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Samson S, Lord É, Makarenkov V. Assessing the emergence time of SARS-CoV-2 zoonotic spillover. PLoS One 2024; 19:e0301195. [PMID: 38574109 PMCID: PMC10994396 DOI: 10.1371/journal.pone.0301195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024] Open
Abstract
Understanding the evolution of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) and its relationship to other coronaviruses in the wild is crucial for preventing future virus outbreaks. While the origin of the SARS-CoV-2 pandemic remains uncertain, mounting evidence suggests the direct involvement of the bat and pangolin coronaviruses in the evolution of the SARS-CoV-2 genome. To unravel the early days of a probable zoonotic spillover event, we analyzed genomic data from various coronavirus strains from both human and wild hosts. Bayesian phylogenetic analysis was performed using multiple datasets, using strict and relaxed clock evolutionary models to estimate the occurrence times of key speciation, gene transfer, and recombination events affecting the evolution of SARS-CoV-2 and its closest relatives. We found strong evidence supporting the presence of temporal structure in datasets containing SARS-CoV-2 variants, enabling us to estimate the time of SARS-CoV-2 zoonotic spillover between August and early October 2019. In contrast, datasets without SARS-CoV-2 variants provided mixed results in terms of temporal structure. However, they allowed us to establish that the presence of a statistically robust clade in the phylogenies of gene S and its receptor-binding (RBD) domain, including two bat (BANAL) and two Guangdong pangolin coronaviruses (CoVs), is due to the horizontal gene transfer of this gene from the bat CoV to the pangolin CoV that occurred in the middle of 2018. Importantly, this clade is closely located to SARS-CoV-2 in both phylogenies. This phylogenetic proximity had been explained by an RBD gene transfer from the Guangdong pangolin CoV to a very recent ancestor of SARS-CoV-2 in some earlier works in the field before the BANAL coronaviruses were discovered. Overall, our study provides valuable insights into the timeline and evolutionary dynamics of the SARS-CoV-2 pandemic.
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Affiliation(s)
- Stéphane Samson
- Department of Computer Sciences, Université du Québec à Montréal, Montréal, Canada
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Québec, Canada
| | - Étienne Lord
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Québec, Canada
| | - Vladimir Makarenkov
- Department of Computer Sciences, Université du Québec à Montréal, Montréal, Canada
- Mila—Quebec AI Institute, Montreal, QC, Canada
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2
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Barua A, Grot N, Plawski A. The basis of mink susceptibility to SARS-CoV-2 infection. J Appl Genet 2022; 63:543-555. [PMID: 35396646 PMCID: PMC8993591 DOI: 10.1007/s13353-022-00689-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
Abstract
Of all known airborne diseases in the twenty-first century, coronavirus disease 19 (COVID-19) has the highest infection and death rate. Over the past few decades, animal origin viral diseases, notably those of bats-linked, have increased many folds in humans with cross-species transmissions noted and the ongoing COVID-19 pandemic has emphasized the importance of understanding the evolution of natural hosts in response to viral pathogens. Cross-species transmissions are possible due to the possession of the angiotensin-converting enzyme 2 (ACE2) receptor in animals. ACE2 recognition by SARS-CoV-2 is a critical determinant of the host range, interspecies transmission, and viral pathogenesis. Thus, the phenomenon of breaking the cross-species barrier is mainly associated with mutations in the receptor-binding domain (RBD) of the spike (S) protein that interacts with ACE2. In this review, we raise the issue of cross-species transmission based on sequence alignment of S protein. Based on previous reports and our observations, we can conclude that the occurrence of one of two mutations D614G or Y453F is sufficient for infection of minks by SARS-CoV-2 from humans. Unfortunately, D614G is observed in the world’s most common line of virus B.1.1.7 and the latest SARS-CoV-2 variants B.1.617.1, B.1.617.2, and B.1.617.3 too.
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Affiliation(s)
- Avishak Barua
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-631, Poznań, Poland
| | - Natalia Grot
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland
| | - Andrzej Plawski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland. .,Department of General and Endocrine Surgery and Gastroenterological Oncology, Poznań University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznań, Poland.
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Wang X, Lam JY, Chen L, Au SWN, To KKW, Yuen KY, Kok KH. Mining of linear B cell epitopes of SARS-CoV-2 ORF8 protein from COVID-19 patients. Emerg Microbes Infect 2021; 10:1016-1023. [PMID: 34003073 PMCID: PMC8186430 DOI: 10.1080/22221751.2021.1931465] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 01/10/2023]
Abstract
Given the on-going SARS-CoV-2 pandemic, identification of immunogenic targets against the viral protein will provide crucial advances towards the development of sensitive diagnostic tools and vaccination strategies. Our previous study has found that ORF8 protein of SARS-CoV-2 is highly immunogenic and shows high sensitivity in identifying COVID-19 disease. In this study, by employing overlapping linear peptides, we characterized the IgG immunodominant regions on SARS-CoV-2 ORF8 protein that are seropositive in the sera from SARS-CoV-2-infected patients. The major immunogenic epitopes are localized at (1) N-termini alpha helix, (2) the resides spanning beta 2 and 3 sheets, and (3) the loop between beta 4 and 5 sheets. Additionally, hamster model infected by SARS-CoV-2 further validates the seropositivity of the linear epitopes in vivo, demonstrating a potential application of the linear peptide-based immunization strategy. Taken together, identification and validation of these B-cell linear epitopes will provide insights into the design of serological diagnostics and peptide-based vaccination approach against this pandemic virus of high priority.
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Affiliation(s)
- Xiaohui Wang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Joy-Yan Lam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Linlei Chen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Shannon Wing-Ngor Au
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Kelvin K. W. To
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Kin-Hang Kok
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
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4
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Gregory DA, Wieberg CG, Wenzel J, Lin CH, Johnson MC. Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. Viruses 2021. [PMID: 34452511 DOI: 10.3390/v13081647.pmid:34452511;pmcid:pmc8402658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Sequencing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from wastewater has become a useful tool in monitoring the spread of viral variants. Approaches to this task have been varied, relying on differing sequencing methods and computational analyses. We used a novel computation workflow based on amplicon sequencing of SARS-CoV-2 spike domains in order to track viral populations in wastewater. As part of this workflow, we developed a program, SAM Refiner, that has a variety of outputs, including novel variant reporting as well as functions designed to remove polymerase chain reaction (PCR) generated chimeric sequences. With these methods, we were able to track viral population dynamics over time. We report here on the emergence of two variants of concern, B.1.1.7 (Alpha) and P.1 (Gamma), and their displacement of the D614G B.1 variant in a Missouri sewershed.
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Affiliation(s)
- Devon A Gregory
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Chris G Wieberg
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65102, USA
| | - Jeff Wenzel
- Bureau of Environmental Epidemiology, Missouri Department of Health and Senior Services, Division of Community and Public Health, Jefferson City, MO 65102, USA
| | - Chung-Ho Lin
- Center for Agroforestry, School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65201, USA
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Gregory DA, Wieberg CG, Wenzel J, Lin CH, Johnson MC. Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. Viruses 2021; 13:1647. [PMID: 34452511 PMCID: PMC8402658 DOI: 10.3390/v13081647] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 12/18/2022] Open
Abstract
Sequencing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from wastewater has become a useful tool in monitoring the spread of viral variants. Approaches to this task have been varied, relying on differing sequencing methods and computational analyses. We used a novel computation workflow based on amplicon sequencing of SARS-CoV-2 spike domains in order to track viral populations in wastewater. As part of this workflow, we developed a program, SAM Refiner, that has a variety of outputs, including novel variant reporting as well as functions designed to remove polymerase chain reaction (PCR) generated chimeric sequences. With these methods, we were able to track viral population dynamics over time. We report here on the emergence of two variants of concern, B.1.1.7 (Alpha) and P.1 (Gamma), and their displacement of the D614G B.1 variant in a Missouri sewershed.
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Affiliation(s)
- Devon A. Gregory
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65201, USA;
| | - Chris G. Wieberg
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65102, USA;
| | - Jeff Wenzel
- Bureau of Environmental Epidemiology, Missouri Department of Health and Senior Services, Division of Community and Public Health, Jefferson City, MO 65102, USA;
| | - Chung-Ho Lin
- Center for Agroforestry, School of Natural Resources, University of Missouri, Columbia, MO 65201, USA;
| | - Marc C. Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65201, USA;
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Islam A, Sayeed MA, Kalam MA, Ferdous J, Rahman MK, Abedin J, Islam S, Shano S, Saha O, Shirin T, Hassan MM. Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. Microorganisms 2021; 9:1696. [PMID: 34442775 PMCID: PMC8401355 DOI: 10.3390/microorganisms9081696] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/27/2021] [Accepted: 08/03/2021] [Indexed: 01/01/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swamped the global environment greatly in the current pandemic. Wastewater-based epidemiology (WBE) effectively forecasts the surge of COVID-19 cases in humans in a particular region. To understand the genomic characteristics/footprints and diversity of SARS-CoV-2 in the environment, we analyzed 807 SARS-CoV-2 sequences from 20 countries deposited in GISAID till 22 May 2021. The highest number of sequences (n = 638) were reported in Austria, followed by the Netherlands, China, and Bangladesh. Wastewater samples were highest (40.0%) to successfully yield the virus genome followed by a 24 h composite wastewater sample (32.6%) and sewage (18.5%). Phylogenetic analysis revealed that SARS-CoV-2 environmental strains are a close congener with the strains mostly circulating in the human population from the same region. Clade GRY (32.7%), G (29.2%), GR (25.3%), O (7.2%), GH (3.4%), GV (1.4%), S (0.5%), and L (0.4%) were found in environmental samples. Various lineages were identified in environmental samples; nevertheless, the highest percentages (49.4%) of the alpha variant (B.1.1.7) were detected in Austria, Liechtenstein, Slovenia, Czech Republic, Switzerland, Germany, and Italy. Other prevalent lineages were B.1 (18.2%), B.1.1 (9.2%), and B.1.160 (3.9%). Furthermore, a significant number of amino acid substitutions were found in environmental strains where the D614G was found in 83.8% of the sequences. However, the key mutations-N501Y (44.6%), S982A (44.4%), A570D (43.3%), T716I (40.4%), and P681H (40.1%) were also recorded in spike protein. The identification of the environmental belvedere of SARS-CoV-2 and its genetic signature is crucial to detect outbreaks, forecast pandemic harshness, and prepare with the appropriate tools to control any impending pandemic. We recommend genomic environmental surveillance to trace the emerging variants and diversity of SARS-CoV-2 viruses circulating in the community. Additionally, proper disposal and treatment of wastewater, sewage, and medical wastes are important to prevent environmental contamination.
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Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, VIC 3216, Australia
| | - Md. Abu Sayeed
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | | | - Jinnat Ferdous
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Md. Kaisar Rahman
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Josefina Abedin
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Shariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Shahanaj Shano
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh;
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Xantus GZ, Burke D, Kanizsai P. How to best handle vaccine decliners: scientific facts and psychological approach. Postgrad Med J 2021; 98:626-632. [PMID: 33837130 DOI: 10.1136/postgradmedj-2021-139835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/25/2021] [Accepted: 03/06/2021] [Indexed: 01/02/2023]
Abstract
There is currently no curative drug therapy for COVID-19. The spread of the virus seems relentless despite the unprecedented epidemiological measures. Prevention remains the only feasible option to stop the pandemic; without population-level vaccination, we are unlikely to regain the quality of social life and the unrestricted economy/commerce we enjoyed before. Anti-vaxxers and conspiracy theorists are seemingly oblivious to the detrimental effect of COVID-19 both at an individual and societal level. These groups have (and probably will) continue to attempt to undermine efforts to eradicate the virus despite the fact that the major reduction in morbidity/and mortality of infectious diseases of the past century was achieved through the development of vaccines and improved hygiene. Conspiracy theories are directly associated with reduced vaccine uptake and unfortunately neither anti-vaxxers nor vaccine hesitants cannot be persuaded (debunked) with logical arguments; hence, prescribers must not only be aware of the truth underlying the dense web of misinformation but must fully understand the psychological aspects as well to be able to efficiently counsel about the potential benefits and harms. Such knowledge is pivotal to help the lay public to make informed decisions about SARS CoV-2 in general and vaccination in particular; as the COVID-19 situation can probably be best controlled with mass inoculation and novel immune therapies. The lessons learnt regarding the importance of efficient communication and the adherence to the proven epidemiological measures hopefully would be leaving us better prepared for the future if challenged by novel communicable diseases of pandemic potential.
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Affiliation(s)
| | - Derek Burke
- Research Department, University of Gibraltar - Europa Point Campus, Gibraltar, Gibraltar
| | - Peter Kanizsai
- Emergency Department, Pecsi Tudomanyegyetem, Pecs, Hungary
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Diagnostic Value of IgM and IgG Detection in COVID-19 Diagnosis by the Mobile Laboratory B-LiFE: A Massive Testing Strategy in the Piedmont Region. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18073372. [PMID: 33805139 PMCID: PMC8036500 DOI: 10.3390/ijerph18073372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/23/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an acute infectious disease caused by the novel coronavirus (SARS-CoV-2) identified in 2019. The COVID-19 outbreak continues to have devastating consequences for human lives and the global economy. The B-LiFe mobile laboratory in Piedmont, Italy, was deployed for the surveillance of COVID-19 cases by large-scale testing of first responders. The objective was to assess the seroconversion among the regional civil protection (CP), police, health care professionals, and volunteers. The secondary objective was to detect asymptomatic individuals within this cohort in the light of age, sex, and residence. In this paper, we report the results of serological testing performed by the B-LiFe mobile laboratory deployed from 10 June to 23 July 2020. The tests included whole blood finger-prick and serum sampling for detection of SARS-CoV-2 spike receptor-binding domain (S-RBD) antibodies. The prevalence of SARS-CoV-2 antibodies was approximately 5% (294/6013). The results of the finger-prick tests and serum sample analyses showed moderate agreement (kappa = 0.77). Furthermore, the detection rates of serum antibodies to the SARS-CoV-2 nucleocapsid protein (NP) and S-RBD among the seroconverted individuals were positively correlated (kappa = 0.60), at least at the IgG level. Seroprevalence studies based on serological testing for the S-RBD protein or SARS-CoV-2 NP antibodies are not sufficient for diagnosis but might help in screening the population to be vaccinated and in determining the duration of seroconversion.
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Jacob Machado D, White RA, Kofsky J, Janies DA. Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2021; 1:e60. [PMID: 36168505 PMCID: PMC9495640 DOI: 10.1017/ash.2021.222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 04/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily Orthocoronavirinae related to 2 other clinically relevant coronaviruses, SARS-CoV and MERS-CoV. Like other coronaviruses and several other viruses, SARS-CoV-2 originated in bats. However, unlike other coronaviruses, SARS-CoV-2 resulted in a devastating pandemic. The SARS-CoV-2 pandemic rages on due to viral evolution that leads to more transmissible and immune evasive variants. Technology such as genomic sequencing has driven the shift from syndromic to molecular epidemiology and promises better understanding of variants. The COVID-19 pandemic has exposed critical impediments that must be addressed to develop the science of pandemics. Much of the progress is being applied in the developed world. However, barriers to the use of molecular epidemiology in low- and middle-income countries (LMICs) remain, including lack of logistics for equipment and reagents and lack of training in analysis. We review the molecular epidemiology literature to understand its origins from the SARS epidemic (2002-2003) through influenza events and the current COVID-19 pandemic. We advocate for improved genomic surveillance of SARS-CoV and understanding the pathogen diversity in potential zoonotic hosts. This work will require training in phylogenetic and high-performance computing to improve analyses of the origin and spread of pathogens. The overarching goals are to understand and abate zoonosis risk through interdisciplinary collaboration and lowering logistical barriers.
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Affiliation(s)
- Denis Jacob Machado
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- Author for correspondence: Denis Jacob Machado, PhD, Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, BINF 224, Charlotte, NC28223. E-mail:
| | - Richard Allen White
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- University of North Carolina at Charlotte, North Carolina Research Campus (NCRC), Kannapolis, North Carolina
| | - Janice Kofsky
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
| | - Daniel A. Janies
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
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Teixeira AIP, Cantarino L. Severe acute respiratory syndrome coronavirus 2 in cats: a systematic review. BRAZILIAN JOURNAL OF VETERINARY MEDICINE 2021; 43:e000421. [PMID: 35749089 PMCID: PMC9179199 DOI: 10.29374/2527-2179.bjvm000421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/11/2021] [Indexed: 11/10/2022] Open
Abstract
The epidemiological role of cats in the coronavirus disease pandemic remains unclear despite of several studies that have been conducted to understand it, in other words it is not yet known whether the cat would be able to transmit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to humans. Taking that into account, the objective of this study was to conduct a systematic review to identify what is known and not known on this topic. Our results revealed that cats can be infected through an airborne (perhaps oral, too) route and that the clinical development of the infection in cats is parallel to that in humans. The majority of infected cats remained asymptomatic, and more severe clinical cases described occurred only in animals with comorbidities. In addition to infection, cats achieved seroconversion with detectable titers. However, the epidemiological role of cats in relation to transmission routes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains unclear and needs to be studied further. We emphasize that, regardless of the conclusion regarding the epidemiological role of cats, this reinforces the concepts of ONE HEALTH to be incorporated into the studies and practices of epidemiological surveillance of infectious diseases, with multidisciplinary teams, to achieve an understanding of the transmission of diseases with zoonotic potential.
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Affiliation(s)
| | - Ligia Cantarino
- Veterinarian, DSc., Faculdade de Agronomia e Veterinária, UNB, Brasília, DF, Brazil.
- Correspondence Ligia Cantarino Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília - UnB Campus Universitário Darcy Ribeiro, s/n CEP 70910-900 - Brasília (DF), Brasil E-mail:
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11
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Sharun K, Tiwari R, Natesan S, Dhama K. SARS-CoV-2 infection in farmed minks, associated zoonotic concerns, and importance of the One Health approach during the ongoing COVID-19 pandemic. Vet Q 2021; 41:50-60. [PMID: 33349165 PMCID: PMC7833041 DOI: 10.1080/01652176.2020.1867776] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has now affected over 72.5 million people worldwide, with nearly 1.6 million deaths reported globally as of December 17, 2020. SARS-CoV-2 has been implicated to have originated from bats and pangolins, and its intermediate animal hosts are being investigated. Crossing of the species barrier and exhibition of zoonosis have been reported in SARS-CoV-2 in farm (minks), domesticated (cats and dogs), and wild animals (tigers, puma, and lions). Recently, the rapid spread of SARS-CoV-2 infection was reported in mink farms, which led to the death of a myriad minks. The clinical and pathological findings of SARS-CoV-2 infection and the rapid animal-to-animal transmission in minks are almost similar to the findings observed in patients with COVID-19. Additionally, the rapid virus transmission among minks and the associated mutations resulted in a new mink-associated variant that was identified in both minks and humans, thereby providing evidence of mink-to-human transmission of SARS-CoV-2. The new mink-associated SARS-CoV-2 variant with a possible reduced sensitivity to neutralizing antibodies poses serious risks and is expected to have a direct effect on the diagnostic techniques, therapeutics, and vaccines that are currently under development. This article highlights the current evidence of SARS-CoV-2 infection in farmed minks, and provides an understanding of the pathogenesis of COVID-19 in minks and the associated zoonotic concerns of SARS-CoV-2 transmission from minks to humans with an emphasis on appropriate mitigation measures and on the necessity of adopting the One Health approach during the COVID-19 pandemic.
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Affiliation(s)
- Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar 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, Uttar Pradesh, India
| | - Senthilkumar Natesan
- Department of Infectious Diseases, Indian Institute of Public Health Gandhinagar, Gandhinagar, Gujarat, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
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