepej S. A Glimpse on the Evolution of RNA Viruses: Implications and Lessons from SARS-CoV-2. Viruses 2022; 15:1. [PMID: 36680042 PMCID: PMC9866536 DOI: 10.3390/v15010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
RNA viruses are characterised by extremely high genetic variability due to fast replication, large population size, low fidelity, and (usually) a lack of proofreading mechanisms of RNA polymerases leading to high mutation rates. Furthermore, viral recombination and reassortment may act as a significant evolutionary force among viruses contributing to greater genetic diversity than obtainable by mutation alone. The above-mentioned properties allow for the rapid evolution of RNA viruses, which may result in difficulties in viral eradication, changes in virulence and pathogenicity, and lead to events such as cross-species transmissions, which are matters of great interest in the light of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemics. In this review, we aim to explore the molecular mechanisms of the variability of viral RNA genomes, emphasising the evolutionary trajectory of SARS-CoV-2 and its variants. Furthermore, the causes and consequences of coronavirus variation are explored, along with theories on the origin of human coronaviruses and features of emergent RNA viruses in general. Finally, we summarise the current knowledge on the circulating variants of concern and highlight the many unknowns regarding SARS-CoV-2 pathogenesis.
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Affiliation(s)
| | - Snježana Židovec-Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, HR-10000 Zagreb, Croatia
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3
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Thakor JC, Dinesh M, Manikandan R, Bindu S, Sahoo M, Sahoo D, Dhawan M, Pandey MK, Tiwari R, Emran TB, Dhama K, Chaicumpa W. Swine coronaviruses (SCoVs) and their emerging threats to swine population, inter-species transmission, exploring the susceptibility of pigs for SARS-CoV-2 and zoonotic concerns. Vet Q 2022; 42:125-147. [PMID: 35584308 PMCID: PMC9225692 DOI: 10.1080/01652176.2022.2079756] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 03/23/2022] [Accepted: 05/16/2022] [Indexed: 12/23/2022] Open
Abstract
Swine coronaviruses (SCoVs) are one of the most devastating pathogens affecting the livelihoods of farmers and swine industry across the world. These include transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine respiratory coronavirus (PRCV), porcine hemagglutinating encephalomyelitis virus (PHEV), swine acute diarrhea syndrome coronavirus (SADS-CoV), and porcine delta coronavirus (PDCoV). Coronaviruses infect a wide variety of animal species and humans because these are having single stranded-RNA that accounts for high mutation rates and thus could break the species barrier. The gastrointestinal, cardiovascular, and nervous systems are the primary organ systems affected by SCoVs. Infection is very common in piglets compared to adult swine causing high mortality in the former. Bat is implicated to be the origin of all CoVs affecting animals and humans. Since pig is the only domestic animal in which CoVs cause a wide range of diseases; new coronaviruses with high zoonotic potential could likely emerge in the future as observed in the past. The recently emerged severe acute respiratory syndrome coronavirus virus-2 (SARS-CoV-2), causing COVID-19 pandemic in humans, has been implicated to have animal origin, also reported from few animal species, though its zoonotic concerns are still under investigation. This review discusses SCoVs and their epidemiology, virology, evolution, pathology, wildlife reservoirs, interspecies transmission, spill-over events and highlighting their emerging threats to swine population. The role of pigs amid ongoing SARS-CoV-2 pandemic will also be discussed. A thorough investigation should be conducted to rule out zoonotic potential of SCoVs and to design appropriate strategies for their prevention and control.
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Affiliation(s)
- Jigarji C. Thakor
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Murali Dinesh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Rajendran Manikandan
- Immunology Section, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Suresh Bindu
- Immunology Section, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Monalisa Sahoo
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Diptimayee Sahoo
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, India
- The Trafford Group of Colleges, Manchester, United Kingdom
| | - Megha Katare Pandey
- Department of Translational Medicine Center, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, India
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Abstract
Our understanding of the still unfolding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic would have been extremely limited without the study of the genetics and evolution of this new human coronavirus. Large-scale genome-sequencing efforts have provided close to real-time tracking of the global spread and diversification of SARS-CoV-2 since its entry into the human population in late 2019. These data have underpinned analysis of its origins, epidemiology, and adaptations to the human population: principally immune evasion and increasing transmissibility. SARS-CoV-2, despite being a new human pathogen, was highly capable of human-to-human transmission. During its rapid spread in humans, SARS-CoV-2 has evolved independent new forms, the so-called "variants of concern," that are better optimized for human-to-human transmission. The most important adaptation of the bat coronavirus progenitor of both SARS-CoV-1 and SARS-CoV-2 for human infection (and other mammals) is the use of the angiotensin-converting enzyme 2 (ACE2) receptor. Relaxed structural constraints provide plasticity to SARS-related coronavirus spike protein permitting it to accommodate significant amino acid replacements of antigenic consequence without compromising the ability to bind to ACE2. Although the bulk of research has justifiably concentrated on the viral spike protein as the main determinant of antigenic evolution and changes in transmissibility, there is accumulating evidence for the contribution of other regions of the viral proteome to virus-host interaction. Whereas levels of community transmission of recombinants compromising genetically distinct variants are at present low, when divergent variants cocirculate, recombination between SARS-CoV-2 clades is being detected, increasing the risk that viruses with new properties emerge. Applying computational and machine learning methods to genome sequence data sets to generate experimentally verifiable predictions will serve as an early warning system for novel variant surveillance and will be important in future vaccine planning. Omicron, the latest SARS-CoV-2 variant of concern, has focused attention on step change antigenic events, "shift," as opposed to incremental "drift" changes in antigenicity. Both an increase in transmissibility and antigenic shift in Omicron led to it readily causing infections in the fully vaccinated and/or previously infected. Omicron's virulence, while reduced relative to the variant of concern it replaced, Delta, is very much premised on the past immune exposure of individuals with a clear signal that boosted vaccination protects from severe disease. Currently, SARS-CoV-2 has proven itself to be a dangerous new human respiratory pathogen with an unpredictable evolutionary capacity, leading to a risk of future variants too great not to ensure all regions of the world are screened by viral genome sequencing, protected through available and affordable vaccines, and have non-punitive strategies in place for detecting and responding to novel variants of concern.
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Affiliation(s)
- Amalio Telenti
- Vir Biotechnology, San Francisco, California 94158, USA
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, USA
| | - Emma B Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
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5
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Wang H, Cui X, Cai X, An T. Recombination in Positive-Strand RNA Viruses. Front Microbiol 2022; 13:870759. [PMID: 35663855 PMCID: PMC9158499 DOI: 10.3389/fmicb.2022.870759] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/21/2022] [Indexed: 12/28/2022] Open
Abstract
RNA recombination is a major driver of genetic shifts tightly linked to the evolution of RNA viruses. Genomic recombination contributes substantially to the emergence of new viral lineages, expansion in host tropism, adaptations to new environments, and virulence and pathogenesis. Here, we review some of the recent progress that has advanced our understanding of recombination in positive-strand RNA viruses, including recombination triggers and the mechanisms behind them. The study of RNA recombination aids in predicting the probability and outcome of viral recombination events, and in the design of viruses with reduced recombination frequency as candidates for the development of live attenuated vaccines. Surveillance of viral recombination should remain a priority in the detection of emergent viral strains, a goal that can only be accomplished by expanding our understanding of how these events are triggered and regulated.
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Affiliation(s)
| | | | | | - Tongqing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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6
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Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic demonstrates the threat posed by novel coronaviruses to human health. Coronaviruses share a highly conserved cell entry mechanism mediated by the spike protein, the sole product of the S gene. The structural dynamics by which the spike protein orchestrates infection illuminate how antibodies neutralize virions and how S mutations contribute to viral fitness. Here, we review the process by which spike engages its proteinaceous receptor, angiotensin converting enzyme 2 (ACE2), and how host proteases prime and subsequently enable efficient membrane fusion between virions and target cells. We highlight mutations common among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern and discuss implications for cell entry. Ultimately, we provide a model by which sarbecoviruses are activated for fusion competency and offer a framework for understanding the interplay between humoral immunity and the molecular evolution of the SARS-CoV-2 Spike. In particular, we emphasize the relevance of the Canyon Hypothesis (M. G. Rossmann, J Biol Chem 264:14587-14590, 1989) for understanding evolutionary trajectories of viral entry proteins during sustained intraspecies transmission of a novel viral pathogen.
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Affiliation(s)
- Kyle A Wolf
- Department of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Interdiscipinary Ph.D. Program in Structural and Computational Biology and Quantitative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason C Kwan
- Department of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jeremy P Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Shreveport, Shreveport, Louisiana, USA
- Center for Excellence in Emerging Viral Threats, Louisiana State University Health Shreveport, Shreveport, Louisiana, USA
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7
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Bentum K, Shaddox S, Ware C, Reddy G, Abebe W, Folitse R, Martin P, Samuel T. Molecular phylogeny of coronaviruses and host receptors among domestic and close-contact animals reveals subgenome-level conservation, crossover, and divergence. BMC Vet Res 2022; 18:124. [PMID: 35365153 PMCID: PMC8972689 DOI: 10.1186/s12917-022-03217-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/14/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Coronaviruses have the potential to cross species barriers. To learn the molecular intersections among the most common coronaviruses of domestic and close-contact animals, we analyzed representative coronavirus genera infecting mouse, rat, rabbit, dog, cat, cattle, white-tailed deer, swine, ferret, mink, alpaca, Rhinolophus bat, dolphin, whale, chicken, duck and turkey hosts; reference or complete genome sequences were available for most of these coronavirus genera. Protein sequence alignments and phylogenetic trees were built for the spike (S), envelope (E), membrane (M) and nucleocapsid (N) proteins. The host receptors and enzymes aminopeptidase N (APN), angiotensin converting enzyme 2 (ACE2), sialic acid synthase (SAS), transmembrane serine protease 2 (TMPRSS2), dipeptidyl peptidase 4 (DPP4), cathepsin L (and its analogs) and furin were also compared. RESULTS Overall, the S, E, M, and N proteins segregated according to their viral genera (α, β, or γ), but the S proteins of alphacoronaviruses lacked conservation of phylogeny. Interestingly, the unique polybasic furin cleavage motif found in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) but not in severe acute respiratory syndrome coronavirus (SARS-CoV) or Middle East respiratory syndrome coronavirus (MERS-CoV) exists in several β-coronaviruses and a few α- or γ-coronaviruses. Receptors and enzymes retained host species-dependent relationships with one another. Among the hosts, critical ACE2 residues essential for SARS-CoV-2 spike protein binding were most conserved in white-tailed deer and cattle. CONCLUSION The polybasic furin cleavage motif found in several β- and other coronaviruses of animals points to the existence of an intermediate host for SARS-CoV-2, and it also offers a counternarrative to the theory of a laboratory-engineered virus. Generally, the S proteins of coronaviruses show crossovers of phylogenies indicative of recombination events. Additionally, the consistency in the segregation of viral proteins of the MERS-like coronavirus (NC_034440.1) from pipistrelle bat supports its classification as a β-coronavirus. Finally, similarities in host enzymes and receptors did not always explain natural cross-infections. More studies are therefore needed to identify factors that determine the cross-species infectivity of coronaviruses.
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Affiliation(s)
- Kingsley Bentum
- Department of Pathobiology, College of Veterinary Medicine, Patterson Hall, Tuskegee University, Patterson Hall, 1200 W. Montgomery Road, Tuskegee, AL, 36088, USA
| | - Sage Shaddox
- Department of Pathobiology, College of Veterinary Medicine, Patterson Hall, Tuskegee University, Patterson Hall, 1200 W. Montgomery Road, Tuskegee, AL, 36088, USA
| | - Crystal Ware
- Department of Pathobiology, College of Veterinary Medicine, Patterson Hall, Tuskegee University, Patterson Hall, 1200 W. Montgomery Road, Tuskegee, AL, 36088, USA
| | - Gopal Reddy
- Department of Pathobiology, College of Veterinary Medicine, Patterson Hall, Tuskegee University, Patterson Hall, 1200 W. Montgomery Road, Tuskegee, AL, 36088, USA
| | - Woubit Abebe
- Department of Pathobiology, College of Veterinary Medicine, Patterson Hall, Tuskegee University, Patterson Hall, 1200 W. Montgomery Road, Tuskegee, AL, 36088, USA
| | - Raphael Folitse
- School of Veterinary Medicine, Kwame Nkrumah University of Science and Technology, University Post Office, Kumasi, Ghana
| | - Pamela Martin
- Department of Pathobiology, College of Veterinary Medicine, Patterson Hall, Tuskegee University, Patterson Hall, 1200 W. Montgomery Road, Tuskegee, AL, 36088, USA
| | - Temesgen Samuel
- Department of Pathobiology, College of Veterinary Medicine, Patterson Hall, Tuskegee University, Patterson Hall, 1200 W. Montgomery Road, Tuskegee, AL, 36088, USA.
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Nikolaidis M, Papakyriakou A, Chlichlia K, Markoulatos P, Oliver SG, Amoutzias GD. Comparative Analysis of SARS-CoV-2 Variants of Concern, Including Omicron, Highlights Their Common and Distinctive Amino Acid Substitution Patterns, Especially at the Spike ORF. Viruses 2022; 14:707. [PMID: 35458441 PMCID: PMC9025783 DOI: 10.3390/v14040707] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 12/13/2022] Open
Abstract
In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant of concern (VoC), a study of amino acid substitution (AAS) patterns was performed and compared with those of the other four successful variants of concern (Alpha, Beta, Gamma, Delta) and one closely related variant of interest (VoI-Lambda). The Spike ORF consistently emerges as an AAS hotspot in all six lineages, but in Omicron this enrichment is significantly higher. The progenitors of each of these VoC/VoI lineages underwent positive selection in the Spike ORF. However, once they were established, their Spike ORFs have been undergoing purifying selection, despite the application of global vaccination schemes from 2021 onwards. Our analyses reject the hypothesis that the heavily mutated receptor binding domain (RBD) of the Omicron Spike was introduced via recombination from another closely related Sarbecovirus. Thus, successive point mutations appear as the most parsimonious scenario. Intriguingly, in each of the six lineages, we observed a significant number of AAS wherein the new residue is not present at any homologous site among the other known Sarbecoviruses. Such AAS should be further investigated as potential adaptations to the human host. By studying the phylogenetic distribution of AAS shared between the six lineages, we observed that the Omicron (BA.1) lineage had the highest number (8/10) of recurrent mutations.
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Affiliation(s)
- Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Athanasios Papakyriakou
- Institute of Biosciences & Applications, National Centre for Scientific Research Demokritos, 15341 Agia Paraskevi, Greece;
| | - Katerina Chlichlia
- Laboratory of Molecular Immunology, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus-Dragana, 68100 Alexandroupolis, Greece;
| | - 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;
| | - Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
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Dezordi FZ, Resende PC, Naveca FG, do Nascimento VA, de Souza VC, Dias Paixão AC, Appolinario L, Lopes RS, da Fonseca Mendonça AC, Barreto da Rocha AS, Martins Venas TM, Pereira EC, Paiva MHS, Docena C, Bezerra MF, Machado LC, Salvato RS, Gregianini TS, Martins LG, Pereira FM, Rovaris DB, Fernandes SB, Ribeiro-Rodrigues R, Costa TO, Sousa JC, Miyajima F, Delatorre E, Gräf T, Bello G, Siqueira MM, Wallau GL. Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection. Microb Genom 2022; 8:000751. [PMID: 35297757 PMCID: PMC9176291 DOI: 10.1099/mgen.0.000751] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has infected almost 200 million people worldwide by July 2021 and the pandemic has been characterized by infection waves of viral lineages showing distinct fitness profiles. The simultaneous infection of a single individual by two distinct SARS-CoV-2 lineages may impact COVID-19 disease progression and provides a window of opportunity for viral recombination and the emergence of new lineages with differential phenotype. Several hundred SARS-CoV-2 lineages are currently well phylogenetically defined, but two main factors have precluded major coinfection/codetection and recombination analysis thus far: (i) the low diversity of SARS-CoV-2 lineages during the first year of the pandemic, which limited the identification of lineage defining mutations necessary to distinguish coinfecting/recombining viral lineages; and the (ii) limited availability of raw sequencing data where abundance and distribution of intrasample/intrahost variability can be accessed. Here, we assembled a large sequencing dataset from Brazilian samples covering a period of 18 May 2020 to 30 April 2021 and probed it for unexpected patterns of high intrasample/intrahost variability. This approach enabled us to detect nine cases of SARS-CoV-2 coinfection with well characterized lineage-defining mutations, representing 0.61 % of all samples investigated. In addition, we matched these SARS-CoV-2 coinfections with spatio-temporal epidemiological data confirming its plausibility with the cocirculating lineages at the timeframe investigated. Our data suggests that coinfection with distinct SARS-CoV-2 lineages is a rare phenomenon, although it is certainly a lower bound estimate considering the difficulty to detect coinfections with very similar SARS-CoV-2 lineages and the low number of samples sequenced from the total number of infections.
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Affiliation(s)
- Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ-Amazonas, Manaus, Amazonas, Brazil
| | - Valdinete Alves do Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ-Amazonas, Manaus, Amazonas, Brazil
| | - Victor Costa de Souza
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ-Amazonas, Manaus, Amazonas, Brazil
| | - Anna Carolina Dias Paixão
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciana Appolinario
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renata Serrano Lopes
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Alice Sampaio Barreto da Rocha
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Taina Moreira Martins Venas
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elisa Cavalcante Pereira
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo Henrique Santos Paiva
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Núcleo de Ciências da Vida, Universidade Federal de Pernambuco (UFPE), Centro Acadêmico do Agreste, Caruaru, Pernambuco, Brazil
| | - Cassia Docena
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Matheus Filgueira Bezerra
- Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Laís Ceschini Machado
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Richard Steiner Salvato
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Tatiana Schäffer Gregianini
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Leticia Garay Martins
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Darcita Buerger Rovaris
- Laboratório Central de Saúde Pública do Estado de Santa Catarina (LACEN-SC), Florianópolis, Santa Catarina, Brazil
| | - Sandra Bianchini Fernandes
- Laboratório Central de Saúde Pública do Estado de Santa Catarina (LACEN-SC), Florianópolis, Santa Catarina, Brazil
| | - Rodrigo Ribeiro-Rodrigues
- Laboratório Central de Saúde Pública do Estado do Espírito Santo (LACEN-ES), Vitória, Espírito Santo, Brazil
| | - Thais Oliveira Costa
- Analytical Competence Molecular Epidemiology Laboratory (ACME), FIOCRUZ-Ceará, Fortaleza, Ceará, Brazil
| | - Joaquim Cesar Sousa
- Analytical Competence Molecular Epidemiology Laboratory (ACME), FIOCRUZ-Ceará, Fortaleza, Ceará, Brazil
| | - Fabio Miyajima
- Analytical Competence Molecular Epidemiology Laboratory (ACME), FIOCRUZ-Ceará, Fortaleza, Ceará, Brazil
| | - Edson Delatorre
- Departamento de Biologia. Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, FIOCRUZ-Bahia, Salvador, Bahia, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- *Correspondence: Gabriel Luz Wallau,
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10
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Nikolaidis M, Markoulatos P, Van de Peer Y, Oliver SG, Amoutzias GD. The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes. Mol Biol Evol 2022; 39:msab292. [PMID: 34638137 PMCID: PMC8549283 DOI: 10.1093/molbev/msab292] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous and nonhomologous recombination, because such events may affect the emergence of novel CoV strains, alter their host range, infection rate, tissue tropism pathogenicity, and their ability to escape vaccination programs. Intratypic recombination among closely related CoVs of the same subgenus has often been reported; however, the patterns and limits of genomic exchange between more distantly related CoV lineages (intertypic recombination) need further investigation. Here, we report computational/evolutionary analyses that clearly demonstrate a substantial ability for CoVs of different subgenera to recombine. Furthermore, we show that CoVs can obtain-through nonhomologous recombination-accessory ORFs from core ORFs, exchange accessory ORFs with different CoV genera, with other viruses (i.e., toroviruses, influenza C/D, reoviruses, rotaviruses, astroviruses) and even with hosts. Intriguingly, most of these radical events result from double crossovers surrounding the Spike ORF, thus highlighting both the instability and mobile nature of this genomic region. Although many such events have often occurred during the evolution of various CoVs, the genomic architecture of the relatively young SARS-CoV/SARS-CoV-2 lineage so far appears to be stable.
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Affiliation(s)
- Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Panayotis Markoulatos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Grigorios D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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11
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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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12
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Fay EJ, Balla KM, Roach SN, Shepherd FK, Putri DS, Wiggen TD, Goldstein SA, Pierson MJ, Ferris MT, Thefaine CE, Tucker A, Salnikov M, Cortez V, Compton SR, Kotenko SV, Hunter RC, Masopust D, Elde NC, Langlois RA. Natural rodent model of viral transmission reveals biological features of virus population dynamics. J Exp Med 2021; 219:212940. [PMID: 34958350 PMCID: PMC8713297 DOI: 10.1084/jem.20211220] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/05/2021] [Accepted: 12/08/2021] [Indexed: 12/21/2022] Open
Abstract
Emerging viruses threaten global health, but few experimental models can characterize the virus and host factors necessary for within- and cross-species transmission. Here, we leverage a model whereby pet store mice or rats-which harbor natural rodent pathogens-are cohoused with laboratory mice. This "dirty" mouse model offers a platform for studying acute transmission of viruses between and within hosts via natural mechanisms. We identified numerous viruses and other microbial species that transmit to cohoused mice, including prospective new members of the Coronaviridae, Astroviridae, Picornaviridae, and Narnaviridae families, and uncovered pathogen interactions that promote or prevent virus transmission. We also evaluated transmission dynamics of murine astroviruses during transmission and spread within a new host. Finally, by cohousing our laboratory mice with the bedding of pet store rats, we identified cross-species transmission of a rat astrovirus. Overall, this model system allows for the analysis of transmission of natural rodent viruses and is a platform to further characterize barriers to zoonosis.
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Affiliation(s)
- Elizabeth J. Fay
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN,Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Keir M. Balla
- Department of Human Genetics, University of Utah, Salt Lake City, UT
| | - Shanley N. Roach
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Frances K. Shepherd
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Dira S. Putri
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN,Microbiology, Immunology and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN
| | - Talia D. Wiggen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | | | - Mark J. Pierson
- Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Claire E. Thefaine
- Microbiology, Immunology and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN
| | - Andrew Tucker
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Mark Salnikov
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Valerie Cortez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA
| | - Susan R. Compton
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT
| | - Sergei V. Kotenko
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ
| | - Ryan C. Hunter
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - David Masopust
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN,Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT
| | - Ryan A. Langlois
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN,Center for Immunology, University of Minnesota, Minneapolis, MN,Correspondence to Ryan A. Langlois:
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13
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Torbati E, Krause KL, Ussher JE. The Immune Response to SARS-CoV-2 and Variants of Concern. Viruses 2021; 13:1911. [PMID: 34696342 PMCID: PMC8537260 DOI: 10.3390/v13101911] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/07/2023] Open
Abstract
At the end of 2019 a newly emerged betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the cause of an outbreak of severe pneumonia, subsequently termed COVID-19, in a number of patients in Wuhan, China. Subsequently, SARS-CoV-2 rapidly spread globally, resulting in a pandemic that has to date infected over 200 million individuals and resulted in more than 4.3 million deaths. While SARS-CoV-2 results in severe disease in 13.8%, with increasing frequency of severe disease with age, over 80% of infections are asymptomatic or mild. The immune response is an important determinant of outcome following SARS-CoV-2 infection. While B cell and T cell responses are associated with control of infection and protection against subsequent challenge with SARS-CoV-2, failure to control viral replication and the resulting hyperinflammation are associated with severe COVID-19. Towards the end of 2020, several variants of concern emerged that demonstrate increased transmissibility and/or evasion of immune responses from prior SARS-CoV-2 infection. This article reviews what is known about the humoral and cellular immune responses to SARS-CoV-2 and how mutation and structural/functional changes in the emerging variants of concern impact upon the immune protection from prior infection or vaccination.
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Affiliation(s)
- Elham Torbati
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand;
- Vaccine Alliance Aotearoa New Zealand, Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Kurt L. Krause
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
| | - James E. Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand;
- Vaccine Alliance Aotearoa New Zealand, Malaghan Institute of Medical Research, Wellington 6242, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
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14
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections trigger viral RNA sensors such as TLR7 and RIG-I, thereby leading to production of type I interferon (IFN) and other inflammatory mediators. Expression of viral proteins in the context of this inflammation leads to stereotypical antigen-specific antibody and T cell responses that clear the virus. Immunity is then maintained through long-lived antibody-secreting plasma cells and by memory B and T cells that can initiate anamnestic responses. Each of these steps is consistent with prior knowledge of acute RNA virus infections. Yet there are certain concepts, while not entirely new, that have been resurrected by the biology of severe SARS-CoV-2 infections and deserve further attention. These include production of anti-IFN autoantibodies, early inflammatory processes that slow adaptive humoral immunity, immunodominance of antibody responses, and original antigenic sin. Moreover, multiple different vaccine platforms allow for comparisons of pathways that promote robust and durable adaptive immunity.
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Affiliation(s)
- Dominik Schenten
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, United States.
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, United States.
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15
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Singh J, Pandit P, McArthur AG, Banerjee A, Mossman K. Evolutionary trajectory of SARS-CoV-2 and emerging variants. Virol J 2021; 18:166. [PMID: 34389034 PMCID: PMC8361246 DOI: 10.1186/s12985-021-01633-w] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.
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Affiliation(s)
- Jalen Singh
- School of Interdisciplinary Science, McMaster University, Hamilton, ON, Canada
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
| | - Karen Mossman
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.
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16
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Telenti A, Arvin A, Corey L, Corti D, Diamond MS, García-Sastre A, Garry RF, Holmes EC, Pang PS, Virgin HW. After the pandemic: perspectives on the future trajectory of COVID-19. Nature 2021; 596:495-504. [PMID: 34237771 DOI: 10.1038/s41586-021-03792-w] [Citation(s) in RCA: 212] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
There is a realistic expectation that the global effort in vaccination will bring the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) under control. Nonetheless, uncertainties remain about the type of long-term association that the virus will establish with the human population and, in particular, whether coronavirus disease 2019 (COVID-19) will become an endemic disease. Although the trajectory is difficult to predict, the conditions, concepts and variables that influence this transition can be anticipated. Persistence of SARS-CoV-2 as an endemic virus, perhaps with seasonal epidemic peaks, may be fuelled by pockets of susceptible individuals and waning immunity after infection or vaccination, changes in the virus through antigenic drift that diminish protection and re-entries from zoonotic reservoirs. Here we review relevant observations from previous epidemics and discuss the potential evolution of SARS-CoV-2 as it adapts during persistent transmission in the presence of a level of population immunity. Lack of effective surveillance or adequate response could enable the emergence of new epidemic or pandemic patterns from an endemic infection of SARS-CoV-2. There are key pieces of data that are urgently needed in order to make good decisions; we outline these and propose a way forward.
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Affiliation(s)
- Amalio Telenti
- Vir Biotechnology, San Francisco, CA, USA. .,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA.
| | - Ann Arvin
- Vir Biotechnology, San Francisco, CA, USA.
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA. .,Department of Medicine, Washington University School of Medicine, St Louis, MO, USA. .,Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA, USA.
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.
| | | | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, USA. .,Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA. .,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.
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