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Nelson CW, Poon LLM, Gu H. Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data. Nat Commun 2024; 15:3239. [PMID: 38627383 PMCID: PMC11021549 DOI: 10.1038/s41467-024-46262-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/21/2024] [Indexed: 04/19/2024] Open
Affiliation(s)
- Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China.
- HKU- Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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Silva MJA, Santana DS, Lima MBM, Silva CS, de Oliveira LG, Monteiro EOL, Dias RDS, Pereira BDKB, Nery PADS, Ferreira MAS, Sarmento MADS, Ayin AAN, Mendes de Oliveira AC, Lima KVB, Lima LNGC. Assessment of the Risk Impact of SARS-CoV-2 Infection Prevalence between Cats and Dogs in America and Europe: A Systematic Review and Meta-Analysis. Pathogens 2024; 13:314. [PMID: 38668269 PMCID: PMC11053406 DOI: 10.3390/pathogens13040314] [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: 03/01/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/29/2024] Open
Abstract
The COVID-19 pandemic represented a huge obstacle for public health and demonstrated weaknesses in surveillance and health promotion systems around the world. Its etiological agent, SARS-CoV-2, of zoonotic origin, has been the target of several studies related to the control and prevention of outbreaks and epidemics of COVID-19 not only for humans but also for animals. Domestic animals, such as dogs and cats, have extensive contact with humans and can acquire the infection both naturally and directly from humans. The objective of this article was to summarize the seroprevalence findings of SARS-CoV-2 in dogs and cats and correlate them with the strength of infection risk between each of them. This is a systematic review and meta-analysis following the recommendations of PRISMA 2020. The search and selection of papers was carried out using in vivo experimental works with animals using the descriptors (MeSH/DeCS) "Animal", "Public Health", "SARS-CoV-2" and "Pandemic" (together with AND) in English, Portuguese or Spanish for Science Direct, PUBMED, LILACS and SciELO databases. The ARRIVE checklist was used for methodological evaluation and the Comprehensive Meta-Analysis v2.2 software with the Difference Risk (RD) test to evaluate statistical inferences (with subgroups by continent). Cats showed greater susceptibility to SARS-CoV-2 compared to dogs both in a joint analysis of studies (RD = 0.017; 95% CI = 0.008-0.025; p < 0.0001) and in the American subgroup (RD = 0.053; 95% CI = 0.032-0.073; p < 0.0001), unlike the lack of significant difference on the European continent (RD = 0.009; 95% CI = -0.001-0.018; p = 0.066). Therefore, it was observed that cats have a greater interest in health surveillance due to the set of biological and ecological aspects of these animals, but also that there are a set of factors that can influence the spread and possible spillover events of the virus thanks to the anthropozoonotic context.
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Affiliation(s)
- Marcos Jessé Abrahão Silva
- Center for Biological and Health Sciences (CCBS), University of the State of Pará (UEPA), Belém 66087-670, PA, Brazil;
| | - Davi Silva Santana
- Institute of Health Sciences (ICS), Institute of Biological Sciences (ICB), Federal University of Pará (UFPA), Belém 66077-830, PA, Brazil; (D.S.S.); (M.B.M.L.); (R.d.S.D.); (M.A.S.F.); (A.C.M.d.O.)
| | - Marceli Batista Martins Lima
- Institute of Health Sciences (ICS), Institute of Biological Sciences (ICB), Federal University of Pará (UFPA), Belém 66077-830, PA, Brazil; (D.S.S.); (M.B.M.L.); (R.d.S.D.); (M.A.S.F.); (A.C.M.d.O.)
| | - Caroliny Soares Silva
- Center for Biological and Health Sciences (CCBS), University of the State of Pará (UEPA), Belém 66087-670, PA, Brazil;
| | - Letícia Gomes de Oliveira
- Evandro Chagas Institute (IEC), Ananindeua 67030-000, PA, Brazil; (L.G.d.O.); (K.V.B.L.); (L.N.G.C.L.)
| | | | - Rafael dos Santos Dias
- Institute of Health Sciences (ICS), Institute of Biological Sciences (ICB), Federal University of Pará (UFPA), Belém 66077-830, PA, Brazil; (D.S.S.); (M.B.M.L.); (R.d.S.D.); (M.A.S.F.); (A.C.M.d.O.)
| | - Bruna de Kássia Barbosa Pereira
- Department of Veterinary Medicine, University of the Amazon (UNAMA), Belém 66120-901, PA, Brazil; (B.d.K.B.P.); (P.A.d.S.N.)
| | - Paula Andresa da Silva Nery
- Department of Veterinary Medicine, University of the Amazon (UNAMA), Belém 66120-901, PA, Brazil; (B.d.K.B.P.); (P.A.d.S.N.)
| | - Márcio André Silva Ferreira
- Institute of Health Sciences (ICS), Institute of Biological Sciences (ICB), Federal University of Pará (UFPA), Belém 66077-830, PA, Brazil; (D.S.S.); (M.B.M.L.); (R.d.S.D.); (M.A.S.F.); (A.C.M.d.O.)
| | | | - Andrea Alexandra Narro Ayin
- Faculty of Medicine, Centro Universitário do Estado do Pará (CESUPA), Belém 66613-903, PA, Brazil; (M.A.d.S.S.); (A.A.N.A.)
| | - Ana Cristina Mendes de Oliveira
- Institute of Health Sciences (ICS), Institute of Biological Sciences (ICB), Federal University of Pará (UFPA), Belém 66077-830, PA, Brazil; (D.S.S.); (M.B.M.L.); (R.d.S.D.); (M.A.S.F.); (A.C.M.d.O.)
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Wang Z, Pei S, Ye R, Chen J, Cheng N, Zhao M, Cao W, Jia Z. Increasing evolution, prevalence, and outbreaks for rift valley fever virus in the process of breaking geographical barriers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170302. [PMID: 38272089 DOI: 10.1016/j.scitotenv.2024.170302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND Rift valley fever (RVF) is listed as one of prioritized diseases by WHO. This study aims to describe RVF virus' landscape distribution globally, and to insight dynamics change of its evolution, prevalence, and outbreaks in the process of breaking geographical barriers. METHODS A systematic literature review and meta-analyses was conducted to estimate RVF prevalence by hosts using a random-effect model. Molecular clock-based phylogenetic analyses were performed to estimate RVF virus nucleotide substitution rates using nucleotide sequences in NCBI database. RVF virus prevalence, nucleotide substitution rates, and outbreaks were compared before and after breaking geographical barriers twice, respectively. RESULTS RVF virus was reported from 26 kinds of hosts covering 48 countries from 1930 to 2022. Since RVF broke geographical barriers, (1) nucleotide substitution rates significantly increased after firstly spreading out of Africa in 2000, (2) prevalence in humans significantly increased from 1.92 % (95 % CI: 0.86-3.25 %) to 3.03 % (95 % CI: 2.09-4.12 %) after it broke Sahara Desert geographical barriers in 1977, and to 5.24 % (95 % CI: 3.81-6.82 %) after 2000, (3) RVF outbreaks in humans and the number of wildlife hosts presented increasing trends. RVF virus spillover may exist between bats and humans, and accelerate viral substitution rates in humans. During outbreaks, the RVF virus substitution rates accelerated in humans. 60.00 % RVF outbreaks occurred 0-2 months after floods and (or) heavy rainfall. CONCLUSION RVF has the increasing risk to cause pandemics, and global collaboration on "One Health" is needed to prevent potential pandemics.
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Affiliation(s)
- Zekun Wang
- School of Public Health, Peking University, Beijing, China
| | - Shaojun Pei
- School of Public Health, Peking University, Beijing, China
| | - Runze Ye
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyuan Chen
- School of Public Health, Peking University, Beijing, China
| | - Nuo Cheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Mingchen Zhao
- School of Public Health, Peking University, Beijing, China
| | - Wuchun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhongwei Jia
- School of Public Health, Peking University, Beijing, China; Center for Intelligent Public Health, Institute for Artificial Intelligence, Peking University, Beijing, China; Center for Drug Abuse Control and Prevention, National Institute of Health Data Science, Peking University, Beijing, China; Peking University Clinical Research Institute, Beijing, China.
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4
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Martínez-González B, Soria ME, Mínguez P, Lorenzo-Redondo R, Salar-Vidal L, López-García A, Esteban-Muñoz M, Durán-Pastor A, Somovilla P, García-Crespo C, de Ávila AI, Gómez J, Esteban J, Fernández-Roblas R, Gadea I, Domingo E, Perales C. SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation? Front Microbiol 2024; 15:1358258. [PMID: 38559344 PMCID: PMC10979541 DOI: 10.3389/fmicb.2024.1358258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/21/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction SARS-CoV-2 isolates of a given clade may contain low frequency genomes that encode amino acids or deletions which are typical of a different clade. Methods Here we use high resolution ultra-deep sequencing to analyze SARS-CoV-2 mutant spectra. Results In 6 out of 11 SARS-CoV-2 isolates from COVID-19 patients, the mutant spectrum of the spike (S)-coding region included two or more amino acids or deletions, that correspond to discordant viral clades. A similar observation is reported for laboratory populations of SARS-CoV-2 USA-WA1/2020, following a cell culture infection in the presence of remdesivir, ribavirin or their combinations. Moreover, some of the clade-discordant genome residues are found in the same haplotype within an amplicon. Discussion We evaluate possible interpretations of these findings, and reviewed precedents for rapid selection of genomes with multiple mutations in RNA viruses. These considerations suggest that intra-host evolution may be sufficient to generate minority sequences which are closely related to sequences typical of other clades. The results provide a model for the origin of variants of concern during epidemic spread─in particular Omicron lineages─that does not require prolonged infection, involvement of immunocompromised individuals, or participation of intermediate, non-human hosts.
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Affiliation(s)
- Brenda Martínez-González
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - María Eugenia Soria
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ramón Lorenzo-Redondo
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Llanos Salar-Vidal
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Alberto López-García
- Health Research Institute IIS-FJD, Fundación Jiménez Diaz University Hospital, Madrid, Spain
| | - Mario Esteban-Muñoz
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Antoni Durán-Pastor
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Pilar Somovilla
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Jordi Gómez
- Instituto de Parasitología y Biomedicina “López-Neyra” (CSIC), Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Jaime Esteban
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Ricardo Fernández-Roblas
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
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Carossino M, Izadmehr S, Trujillo JD, Gaudreault NN, Dittmar W, Morozov I, Balasuriya UBR, Cordon-Cardo C, García-Sastre A, Richt JA. ACE2 and TMPRSS2 distribution in the respiratory tract of different animal species and its correlation with SARS-CoV-2 tissue tropism. Microbiol Spectr 2024; 12:e0327023. [PMID: 38230954 PMCID: PMC10846196 DOI: 10.1128/spectrum.03270-23] [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: 09/07/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024] Open
Abstract
A wide range of animal species show variable susceptibility to SARS-CoV-2; however, host factors associated with varied susceptibility remain to be defined. Here, we examined whether susceptibility to SARS-CoV-2 and virus tropism in different animal species are dependent on the expression and distribution of the virus receptor angiotensin-converting enzyme 2 (ACE2) and the host cell factor transmembrane serine protease 2 (TMPRSS2). We cataloged the upper and lower respiratory tract of multiple animal species and humans in a tissue-specific manner and quantitatively evaluated the distribution and abundance of ACE2 and TMPRSS2 mRNA in situ. Our results show that: (i) ACE2 and TMPRSS2 mRNA are abundant in the conduction portion of the respiratory tract, (ii) ACE2 mRNA occurs at a lower abundance compared to TMPRSS2 mRNA, (iii) co-expression of ACE2-TMPRSS2 mRNAs is highest in those species with the highest susceptibility to SARS-CoV-2 infection (i.e., cats, Syrian hamsters, and white-tailed deer), and (iv) expression of ACE2 and TMPRSS2 mRNA was not altered following SARS-CoV-2 infection. Our results demonstrate that while specific regions of the respiratory tract are enriched in ACE2 and TMPRSS2 mRNAs in different animal species, this is only a partial determinant of susceptibility to SARS-CoV-2 infection.IMPORTANCESARS-CoV-2 infects a wide array of domestic and wild animals, raising concerns regarding its evolutionary dynamics in animals and potential for spillback transmission of emerging variants to humans. Hence, SARS-CoV-2 infection in animals has significant public health relevance. Host factors determining animal susceptibility to SARS-CoV-2 are vastly unknown, and their characterization is critical to further understand susceptibility and viral dynamics in animal populations and anticipate potential spillback transmission. Here, we quantitatively assessed the distribution and abundance of the two most important host factors, angiotensin-converting enzyme 2 and transmembrane serine protease 2, in the respiratory tract of various animal species and humans. Our results demonstrate that while specific regions of the respiratory tract are enriched in these two host factors, they are only partial determinants of susceptibility. Detailed analysis of additional host factors is critical for our understanding of the underlying mechanisms governing viral susceptibility and reservoir hosts.
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Affiliation(s)
- Mariano Carossino
- Department of Pathobiological Sciences and Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Sudeh Izadmehr
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jessie D. Trujillo
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Wellesley Dittmar
- Department of Pathobiological Sciences and Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Igor Morozov
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Udeni B. R. Balasuriya
- Department of Pathobiological Sciences and Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo García-Sastre
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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Sparrer MN, Hodges NF, Ragan I, Yamashita T, Reed KJ, Sherman TJ, Mayer T, Maichak C, Adney DR, Carpenter M, Webb TL, Mayo C. SARS-CoV-2 surveillance in a veterinary health system provides insight into transmission risks. J Am Vet Med Assoc 2024; 262:93-99. [PMID: 38103381 PMCID: PMC11234244 DOI: 10.2460/javma.23.05.0229] [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: 05/16/2023] [Accepted: 09/12/2023] [Indexed: 12/19/2023]
Abstract
OBJECTIVE To investigate the prevalence and seropositivity of SARS-CoV-2 in companion and exotic animals in a veterinary healthcare system. SAMPLE A total of 341 animals were sampled by a combination of oral and nasal swabs. Serum from whole blood was collected from a subset of animals (86 canines, 25 felines, and 6 exotic animals). METHODS After informed owner consent, convenience samples from client-owned animals and the pets of students and staff members associated with Colorado State University's Veterinary Health System were collected between May 2021 and September 2022. Study samples were collected by trained veterinarians, Veterinary Health System staff, and veterinary students. RESULTS SARS-CoV-2 RNA was detected by reverse transcription PCR in 1.6% (95% CI, 0.5% to 4.6%) of domestic canines and 1.1% (95% CI, 0.2% to 6.1%) of domestic felines. No RNA was detected in any of the exotic animal species tested (n = 66). Plaque reduction neutralization tests indicated that 12.8% (95% CI, 7.3% to 21.5%) of canines and 12.0% (95% CI, 4.2% to 30.0%) of felines had neutralizing antibodies against SARS-CoV-2. CLINICAL RELEVANCE This study provides insight regarding SARS-CoV-2 spillover in domestic companion and exotic animals and contributes to our understanding of transmission risk in the veterinary setting.
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Affiliation(s)
- McKenzie N Sparrer
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
- 2Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Natasha F Hodges
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Izabela Ragan
- 3Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Tyler Yamashita
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Kirsten J Reed
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Tyler J Sherman
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Treana Mayer
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Courtney Maichak
- 4Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Danielle R Adney
- 5Department of Life Sciences, Lovelace Biomedical, Albuquerque, NM
| | - Molly Carpenter
- 3Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Tracy L Webb
- 2Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Christie Mayo
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
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Piewbang C, Poonsin P, Lohavicharn P, Punyathi P, Kesdangsakonwut S, Kasantikul T, Techangamsuwan S. Natural SARS-CoV-2 infection in dogs: Determination of viral loads, distributions, localizations, and pathology. Acta Trop 2024; 249:107070. [PMID: 37956819 DOI: 10.1016/j.actatropica.2023.107070] [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: 08/30/2023] [Revised: 10/13/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023]
Abstract
Instances of reverse zoonosis involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been documented in both controlled experiments and spontaneous cases. Although dogs are susceptible to infection, clinical significance is limited to mild or asymptomatic. Here, we investigate the fatal cases of natural SARS-CoV-2 infection in dogs in Thailand. Pathological findings of SARS-CoV-2-infected dogs reveal severe diffuse alveolar damage, pulmonary hyalinization and fibrosis, and syncytial formation, together with minor lesions in brain and kidney. Employing reverse transcription-digital PCR, substantial viral loads of SARS-CoV-2 were detected in lung, kidney, brain, trachea, tonsil, tracheobronchial lymph node, liver, and intestine, respectively. Localization of SARS-CoV-2 within various tissues was examined through immunohistochemistry (IHC), where the co-localization of the viral spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor was illustrated using double IHC. SARS-CoV-2 localization was markedly identified in the epithelial cells of the lung, trachea, intestine and kidneys, and moderately presented in the salivary gland and gall bladder, where the co-localization with the ACE2 was also evident. Neurons in the brainstem where exhibited lymphocytic perivascular cuffing were also found to be positive for SARS-CoV-2 in IHC testing, despite lacking ACE2 receptor expression. In addition, SARS-CoV-2 replication within the lungs of infected dogs was confirmed by transmission electron microscopy, visualizing free viral particles within the cytosol or the endoplasmic reticulum of syncytial cells within the lung. This study considerably expanded on the knowledge of the pathology associated with natural SARS-CoV-2 infection in dogs, a scenario that is relatively infrequent but occasionally leads to fatal outcome. Furthermore, these findings suggest the potential utility of dogs as a model for studying SARS-CoV-2 infection in humans, warranting further investigation.
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Affiliation(s)
- Chutchai Piewbang
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panida Poonsin
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattiya Lohavicharn
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panitnan Punyathi
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sawang Kesdangsakonwut
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tanit Kasantikul
- Veterinary Diagnostic Laboratory, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Kotwa JD, Lobb B, Massé A, Gagnier M, Aftanas P, Banerjee A, Banete A, Blais-Savoie J, Bowman J, Buchanan T, Chee HY, Kruczkiewicz P, Nirmalarajah K, Soos C, Vernygora O, Yip L, Lindsay LR, McGeer AJ, Maguire F, Lung O, Doxey AC, Pickering B, Mubareka S. Genomic and transcriptomic characterization of delta SARS-CoV-2 infection in free-ranging white-tailed deer ( Odocoileus virginianus). iScience 2023; 26:108319. [PMID: 38026171 PMCID: PMC10665813 DOI: 10.1016/j.isci.2023.108319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/12/2023] [Accepted: 10/20/2023] [Indexed: 11/29/2023] Open
Abstract
White-tailed deer (WTD) are susceptible to SARS-CoV-2 and represent an important species for surveillance. Samples from WTD (n = 258) collected in November 2021 from Québec, Canada were analyzed for SARS-CoV-2 RNA. We employed viral genomics and host transcriptomics to further characterize infection and investigate host response. We detected Delta SARS-CoV-2 (B.1.617.2) in WTD from the Estrie region; sequences clustered with human sequences from October 2021 from Vermont, USA, which borders this region. Mutations in the S-gene and a deletion in ORF8 were detected. Host expression patterns in SARS-CoV-2 infected WTD were associated with the innate immune response, including signaling pathways related to anti-viral, pro- and anti-inflammatory signaling, and host damage. We found limited correlation between genes associated with innate immune response from human and WTD nasal samples, suggesting differences in responses to SARS-CoV-2 infection. Our findings provide preliminary insights into host response to SARS-CoV-2 infection in naturally infected WTD.
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Affiliation(s)
| | - Briallen Lobb
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Ariane Massé
- Ministère de l’Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs, Québec City, QC G1S 4X4, Canada
| | - Marianne Gagnier
- Ministère de l’Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs, Québec City, QC G1S 4X4, Canada
| | | | - Arinjay Banerjee
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andra Banete
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | | | - Jeff Bowman
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON K9J 8M5, Canada
| | - Tore Buchanan
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON K9J 8M5, Canada
| | - Hsien-Yao Chee
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
- Global Health Research Center and Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu 215316, China
| | - Peter Kruczkiewicz
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | | | - Catherine Soos
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Saskatoon, SK S7N 3H5, Canada
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Oksana Vernygora
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Lily Yip
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | - L. Robbin Lindsay
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada
| | - Allison J. McGeer
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
- Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Community Health & Epidemiology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Shared Hospital Laboratory, Toronto, ON M4N 3M5, Canada
| | - Oliver Lung
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Andrew C. Doxey
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Bradley Pickering
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
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9
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Gomez-Romero N, Basurto-Alcantara FJ, Velazquez-Salinas L. Assessing the Potential Role of Cats ( Felis catus) as Generators of Relevant SARS-CoV-2 Lineages during the Pandemic. Pathogens 2023; 12:1361. [PMID: 38003825 PMCID: PMC10675002 DOI: 10.3390/pathogens12111361] [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: 10/07/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Several questions regarding the evolution of SARS-CoV-2 remain poorly elucidated. One of these questions is the possible evolutionary impact of SARS-CoV-2 after the infection in domestic animals. In this study, we aimed to evaluate the potential role of cats as generators of relevant SARS-CoV-2 lineages during the pandemic. A total of 105 full-length genome viral sequences obtained from naturally infected cats during the pandemic were evaluated by distinct evolutionary algorithms. Analyses were enhanced, including a set of highly related SARS-CoV-2 sequences recovered from human populations. Our results showed the apparent high susceptibility of cats to the infection SARS-CoV-2 compared with other animal species. Evolutionary analyses indicated that the phylogenomic characteristics displayed by cat populations were influenced by the dominance of specific SARS-CoV-2 genetic groups affecting human populations. However, disparate dN/dS rates at some genes between populations recovered from cats and humans suggested that infection in these two species may suggest a different evolutionary constraint for SARS-CoV-2. Interestingly, the branch selection analysis showed evidence of the potential role of natural selection in the emergence of five distinct cat lineages during the pandemic. Although these lineages were apparently irrelevant to public health during the pandemic, our results suggested that additional studies are needed to understand the role of other animal species in the evolution of SARS-CoV-2 during the pandemic.
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Affiliation(s)
- Ninnet Gomez-Romero
- Comisión México-Estados Unidos para la Prevención de Fiebre Aftosa y Otras Enfermedades Exóticas de los Animales, Carretera Mexico-Toluca Km 15.5 Piso 4 Col. Palo Alto, Cuajimalpa de Morelos, Mexico City 05110, Mexico;
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Av. Universidad No. 3000 Col Copilco Universidad, Mexico City 14510, Mexico;
| | - Francisco Javier Basurto-Alcantara
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Av. Universidad No. 3000 Col Copilco Universidad, Mexico City 14510, Mexico;
| | - Lauro Velazquez-Salinas
- Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY 11944, USA
- National Bio and Agro-Defense Facility (NBAF), Agricultural Research Service, United States Department of Agriculture, Manhattan, KS 66502, USA
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10
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Kim D, Kim J, Kim M, Park H, Park S, Maharjan S, Baek K, Kang BM, Kim S, Park MS, Lee Y, Kwon HJ. Analysis of spike protein variants evolved in a novel in vivo long-term replication model for SARS-CoV-2. Front Cell Infect Microbiol 2023; 13:1280686. [PMID: 38029235 PMCID: PMC10655031 DOI: 10.3389/fcimb.2023.1280686] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The spectrum of SARS-CoV-2 mutations have increased over time, resulting in the emergence of several variants of concern. Persistent infection is assumed to be involved in the evolution of the variants. Calu-3 human lung cancer cells persistently grow without apoptosis and release low virus titers after infection. Methods We established a novel in vivo long-term replication model using xenografts of Calu-3 human lung cancer cells in immunodeficient mice. Virus replication in the tumor was monitored for 30 days and occurrence of mutations in the viral genome was determined by whole-genome deep sequencing. Viral isolates with mutations were selected after plaque forming assays and their properties were determined in cells and in K18-hACE2 mice. Results After infection with parental SARS-CoV-2, viruses were found in the tumor tissues for up to 30 days and acquired various mutations, predominantly in the spike (S) protein, some of which increased while others fluctuated for 30 days. Three viral isolates with different combination of mutations produced higher virus titers than the parental virus in Calu-3 cells without cytopathic effects. In K18-hACE2 mice, the variants were less lethal than the parental virus. Infection with each variant induced production of cross-reactive antibodies to the receptor binding domain of parental SARS-CoV-2 S protein and provided protective immunity against subsequent challenge with parental virus. Discussion These results suggest that most of the SARS-CoV-2 variants acquired mutations promoting host adaptation in the Calu-3 xenograft mice. This model can be used in the future to further study SARS-CoV-2 variants upon long-term replication in vivo.
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Affiliation(s)
- Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jinsoo Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Sony Maharjan
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Bo Min Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Suyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyung-Joo Kwon
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
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11
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Llanco L, Retamozo K, Oviedo N, Manchego A, Lázaro C, Navarro-Mamani DA, Santos N, Rojas M. Co-Circulation of Multiple Coronavirus Genera and Subgenera during an Epizootic of Lethal Respiratory Disease in Newborn Alpacas ( Vicugna pacos) in Peru: First Report of Bat-like Coronaviruses in Alpacas. Animals (Basel) 2023; 13:2983. [PMID: 37760383 PMCID: PMC10525639 DOI: 10.3390/ani13182983] [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: 08/16/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Coronaviruses (CoVs) infect a wide range of hosts, including humans, domestic animals, and wildlife, typically causing mild-to-severe respiratory or enteric disease. The main objective of this study was to identify CoV genera and subgenera detected in Peruvian alpacas. Lung lavage specimens were collected from 32 animals aged 1 to 6 weeks. CoVs were identified by using RT-PCR to amplify a pan-CoV conserved region of the RNA-dependent RNA polymerase-encoding gene. A nested PCR was performed to identify β-CoVs. Then, β-CoV-positive samples were subjected to RT-PCR using specific primers to identify the Embecovirus subgenus. Out of 32 analyzed samples, 30 (93.8%) tested positive for at least one CoV genus. β-, α-, or unclassified CoVs were identified in 24 (80%), 1 (3.3%), and 1 (3.3%) of the positive samples, respectively. A CoV genus could not be identified in two (6.7%) samples. A mixture of different CoV genera was detected in two (6.7%) samples: one was co-infected with β- and α-CoVs, and the other contained a β- and an unclassified CoV. A sequence analysis of the amplicons generated by the PCR identified 17 β-CoV strains belonging to the subgenus Embecovirus and two α-CoV strains belonging to Decacovirus. A phylogenetic analysis of two strains revealed a relationship with an unclassified Megaderma BatCoV strain. A subgenus could not be identified in nine β-CoV samples. Our data show a high prevalence and a high genetic diversity of CoV genera and subgenera that infect alpacas, in which the β-CoV subgenus Embecovirus predominated. Our data also suggest a new role for bats in the dissemination and transmission of uncommon CoVs to alpacas raised in rural Peru.
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Affiliation(s)
- Luis Llanco
- Escuela de Medicina Humana, Universidad Privada San Juan Bautista, Apartado, Chincha 15067, Peru;
| | - Karubya Retamozo
- Laboratório de Inmunología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru; (K.R.); (N.O.); (A.M.)
| | - Noriko Oviedo
- Laboratório de Inmunología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru; (K.R.); (N.O.); (A.M.)
| | - Alberto Manchego
- Laboratório de Inmunología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru; (K.R.); (N.O.); (A.M.)
| | - César Lázaro
- Laboratório de Farmacología y Toxicología Veterinaria, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru;
| | - Dennis A. Navarro-Mamani
- Laboratório de Virología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru;
| | - Norma Santos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil;
| | - Miguel Rojas
- Laboratório de Inmunología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Apartado, Lima 03-5137, Peru; (K.R.); (N.O.); (A.M.)
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12
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Barroso-Arévalo S, Díaz-Frutos M, Domínguez L, Sánchez-Vizcaíno JM. Importance of genomic surveillance of SARS-CoV-2 in cats during reverse zoonosis events: potential viral evolution may occur. Microbiol Spectr 2023; 11:e0068023. [PMID: 37565759 PMCID: PMC10581217 DOI: 10.1128/spectrum.00680-23] [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: 02/16/2023] [Accepted: 06/29/2023] [Indexed: 08/12/2023] Open
Abstract
The apparition of new variants of severe acute respiratory syndrome coronavirus 2 and lineages is constantly happening because of the high viral mutation rate. Since numerous reverse zoonosis events have been reported so far, genomic surveillance should be conducted in susceptible species to evaluate potential adaptations that may trigger the apparition of new variants. Here, we evaluate the evolution of the infection in a cat naturally infected in parallel with its owner, performing a comparative phylogenetic analysis. Sequencing analysis showed that both were infected with the Omicron BA.5/BF.1 lineage and revealed the presence of nucleotide substitution in the viral genome recovered from the cat with respect to the viral genome from the human sample. This nucleotide substitution (C11897A) produced the amino acid change Orf1a: Q3878K. Therefore, genomic surveillance in the case of reverse zoonosis events is still necessary in order to control possible adaptations of the virus to other susceptible species. IMPORTANCE Genomic surveillance of pets for severe acute respiratory syndrome coronavirus 2 is important to monitor the emergence of new variants of the virus associated with these animals. Pets can serve as a potential reservoir for the virus, and their close contact with humans increases the risk of transmission. By conducting genomic surveillance in pets, it is possible to detect and track new variants early on, allowing for more effective control measures to be put in place. This can help prevent the spread of these variants to human populations and potentially mitigate the impact of the pandemic. Furthermore, it may also provide insight into the evolution and spread of the virus within the animal population.
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Affiliation(s)
- Sandra Barroso-Arévalo
- VISAVET Health Surveillance Center, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - Marta Díaz-Frutos
- VISAVET Health Surveillance Center, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Center, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - José M. Sánchez-Vizcaíno
- VISAVET Health Surveillance Center, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
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13
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Feng A, Bevins S, Chandler J, DeLiberto TJ, Ghai R, Lantz K, Lenoch J, Retchless A, Shriner S, Tang CY, Tong SS, Torchetti M, Uehara A, Wan XF. Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States. Nat Commun 2023; 14:4078. [PMID: 37429851 DOI: 10.1038/s41467-023-39782-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023] Open
Abstract
SARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of SARS-CoV-2 from humans to free-ranging white-tailed deer (Odocoileus virginianus) poses a unique public health risk due to the potential for reservoir establishment where variants may persist and evolve. We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants. Evolutionary analyses showed these white-tailed deer viruses originated from at least 109 independent spillovers from humans, which resulted in 39 cases of subsequent local deer-to-deer transmission and three cases of potential spillover from white-tailed deer back to humans. Viruses repeatedly adapted to white-tailed deer with recurring amino acid substitutions across spike and other proteins. Overall, our findings suggest that multiple SARS-CoV-2 lineages were introduced, became enzootic, and co-circulated in white-tailed deer.
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Affiliation(s)
- Aijing Feng
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Sarah Bevins
- USDA APHIS Wildlife Services National Wildlife Disease Program, Fort Collins, CO, USA
| | - Jeff Chandler
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO, USA
| | | | - Ria Ghai
- One Health Office, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kristina Lantz
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Julianna Lenoch
- USDA APHIS Wildlife Services National Wildlife Disease Program, Fort Collins, CO, USA
| | - Adam Retchless
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Susan Shriner
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO, USA
| | - Cynthia Y Tang
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Suxiang Sue Tong
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mia Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Anna Uehara
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
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14
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Hamdy ME, El Deeb AH, Hagag NM, Shahein MA, Alaidi O, Hussein HA. Interspecies transmission of SARS CoV-2 with special emphasis on viral mutations and ACE-2 receptor homology roles. Int J Vet Sci Med 2023; 11:55-86. [PMID: 37441062 PMCID: PMC10334861 DOI: 10.1080/23144599.2023.2222981] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 05/11/2023] [Accepted: 05/19/2023] [Indexed: 07/15/2023] Open
Abstract
COVID-19 outbreak was first reported in 2019, Wuhan, China. The spillover of the disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), to a wide range of pet, zoo, wild, and farm animals has emphasized potential zoonotic and reverse zoonotic viral transmission. Furthermore, it has evoked inquiries about susceptibility of different animal species to SARS-CoV-2 infection and role of these animals as viral reservoirs. Therefore, studying susceptible and non-susceptible hosts for SARS-CoV-2 infection could give a better understanding for the virus and will help in preventing further outbreaks. Here, we review structural aspects of SARS-CoV-2 spike protein, the effect of the different mutations observed in the spike protein, and the impact of ACE2 receptor variations in different animal hosts on inter-species transmission. Moreover, the SARS-CoV-2 spillover chain was reviewed. Combination of SARS-CoV-2 high mutation rate and homology of cellular ACE2 receptors enable the virus to transcend species barriers and facilitate its transmission between humans and animals.
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Affiliation(s)
- Mervat E. Hamdy
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Ayman H. El Deeb
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
- Department of Virology, Faculty of Veterinary Medicine, King Salman International University, South Sinai, Egypt
| | - Naglaa M. Hagag
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Momtaz A. Shahein
- Department of Virology, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Osama Alaidi
- Biocomplexity for Research and Consulting Co., Cairo, Egypt
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Hussein A. Hussein
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
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15
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Dehesa-Canseco F, Pastrana-Unzueta R, Carrillo-Guzmán N, Liljehult-Fuentes F, Pérez-De la Rosa JD, Ramírez-Mendoza H, Estrada-Franco JG, Navarro-López R, Hernández J, Solís-Hernández M. Neutralizing Antibodies against the SARS-CoV-2 Ancestral Strain and Omicron BA.1 Subvariant in Dogs and Cats in Mexico. Pathogens 2023; 12:835. [PMID: 37375525 DOI: 10.3390/pathogens12060835] [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: 05/18/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
SARS-CoV-2 mainly affects humans; however, it is important to monitor the infection of companion and wild animals as possible reservoirs of this virus. In this sense, seroprevalence studies in companion animals, such as dogs and cats, provide important information about the epidemiology of SARS-CoV-2. This study aimed to evaluate the seroprevalence of neutralizing antibodies (nAbs) against the ancestral strain and the Omicron BA.1 subvariant in dogs and cats in Mexico. Six hundred and two samples were obtained from dogs (n = 574) and cats (n = 28). These samples were collected from the end of 2020 to December 2021 from different regions of Mexico. The presence of nAbs was evaluated using a plaque reduction neutralization test (PRNT) and microneutralization (MN) assays. The results showed that 14.2% of cats and 1.5% of dogs presented nAbs against the ancestral strain of SARS-CoV-2. The analysis of nAbs against Omicron BA.1 in cats showed the same percentage of positive animals but a reduced titer. In dogs, 1.2% showed nAbs against Omicron BA.1. These results indicate that nAbs were more frequent in cats than in dogs and that these nAbs have a lower capacity to neutralize the subvariant Omicron BA.1.
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Affiliation(s)
- Freddy Dehesa-Canseco
- Comisión México-Estados Unidos para la Prevención de la Fiebre Aftosa y otras Enfermedades Exóticas de los Animales (CPA), Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Secretaría de Agricultura y Desarrollo Rural (SADER), Ciudad de Mexico 05110, Mexico
| | - Roxana Pastrana-Unzueta
- Comisión México-Estados Unidos para la Prevención de la Fiebre Aftosa y otras Enfermedades Exóticas de los Animales (CPA), Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Secretaría de Agricultura y Desarrollo Rural (SADER), Ciudad de Mexico 05110, Mexico
| | - Nadia Carrillo-Guzmán
- Comisión México-Estados Unidos para la Prevención de la Fiebre Aftosa y otras Enfermedades Exóticas de los Animales (CPA), Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Secretaría de Agricultura y Desarrollo Rural (SADER), Ciudad de Mexico 05110, Mexico
| | - Francisco Liljehult-Fuentes
- Comisión México-Estados Unidos para la Prevención de la Fiebre Aftosa y otras Enfermedades Exóticas de los Animales (CPA), Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Secretaría de Agricultura y Desarrollo Rural (SADER), Ciudad de Mexico 05110, Mexico
| | - Juan Diego Pérez-De la Rosa
- Centro Nacional de Servicios de Constatación en Salud Animal (CENAPA), Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Secretaría de Agricultura y Desarrollo Rural (SADER), Cuernavaca 62574, Mexico
| | - Humberto Ramírez-Mendoza
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Universidad Nacional Autónoma de México (UNAM), Ciudad de Mexico 04510, Mexico
| | | | - Roberto Navarro-López
- Comisión México-Estados Unidos para la Prevención de la Fiebre Aftosa y otras Enfermedades Exóticas de los Animales (CPA), Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Secretaría de Agricultura y Desarrollo Rural (SADER), Ciudad de Mexico 05110, Mexico
| | - Jesús Hernández
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A. C. (CIAD), Hermosillo Sonora 83304, Mexico
| | - Mario Solís-Hernández
- Comisión México-Estados Unidos para la Prevención de la Fiebre Aftosa y otras Enfermedades Exóticas de los Animales (CPA), Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Secretaría de Agricultura y Desarrollo Rural (SADER), Ciudad de Mexico 05110, Mexico
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16
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Qerqez AN, Silva RP, Maynard JA. Outsmarting Pathogens with Antibody Engineering. Annu Rev Chem Biomol Eng 2023; 14:217-241. [PMID: 36917814 PMCID: PMC10330301 DOI: 10.1146/annurev-chembioeng-101121-084508] [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] [Indexed: 03/16/2023]
Abstract
There is growing interest in identifying antibodies that protect against infectious diseases, especially for high-risk individuals and pathogens for which no vaccine is yet available. However, pathogens that manifest as opportunistic or latent infections express complex arrays of virulence-associated proteins and are adept at avoiding immune responses. Some pathogens have developed strategies to selectively destroy antibodies, whereas others create decoy epitopes that trick the host immune system into generating antibodies that are at best nonprotective and at worst enhance pathogenesis. Antibody engineering strategies can thwart these efforts by accessing conserved neutralizing epitopes, generating Fc domains that resist capture or degradation and even accessing pathogens hidden inside cells. Design of pathogen-resistant antibodies can enhance protection and guide development of vaccine immunogens against these complex pathogens. Here, we discuss general strategies for design of antibodies resistant to specific pathogen defense mechanisms.
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Affiliation(s)
- Ahlam N Qerqez
- Department of Chemical Engineering, The University of Texas, Austin, Texas, USA;
| | - Rui P Silva
- Department of Molecular Biosciences, The University of Texas, Austin, Texas, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas, Austin, Texas, USA;
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17
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Devaux CA, Fantini J. Unravelling Antigenic Cross-Reactions toward the World of Coronaviruses: Extent of the Stability of Shared Epitopes and SARS-CoV-2 Anti-Spike Cross-Neutralizing Antibodies. Pathogens 2023; 12:713. [PMID: 37242383 PMCID: PMC10220573 DOI: 10.3390/pathogens12050713] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
The human immune repertoire retains the molecular memory of a very great diversity of target antigens (epitopes) and can recall this upon a second encounter with epitopes against which it has previously been primed. Although genetically diverse, proteins of coronaviruses exhibit sufficient conservation to lead to antigenic cross-reactions. In this review, our goal is to question whether pre-existing immunity against seasonal human coronaviruses (HCoVs) or exposure to animal CoVs has influenced the susceptibility of human populations to SARS-CoV-2 and/or had an impact upon the physiopathological outcome of COVID-19. With the hindsight that we now have regarding COVID-19, we conclude that although antigenic cross-reactions between different coronaviruses exist, cross-reactive antibody levels (titers) do not necessarily reflect on memory B cell frequencies and are not always directed against epitopes which confer cross-protection against SARS-CoV-2. Moreover, the immunological memory of these infections is short-term and occurs in only a small percentage of the population. Thus, in contrast to what might be observed in terms of cross-protection at the level of a single individual recently exposed to circulating coronaviruses, a pre-existing immunity against HCoVs or other CoVs can only have a very minor impact on SARS-CoV-2 circulation at the level of human populations.
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Affiliation(s)
- Christian A. Devaux
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM Institut Hospitalo-Universitaire—Méditerranée Infection, 13005 Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), 13009 Marseille, France
| | - Jacques Fantini
- Aix-Marseille Université, INSERM UMR_S 1072, 13015 Marseille, France
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18
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Kim SH, Kearns FL, Rosenfeld MA, Votapka L, Casalino L, Papanikolas M, Amaro RE, Freeman R. SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101346. [PMID: 37077408 PMCID: PMC10080732 DOI: 10.1016/j.xcrp.2023.101346] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/07/2023] [Accepted: 03/07/2023] [Indexed: 05/03/2023]
Abstract
Viral variants of concern continue to arise for SARS-CoV-2, potentially impacting both methods for detection and mechanisms of action. Here, we investigate the effect of an evolving spike positive charge in SARS-CoV-2 variants and subsequent interactions with heparan sulfate and the angiotensin converting enzyme 2 (ACE2) in the glycocalyx. We show that the positively charged Omicron variant evolved enhanced binding rates to the negatively charged glycocalyx. Moreover, we discover that while the Omicron spike-ACE2 affinity is comparable to that of the Delta variant, the Omicron spike interactions with heparan sulfate are significantly enhanced, giving rise to a ternary complex of spike-heparan sulfate-ACE2 with a large proportion of double-bound and triple-bound ACE2. Our findings suggest that SARS-CoV-2 variants evolve to be more dependent on heparan sulfate in viral attachment and infection. This discovery enables us to engineer a second-generation lateral-flow test strip that harnesses both heparin and ACE2 to reliably detect all variants of concern, including Omicron.
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Affiliation(s)
- Sang Hoon Kim
- Department of Applied Physical Sciences, University of North Carolina - Chapel Hill, 1112 Murray Hall, CB#3050, Chapel Hill, NC 27599-2100, USA
| | - Fiona L Kearns
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Mia A Rosenfeld
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Lane Votapka
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Micah Papanikolas
- Department of Applied Physical Sciences, University of North Carolina - Chapel Hill, 1112 Murray Hall, CB#3050, Chapel Hill, NC 27599-2100, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina - Chapel Hill, 1112 Murray Hall, CB#3050, Chapel Hill, NC 27599-2100, USA
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19
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Peka M, Balatsky V. The impact of mutation sets in receptor-binding domain of SARS-CoV-2 variants on the stability of RBD–ACE2 complex. Future Virol 2023. [PMID: 37064325 PMCID: PMC10089296 DOI: 10.2217/fvl-2022-0152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/01/2023] [Indexed: 04/08/2023]
Abstract
Aim: Bioinformatic analysis of mutation sets in receptor-binding domain (RBD) of currently and previously circulating SARS-CoV-2 variants of concern (VOCs) and interest (VOIs) to assess their ability to bind the ACE2 receptor. Methods: In silico sequence and structure-oriented approaches were used to evaluate the impact of single and multiple mutations. Results: Mutations detected in VOCs and VOIs led to the reduction of binding free energy of the RBD–ACE2 complex, forming additional chemical bonds with ACE2, and to an increase of RBD–ACE2 complex stability. Conclusion: Mutation sets characteristic of SARS-CoV-2 variants have complex effects on the ACE2 receptor-binding affinity associated with amino acid interactions at mutation sites, as well as on the acquisition of other viral adaptive advantages.
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Affiliation(s)
- Mykyta Peka
- V. N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine
- Institute of Pig Breeding & Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, Poltava, 36013, Ukraine
| | - Viktor Balatsky
- V. N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine
- Institute of Pig Breeding & Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, Poltava, 36013, Ukraine
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20
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Klestova Z. Possible spread of SARS-CoV-2 in domestic and wild animals and body temperature role. Virus Res 2023; 327:199066. [PMID: 36754290 PMCID: PMC9911306 DOI: 10.1016/j.virusres.2023.199066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023]
Abstract
The COVID-19 pandemic was officially announced in March 2020 and is still moving around the world. Virus strains, their pathogenicity and infectivity are changing, but the ability is fast to spread and harm people's health remained, despite the seasonality seasons and other circumstances. Most likely, humanity is doomed for a long time to coexistence with this emergent pathogen, since it is already circulating not only among the human population, but and among fauna, especially among wild animals in different regions of the planet. Thus, the range the virus has expanded, the material and conditions for its evolution are more than enough. The detection of SARS-CoV-2 in known infected fauna species is analyzed and possible spread and ongoing circulation of the virus in domestic and wild animals are discussed. One of the main focus of the article is the role of animal body temperature, its fluctuations and the presence of entry receptors in the susceptibility of different animal species to SARS-CoV-2 infection and virus spreading in possible new ecological niches. The possibility of long-term circulation of the pathogen among susceptible organisms is discussed.
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Affiliation(s)
- Zinaida Klestova
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Elfriede-Aulhorn-Straße 6, Tübingen 72076, Germany.
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21
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Akaishi T, Fujiwara K. Insertion and deletion mutations preserved in SARS-CoV-2 variants. Arch Microbiol 2023; 205:154. [PMID: 37000302 PMCID: PMC10064622 DOI: 10.1007/s00203-023-03493-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 04/01/2023]
Abstract
The insertion/deletion (indel) mutation profiles of SARS-CoV-2 variants, including Omicron, remain unclear. We compared whole-genome sequences from various lineages and used preserved indels to infer the ancestral relationships between different lineages. Thirteen indel patterns from twelve sites were seen in ≥ 2 sequences; six of these sites were located in the N-terminal domain of the viral spike gene. Preserved indels in the coding regions were also identified in the non-structural protein 3 (Nsp3), Nsp6, and nucleocapsid genes. Seven of the thirteen indel patterns were specific to the Omicron variants, four of which were observed in BA.1, making it the most mutated variant. Other preserved indels observed in the Omicron variants were also seen in Alpha and/or Gamma, but not Delta, suggesting that Omicron is phylogenetically more proximal to Alpha. We demonstrated distinct profiles of preserved indels among SARS-CoV-2 variants and sublineages, suggesting the importance of indels in viral evolution.
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Affiliation(s)
- Tetsuya Akaishi
- Department of Education and Support for Regional Medicine, Tohoku University, Seiryo-Machi 1-1, Aoba-Ku, Sendai, Miyagi, 980-8574, Japan.
- COVID-19 Testing Center, Tohoku University, Sendai, Japan.
| | - Kei Fujiwara
- Department of Gastroenterology and Metabolism, Nagoya City University, Nagoya, Japan
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22
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Gu H, Quadeer AA, Krishnan P, Ng DYM, Chang LDJ, Liu GYZ, Cheng SMS, Lam TTY, Peiris M, McKay MR, Poon LLM. Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals. Nat Commun 2023; 14:1793. [PMID: 37002233 PMCID: PMC10063955 DOI: 10.1038/s41467-023-37468-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Viral and host factors can shape SARS-CoV-2 evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here, we analysed deep sequencing data from 2,820 SARS-CoV-2 respiratory samples with different viral lineages to describe the patterns of within-host diversity under different conditions, including vaccine-breakthrough infections. In unvaccinated individuals, variant of Concern (VOC) Alpha, Delta, and Omicron respiratory samples were found to have higher within-host diversity and were under neutral to purifying selection at the full genome level compared to non-VOC SARS-CoV-2. Breakthrough infections in 2-dose or 3-dose Comirnaty and CoronaVac vaccinated individuals did not increase levels of non-synonymous mutations and did not change the direction of selection pressure. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 sequence diversification. Our findings suggest that vaccination does not increase exploration of SARS-CoV-2 protein sequence space and may not facilitate emergence of viral variants.
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Affiliation(s)
- Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ahmed Abdul Quadeer
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Daisy Y M Ng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lydia D J Chang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Gigi Y Z Liu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Samuel M S Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tommy T Y Lam
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Matthew R McKay
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electrical and Electronic Engineering, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China.
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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23
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Ong'era EM, Mohammed KS, Makori TO, Bejon P, Ocholla-Oyier LI, Nokes DJ, Agoti CN, Githinji G. High-throughput sequencing approaches applied to SARS-CoV-2. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18701.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
High-throughput sequencing is crucial for surveillance and control of viral outbreaks. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, advances in the high-throughput sequencing technology resources have enhanced diagnosis, surveillance, and vaccine discovery. From the onset of the pandemic in December 2019, several genome-sequencing approaches have been developed and supported across the major sequencing platforms such as Illumina, Oxford Nanopore, PacBio, MGI DNBSEQTM and Ion Torrent. Here, we share insights from the sequencing approaches developed for sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between December 2019 and October 2022.
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24
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Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J, Peacock SJ, Barclay WS, de Silva TI, Towers GJ, Robertson DL. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol 2023; 21:162-177. [PMID: 36653446 PMCID: PMC9847462 DOI: 10.1038/s41579-022-00841-7] [Citation(s) in RCA: 279] [Impact Index Per Article: 279.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/19/2023]
Abstract
In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited a major step change in its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates of transmission relative to previous variants and were termed 'variants of concern' (VOCs). Designated Alpha, Beta, Gamma, Delta and Omicron, the VOCs emerged independently from one another, and in turn each rapidly became dominant, regionally or globally, outcompeting previous variants. The success of each VOC relative to the previously dominant variant was enabled by altered intrinsic functional properties of the virus and, to various degrees, changes to virus antigenicity conferring the ability to evade a primed immune response. The increased virus fitness associated with VOCs is the result of a complex interplay of virus biology in the context of changing human immunity due to both vaccination and prior infection. In this Review, we summarize the literature on the relative transmissibility and antigenicity of SARS-CoV-2 variants, the role of mutations at the furin spike cleavage site and of non-spike proteins, the potential importance of recombination to virus success, and SARS-CoV-2 evolution in the context of T cells, innate immunity and population immunity. SARS-CoV-2 shows a complicated relationship among virus antigenicity, transmission and virulence, which has unpredictable implications for the future trajectory and disease burden of COVID-19.
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Affiliation(s)
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Wendy S Barclay
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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25
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Tosta S, Moreno K, Schuab G, Fonseca V, Segovia FMC, Kashima S, Elias MC, Sampaio SC, Ciccozzi M, Alcantara LCJ, Slavov SN, Lourenço J, Cella E, Giovanetti M. Global SARS-CoV-2 genomic surveillance: What we have learned (so far). INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 108:105405. [PMID: 36681102 PMCID: PMC9847326 DOI: 10.1016/j.meegid.2023.105405] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023]
Abstract
The COVID-19 pandemic has brought significant challenges for genomic surveillance strategies in public health systems worldwide. During the past thirty-four months, many countries faced several epidemic waves of SARS-CoV-2 infections, driven mainly by the emergence and spread of novel variants. In that line, genomic surveillance has been a crucial toolkit to study the real-time SARS-CoV-2 evolution, for the assessment and optimization of novel diagnostic assays, and to improve the efficacy of existing vaccines. During the pandemic, the identification of emerging lineages carrying lineage-specific mutations (particularly those in the Receptor Binding domain) showed how these mutations might significantly impact viral transmissibility, protection from reinfection and vaccination. So far, an unprecedented number of SARS-CoV-2 viral genomes has been released in public databases (i.e., GISAID, and NCBI), achieving 14 million genome sequences available as of early-November 2022. In the present review, we summarise the global landscape of SARS-CoV-2 during the first thirty-four months of viral circulation and evolution. It demonstrates the urgency and importance of sustained investment in genomic surveillance strategies to timely identify the emergence of any potential viral pathogen or associated variants, which in turn is key to epidemic and pandemic preparedness.
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Affiliation(s)
- Stephane Tosta
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Keldenn Moreno
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Schuab
- Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil; Laboratório de Flavivirus, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vagner Fonseca
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil.
| | | | - Simone Kashima
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo,Brazil
| | | | | | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy
| | - Luiz Carlos Junior Alcantara
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivirus, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo,Brazil; Butantan Institute, São Paulo, Brazil
| | - José Lourenço
- BioISI (Biosystems and Integrative Sciences Institute), Faculdade de Ciências da Universidade de Lisboa, Lisboa,Portugal
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA.
| | - Marta Giovanetti
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivirus, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil; Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy.
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26
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Arai Y, Yamanaka I, Okamoto T, Isobe A, Nakai N, Kamimura N, Suzuki T, Daidoji T, Ono T, Nakaya T, Matsumoto K, Okuzaki D, Watanabe Y. Stimulation of interferon-β responses by aberrant SARS-CoV-2 small viral RNAs acting as retinoic acid-inducible gene-I agonists. iScience 2023; 26:105742. [PMID: 36507221 PMCID: PMC9726650 DOI: 10.1016/j.isci.2022.105742] [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: 05/27/2022] [Revised: 07/03/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Patients with severe COVID-19 exhibit a cytokine storm characterized by greatly elevated levels of cytokines. Despite this, the interferon (IFN) response is delayed, contributing to disease progression. Here, we report that SARS-CoV-2 excessively generates small viral RNAs (svRNAs) encoding exact 5' ends of positive-sense genes in human cells in vitro and ex vivo, whereas endemic human coronaviruses (OC43 and 229E) produce significantly fewer similar svRNAs. SARS-CoV-2 5' end svRNAs are RIG-I agonists and induce the IFN-β response in the later stages of infection. The first 60-nt ends bearing duplex structures and 5'-triphosphates are responsible for immune-stimulation. We propose that RIG-I activation by accumulated SARS-CoV-2 5' end svRNAs may contribute to later drive over-exuberant IFN production. Additionally, the differences in the amounts of svRNAs produced and the corresponding IFN response among CoV strains suggest that lower svRNA production during replication may correlate with the weaker immune response seen in less pathogenic CoVs.
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Affiliation(s)
- Yasuha Arai
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Itaru Yamanaka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Ayana Isobe
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Naomi Nakai
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Naoko Kamimura
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Tomo Daidoji
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Takao Ono
- SANKEN, Osaka University, Osaka 567-0047, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | | | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan,Single Cell Genomics, Human Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Yohei Watanabe
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan,Corresponding author
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27
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Kuhlmeier E, Chan T, Agüí CV, Willi B, Wolfensberger A, Beisel C, Topolsky I, Beerenwinkel N, Stadler T, Jones S, Tyson G, Hosie MJ, Reitt K, Hüttl J, Meli ML, Hofmann-Lehmann R. Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland. Viruses 2023; 15:245. [PMID: 36680285 PMCID: PMC9864232 DOI: 10.3390/v15010245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
In human beings, there are five reported variants of concern of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). However, in contrast to human beings, descriptions of infections of animals with specific variants are still rare. The aim of this study is to systematically investigate SARS-CoV-2 infections in companion animals in close contact with SARS-CoV-2-positive owners ("COVID-19 households") with a focus on the Delta variant. Samples, obtained from companion animals and their owners were analyzed using a real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) and next-generation sequencing (NGS). Animals were also tested for antibodies and neutralizing activity against SARS-CoV-2. Eleven cats and three dogs in nine COVID-19-positive households were RT-qPCR and/or serologically positive for the SARS-CoV-2 Delta variant. For seven animals, the genetic sequence could be determined. The animals were infected by one of the pangolin lineages B.1.617.2, AY.4, AY.43 and AY.129 and between zero and three single-nucleotide polymorphisms (SNPs) were detected between the viral genomes of animals and their owners, indicating within-household transmission between animal and owner and in multi-pet households also between the animals. NGS data identified SNPs that occur at a higher frequency in the viral sequences of companion animals than in viral sequences of humans, as well as SNPs, which were exclusively found in the animals investigated in the current study and not in their owners. In conclusion, our study is the first to describe the SARS-CoV-2 Delta variant transmission to animals in Switzerland and provides the first-ever description of Delta-variant pangolin lineages AY.129 and AY.4 in animals. Our results reinforce the need of a One Health approach in the monitoring of SARS-CoV-2 in animals.
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Affiliation(s)
- Evelyn Kuhlmeier
- Clinical Laboratory, Department of Clinical Diagnostics and Services, Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Tatjana Chan
- Clinical Laboratory, Department of Clinical Diagnostics and Services, Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Cecilia Valenzuela Agüí
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Barbara Willi
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Aline Wolfensberger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | | | - Sarah Jones
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
- MRC-University of Glasgow Centre for Virus, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Grace Tyson
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Margaret J. Hosie
- MRC-University of Glasgow Centre for Virus, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Katja Reitt
- Center for Laboratory Medicine, Veterinary Diagnostic Services, Frohbergstrasse 3, 9001 St. Gallen, Switzerland
| | - Julia Hüttl
- Center for Laboratory Medicine, Veterinary Diagnostic Services, Frohbergstrasse 3, 9001 St. Gallen, Switzerland
| | - Marina L. Meli
- Clinical Laboratory, Department of Clinical Diagnostics and Services, Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Regina Hofmann-Lehmann
- Clinical Laboratory, Department of Clinical Diagnostics and Services, Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
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28
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Wang Q, Ye S, Zhou Z, Song A, Zhu X, Peng J, Liang R, Yang C, Yu X, Huang X, Yu J, Qiu Y, Ge X. Key mutations in the spike protein of SARS-CoV-2 affecting neutralization resistance and viral internalization. J Med Virol 2023; 95:e28407. [PMID: 36519597 PMCID: PMC9877909 DOI: 10.1002/jmv.28407] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/17/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
To control the ongoing COVID-19 pandemic, a variety of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines have been developed. However, the rapid mutations of SARS-CoV-2 spike (S) protein may reduce the protective efficacy of the existing vaccines which is mainly determined by the level of neutralizing antibodies targeting S. In this study, we screened prevalent S mutations and constructed 124 pseudotyped lentiviral particles carrying these mutants. We challenged these pseudoviruses with sera vaccinated by Sinovac CoronaVac and ZF2001 vaccines, two popular vaccines designed for the initial strain of SARS-CoV-2, and then systematically assessed the susceptivity of these SARS-CoV-2 variants to the immune sera of vaccines. As a result, 14 S mutants (H146Y, V320I + S477N, V382L, K444R, L455F + S477N, L452M + F486L, F486L, Y508H, P521R, A626S, S477N + S698L, A701V, S477N + T778I, E1144Q) were found to be significantly resistant to neutralization, indicating reduced protective efficacy of the vaccines against these SARS-CoV-2 variants. In addition, F486L and Y508H significantly enhanced the utilization of human angiotensin-converting enzyme 2, suggesting a potentially elevated infectivity of these two mutants. In conclusion, our results show that some prevalent S mutations of SARS-CoV-2 reduced the protective efficacy of current vaccines and enhance the infectivity of the virus, indicating the necessity of vaccine renewal and providing direction for the development of new vaccines.
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Affiliation(s)
- Qiong Wang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Sheng‐Bao Ye
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Zhi‐Jian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - A‐Ling Song
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Xi Zhu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Jia‐Mei Peng
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Rui‐Min Liang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Chen‐Hui Yang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Xiao‐Wei Yu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina,Hunan Prevention and Treatment Institute for Occupational DiseasesChangshaHunanChina
| | - Xun Huang
- Department of Hospital Infection Control CenterXiangya Hospital of Central South UniversityChangshaChina
| | - Jie Yu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina
| | - Xing‐Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of BiologyHunan UniversityChangshaHunanChina,Department of Hospital Infection Control CenterXiangya Hospital of Central South UniversityChangshaChina
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29
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Bellinati L, Campalto M, Mazzotta E, Ceglie L, Cavicchio L, Mion M, Lucchese L, Salomoni A, Bortolami A, Quaranta E, Magarotto J, Favarato M, Squarzon L, Natale A. One-Year Surveillance of SARS-CoV-2 Exposure in Stray Cats and Kennel Dogs from Northeastern Italy. Microorganisms 2022; 11:microorganisms11010110. [PMID: 36677401 PMCID: PMC9866628 DOI: 10.3390/microorganisms11010110] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Dogs and cats are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). During the pandemic, several studies have been performed on owned cats and dogs, whereas limited data are available on the exposure to stray animals. The objective of this study was to investigate the exposure to SARS-CoV-2 of feral cats and kennel dogs in northeastern Italy, through serological and molecular methods. From May 2021 to September 2022, public health veterinary services collected serum, oropharyngeal, and rectal swab samples from 257 free-roaming dogs newly introduced to shelters, and from 389 feral cats examined during the routinely trap-neutered-return programs. The swabs were analyzed for viral RNA through a real-time reverse transcriptase PCR (rRT-PCR), and sera were tested for the presence of the specific antibody against SARS-CoV-2 (enzyme-linked immunosorbent assay). Serology was positive in nine dogs (9/257) and three cats (3/389), while two asymptomatic cats tested positive to rRT-PCR. One cat turned out to be positive both for serology and molecular analysis. In addition, this study described the case of a possible human-to-animal SARS-CoV-2 transmission in a cat that travelled in close contact to a COVID-19-positive refugee from Ukraine. This study shows that SARS-CoV-2 can infect, in natural conditions, stray cats and kennel dogs in northeastern Italy, although with a low prevalence.
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Affiliation(s)
- Laura Bellinati
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Mery Campalto
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
- Correspondence:
| | - Elisa Mazzotta
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Letizia Ceglie
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Lara Cavicchio
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Monica Mion
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Laura Lucchese
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Angela Salomoni
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Alessio Bortolami
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Erika Quaranta
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | | | - Mosè Favarato
- UOSD Genetica e Citogenetica e Diagnostica Molecolare-Azienda ULSS 3 Serenissima, 30174 Venice, Italy
| | - Laura Squarzon
- UOSD Genetica e Citogenetica e Diagnostica Molecolare-Azienda ULSS 3 Serenissima, 30174 Venice, Italy
| | - Alda Natale
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
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30
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Vandegrift KJ, Yon M, Surendran Nair M, Gontu A, Ramasamy S, Amirthalingam S, Neerukonda S, Nissly RH, Chothe SK, Jakka P, LaBella L, Levine N, Rodriguez S, Chen C, Sheersh Boorla V, Stuber T, Boulanger JR, Kotschwar N, Aucoin SG, Simon R, Toal KL, Olsen RJ, Davis JJ, Bold D, Gaudreault NN, Dinali Perera K, Kim Y, Chang KO, Maranas CD, Richt JA, Musser JM, Hudson PJ, Kapur V, Kuchipudi SV. SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City. Viruses 2022; 14:2770. [PMID: 36560774 PMCID: PMC9785669 DOI: 10.3390/v14122770] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/19/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
There is mounting evidence of SARS-CoV-2 spillover from humans into many domestic, companion, and wild animal species. Research indicates that humans have infected white-tailed deer, and that deer-to-deer transmission has occurred, indicating that deer could be a wildlife reservoir and a source of novel SARS-CoV-2 variants. We examined the hypothesis that the Omicron variant is actively and asymptomatically infecting the free-ranging deer of New York City. Between December 2021 and February 2022, 155 deer on Staten Island, New York, were anesthetized and examined for gross abnormalities and illnesses. Paired nasopharyngeal swabs and blood samples were collected and analyzed for the presence of SARS-CoV-2 RNA and antibodies. Of 135 serum samples, 19 (14.1%) indicated SARS-CoV-2 exposure, and 11 reacted most strongly to the wild-type B.1 lineage. Of the 71 swabs, 8 were positive for SARS-CoV-2 RNA (4 Omicron and 4 Delta). Two of the animals had active infections and robust neutralizing antibodies, revealing evidence of reinfection or early seroconversion in deer. Variants of concern continue to circulate among and may reinfect US deer populations, and establish enzootic transmission cycles in the wild: this warrants a coordinated One Health response, to proactively surveil, identify, and curtail variants of concern before they can spill back into humans.
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Affiliation(s)
- Kurt J. Vandegrift
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michele Yon
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Abhinay Gontu
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Santhamani Ramasamy
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Saranya Amirthalingam
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shubhada K. Chothe
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Padmaja Jakka
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lindsey LaBella
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nicole Levine
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sophie Rodriguez
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chen Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, IA 50010, USA
| | | | | | | | - Richard Simon
- City of New York Parks & Recreation, New York, NY 10029, USA
| | - Katrina L. Toal
- City of New York Parks & Recreation, New York, NY 10029, USA
| | - Randall J. Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Dashzeveg Bold
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - James M. Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Peter J. Hudson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Vivek Kapur
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Suresh V. Kuchipudi
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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31
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Barua S, Newbolt CH, Ditchkoff SS, Johnson C, Zohdy S, Smith R, Wang C. Absence of SARS-CoV-2 in a captive white-tailed deer population in Alabama, USA. Emerg Microbes Infect 2022; 11:1707-1710. [PMID: 35707965 PMCID: PMC9246038 DOI: 10.1080/22221751.2022.2090282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Subarna Barua
- College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Chad H Newbolt
- College of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, USA
| | - Stephen S Ditchkoff
- College of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, USA
| | - Calvin Johnson
- College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Sarah Zohdy
- College of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, USA
| | - Rachel Smith
- College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Chengming Wang
- College of Veterinary Medicine, Auburn University, Auburn, AL, USA
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32
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Frutos R, Yahi N, Gavotte L, Fantini J, Devaux CA. Role of spike compensatory mutations in the interspecies transmission of SARS-CoV-2. One Health 2022; 15:100429. [PMID: 36060458 PMCID: PMC9420691 DOI: 10.1016/j.onehlt.2022.100429] [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: 07/15/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2, the virus responsible for COVID-19 in humans, can efficiently infect a large number of animal species. Like any virus, and particularly RNA viruses, SARS-CoV-2 undergoes mutations during its life cycle some of which bring a selective advantage, leading to the selection of a given lineage. Minks are very susceptible to SARS-CoV-2 and owing to their presence in mass rearing, they make a good model for studying the relative importance of mutations in viral adaptation to host species. Variants, such as the mink-selected SARS-CoV-2 Y453F and D614G or H69del/V70del, Y453F, I692V and M1229I were identified in humans after spreading through densely caged minks. However, not all mink-specific mutations are conserved when the virus infects human populations back. Many questions remain regarding the interspecies evolution of SARS-CoV-2 and the dynamics of transmission leading to the emergence of new variant strains. We compared the human and mink ACE2 receptor structures and their interactions with SARS-CVoV-2 variants. In minks, ACE2 presents a Y34 amino acid instead of the H34 amino acid found in the human ACE2. H34 is essential for the interaction with the Y453 residue of the SARS-CoV-2 Spike protein. The Y453F mink mutation abolishes this conflict. A series of 18 mutations not involved in the direct ACE2 interaction was observed in addition to the Y453F and D614G in 16 different SARS-CoV-2 strains following bidirectional infections between humans and minks. These mutations were not random and were distributed into five different functional groups having an effect on the kinetics of ACE2-RD interaction. The interspecies transmission of SARS-CoV-2 from humans to minks and back to humans, generated specific mutations in each species which improved the affinity for the ACE2 receptor either by direct mutation of the core 453 residue or by associated compensatory mutations.
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33
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Sangkachai N, Chaiwattanarungruengpaisan S, Thongdee M, Suksai P, Tangsudjai S, Wongluechai P, Suwanpakdee S, Wiriyarat W, Buddhirongawatr R, Prasittichai L, Skulpong A, Okada PA, Puthavathana P, Paungpin W. Serological and Molecular Surveillance for SARS-CoV-2 Infection in Captive Tigers ( Panthera tigris), Thailand. Animals (Basel) 2022; 12:ani12233350. [PMID: 36496872 PMCID: PMC9736889 DOI: 10.3390/ani12233350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022] Open
Abstract
Coronavirus disease (COVID-19) is an emerging infectious disease caused by SARS-CoV-2. Given the emergence of SARS-CoV-2 variants, continuous surveillance of SARS-CoV-2 in animals is important. To monitor SARS-CoV-2 infection in wildlife in Thailand, we collected 62 blood samples and nine nasal- and rectal-swab samples from captive tigers (Panthera tigris) in Ratchaburi province in Thailand during 2020-2021. A plaque reduction neutralization test (PRNT) was employed to detect SARS-CoV-2 neutralizing antibodies. A real-time RT-PCR assay was performed to detect SARS-CoV-2 RNA. Our findings demonstrated that four captive tigers (6.5%, 4/62) had SARS-CoV-2 neutralizing antibodies against Wuhan Hu-1 and the Delta variant, while no SARS-CoV-2 RNA genome could be detected in all swab samples. Moreover, a low-level titer of neutralizing antibodies against the Omicron BA.2 subvariant could be found in only one seropositive tiger. The source of SARS-CoV-2 infection in these tigers most likely came from close contact with the infected animals' caretakers who engaged in activities such as tiger petting and feeding. In summary, we described the first case of natural SARS-CoV-2 infection in captive tigers during the COVID-19 outbreak in Thailand and provided seroepidemiological-based evidence of human-to-animal transmission. Our findings highlight the need for continuous surveillance of COVID-19 among the captive tiger population and emphasize the need to adopt a One Health approach for preventing and controlling outbreaks of COVID-19 zoonotic disease.
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Affiliation(s)
- Nareerat Sangkachai
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Somjit Chaiwattanarungruengpaisan
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Metawee Thongdee
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Parut Suksai
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Siriporn Tangsudjai
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Peerawat Wongluechai
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Sarin Suwanpakdee
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Witthawat Wiriyarat
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Ruangrat Buddhirongawatr
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | | | - Anurux Skulpong
- Wildlife Rescue Center III (Khao Prathap Chang), Ratchaburi 70110, Thailand
| | | | - Pilaipan Puthavathana
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Weena Paungpin
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
- Correspondence: ; Tel.: +66-896-701-400
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SARS-CoV-2 Transmission from Human to Pet and Suspected Transmission from Pet to Human, Thailand. J Clin Microbiol 2022; 60:e0105822. [DOI: 10.1128/jcm.01058-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been the cause of human pandemic infection since late 2019. SARS-CoV-2 infection in animals has also been reported both naturally and experimentally, rendering awareness about a potential source of infection for one health concern.
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Saied AA, Metwally AA. SARS-CoV-2 variants of concerns in animals: An unmonitored rising health threat. Virusdisease 2022; 33:466-476. [PMID: 36405954 PMCID: PMC9648878 DOI: 10.1007/s13337-022-00794-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/19/2022] [Indexed: 11/12/2022] Open
Abstract
Recent findings have highlighted the urgency for rapidly detecting and characterizing SARS-CoV-2 variants of concern in companion and wild animals. The significance of active surveillance and genomic investigation on these animals could pave the way for more understanding of the viral circulation and how the variants emerge. It enables us to predict the next viral challenges and prepare for or prevent these challenges. Horrible neglect of this issue could make the COVID-19 pandemic a continuous threat. Continuing to monitor the animal-origin SARS-CoV-2, and tailoring prevention and control measures to avoid large-scale community transmission in the future caused by the virus leaping from animals to humans, is essential. The reliance on only developing vaccines with ignoring this strategy could cost us many lives. Here, we discuss the most recent data about the transmissibility of SARS-CoV-2 variants of concern (VOCs) among animals and humans.
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Affiliation(s)
- AbdulRahman A. Saied
- National Food Safety Authority (NFSA), Aswan Branch, 81511 Aswan, Egypt
- Ministry of Tourism and Antiquities, Aswan Office, 81511 Aswan, Egypt
| | - Asmaa A. Metwally
- Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Aswan University, 81528 Aswan, Egypt
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Akaishi T, Fujiwara K, Ishii T. Insertion/deletion hotspots in the Nsp2, Nsp3, S1, and ORF8 genes of SARS-related coronaviruses. BMC Ecol Evol 2022; 22:123. [PMID: 36307763 PMCID: PMC9616624 DOI: 10.1186/s12862-022-02078-7] [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: 07/01/2022] [Accepted: 10/11/2022] [Indexed: 11/20/2022] Open
Abstract
The genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains many insertions/deletions (indels) from the genomes of other SARS-related coronaviruses. Some of the identified indels have recently reported to involve relatively long segments of 10-300 consecutive bases and with diverse RNA sequences around gaps between virus species, both of which are different characteristics from the classical shorter in-frame indels. These non-classical complex indels have been identified in non-structural protein 3 (Nsp3), the S1 domain of the spike (S), and open reading frame 8 (ORF8). To determine whether the occurrence of these non-classical indels in specific genomic regions is ubiquitous among broad species of SARS-related coronaviruses in different animal hosts, the present study compared SARS-related coronaviruses from humans (SARS-CoV and SARS-CoV-2), bats (RaTG13 and Rc-o319), and pangolins (GX-P4L), by performing multiple sequence alignment. As a result, indel hotspots with diverse RNA sequences of different lengths between the viruses were confirmed in the Nsp2 gene (approximately 2500-2600 base positions in the overall 29,900 bases), Nsp3 gene (approximately 3000-3300 and 3800-3900 base positions), N-terminal domain of the spike protein (21,500-22,500 base positions), and ORF8 gene (27,800-28,200 base positions). Abnormally high rate of point mutations and complex indels in these regions suggest that the occurrence of mutations in these hotspots may be selectively neutral or even benefit the survival of the viruses. The presence of such indel hotspots has not been reported in different human SARS-CoV-2 strains in the last 2 years, suggesting a lower rate of indels in human SARS-CoV-2. Future studies to elucidate the mechanisms enabling the frequent development of long and complex indels in specific genomic regions of SARS-related coronaviruses would offer deeper insights into the process of viral evolution.
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Affiliation(s)
- Tetsuya Akaishi
- grid.69566.3a0000 0001 2248 6943Department of Education and Support for Regional Medicine, Tohoku University, Seiryo-machi 1-1, Aoba-ku, 980-8574 Sendai, Miyagi Japan ,grid.69566.3a0000 0001 2248 6943COVID-19 Testing Center, Tohoku University, Sendai, Japan
| | - Kei Fujiwara
- grid.260433.00000 0001 0728 1069Department of Gastroenterology and Metabolism, Nagoya City University, Nagoya, Japan
| | - Tadashi Ishii
- grid.69566.3a0000 0001 2248 6943Department of Education and Support for Regional Medicine, Tohoku University, Seiryo-machi 1-1, Aoba-ku, 980-8574 Sendai, Miyagi Japan ,grid.69566.3a0000 0001 2248 6943COVID-19 Testing Center, Tohoku University, Sendai, Japan
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Marques AD, Sherrill-Mix S, Everett JK, Adhikari H, Reddy S, Ellis JC, Zeliff H, Greening SS, Cannuscio CC, Strelau KM, Collman RG, Kelly BJ, Rodino KG, Bushman FD, Gagne RB, Anis E. Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania. mBio 2022; 13:e0210122. [PMID: 36000731 PMCID: PMC9600874 DOI: 10.1128/mbio.02101-22] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/08/2022] [Indexed: 12/11/2022] Open
Abstract
The SARS-CoV-2 pandemic began by viral spillover from animals to humans; today multiple animal species are known to be susceptible to infection. White-tailed deer, Odocoileus virginianus, are infected in North America at substantial levels, and genomic data suggests that a variant in deer may have spilled back to humans. Here, we characterize SARS-CoV-2 in deer from Pennsylvania (PA) sampled during fall and winter 2021. Of 123 nasal swab samples analyzed by RT-qPCR, 20 (16.3%) were positive for SARS-CoV-2. Seven whole genome sequences were obtained, together with six more partial spike gene sequences. These annotated as alpha and delta variants, the first reported observations of these lineages in deer, documenting multiple new jumps from humans to deer. The alpha lineage persisted in deer after its displacement by delta in humans, and deer-derived alpha variants diverged significantly from those in humans, consistent with a distinctive evolutionary trajectory in deer. IMPORTANCE Coronaviruses have been documented to replicate in numerous species of vertebrates, and multiple spillovers of coronaviruses from animals into humans have founded human epidemics. The COVID-19 epidemic likely derived from a spillover of SARS-CoV-2 from bats into humans, possibly via an intermediate host. There are now several examples of SARS-CoV-2 jumping from humans into other mammals, including mink and deer, creating the potential for new animal reservoirs from which spillback into humans could occur. For this reason, data on formation of new animal reservoirs is of great importance for understanding possible sources of future infection. Here, we identify extensive infection in white-tailed deer in Pennsylvania, including what appear to be multiple independent transmissions. Data further suggests possible transmission among deer. These data thus help identify a potential new animal reservoir and provide background information relevant to its management.
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Affiliation(s)
- Andrew D. Marques
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John K. Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hriju Adhikari
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shantan Reddy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julie C. Ellis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania, USA
| | - Haley Zeliff
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania, USA
| | - Sabrina S. Greening
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania, USA
| | - Carolyn C. Cannuscio
- Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Family Medicine and Community Health, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katherine M. Strelau
- Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Family Medicine and Community Health, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Division of Infectious Diseases; Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle G. Rodino
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Roderick B. Gagne
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania, USA
| | - Eman Anis
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania, USA
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Keyel AC, Russell A, Plitnick J, Rowlands JV, Lamson DM, Rosenberg E, St George K. SARS-CoV-2 Vaccine Breakthrough by Omicron and Delta Variants, New York, USA. Emerg Infect Dis 2022; 28:1990-1998. [PMID: 36048774 PMCID: PMC9514330 DOI: 10.3201/eid2810.221058] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recently emerged SARS-CoV-2 variants have greater potential than earlier variants to cause vaccine breakthrough infections. During emergence of the Delta and Omicron variants, a matched case-control analysis used a viral genomic sequence dataset linked with demographic and vaccination information from New York, USA, to examine associations between virus lineage and patient vaccination status, patient age, vaccine type, and time since vaccination. Case-patients were persons infected with the emerging virus lineage, and controls were persons infected with any other virus lineage. Infections in fully vaccinated and boosted persons were significantly associated with the Omicron lineage. Odds of infection with Omicron relative to Delta generally decreased with increasing patient age. A similar pattern was observed with vaccination status during Delta emergence but was not significant. Vaccines offered less protection against Omicron, thereby increasing the number of potential hosts for emerging variants.
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39
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Bashor L, Gagne RB, Bosco-Lauth A, Stenglein M, VandeWoude S. Rapid evolution of SARS-CoV-2 in domestic cats. Virus Evol 2022; 8:veac092. [PMID: 36398096 PMCID: PMC9619536 DOI: 10.1093/ve/veac092] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/05/2022] [Accepted: 09/29/2022] [Indexed: 11/26/2023] Open
Abstract
SARS-CoV-2 (SARS2) infection of a novel permissive host species can result in rapid viral evolution. Data suggest that felids are highly susceptible to SARS2 infection, and species-specific adaptation following human-to-felid transmission may occur. We employed experimental infection and analysis of publicly available SARS2 sequences to observe variant emergence and selection in domestic cats. Three cohorts of cats (N = 23) were inoculated with SARS-CoV-2 USA-WA1/2020 or infected via cat-to-cat contact transmission. Full viral genomes were recovered from RNA obtained from nasal washes 1-3 days post-infection and analyzed for within-host viral variants. We detected 118 unique variants at ≥3 per cent allele frequency in two technical replicates. Seventy of these (59 per cent) were nonsynonymous single nucleotide variants (SNVs); the remainder were synonymous SNVs or structural variants. On average, we observed twelve variants per cat, nearly 10-fold higher than what is commonly reported in human patients. We observed signatures of positive selection in the spike protein and the emergence of eleven within-host variants located at the same genomic positions as mutations in SARS2 variant lineages that have emerged during the pandemic. Fewer variants were noted in cats infected from contact with other cats and in cats exposed to lower doses of cultured inoculum. An analysis of ninety-three publicly available SARS2 consensus genomes recovered from naturally infected domestic cats reflected variant lineages circulating in the local human population at the time of sampling, illustrating that cats are susceptible to SARS2 variants that have emerged in humans, and suggesting human-to-felid transmission occurring in domestic settings is typically unidirectional. These experimental results underscore the rapidity of SARS2 adaptation in felid hosts, representing a theoretical potential origin for variant lineages in human populations. Further, cats should be considered susceptible hosts capable of shedding virus during infections occurring within households.
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Affiliation(s)
- Laura Bashor
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Roderick B Gagne
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kenneth Square, Pennsylvania, USA
| | - Angela Bosco-Lauth
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Mark Stenglein
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Sue VandeWoude
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
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40
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Nuismer SL, Basinski AJ, Schreiner C, Whitlock A, Remien CH. Reservoir population ecology, viral evolution and the risk of emerging infectious disease. Proc Biol Sci 2022; 289:20221080. [PMID: 36100013 PMCID: PMC9470272 DOI: 10.1098/rspb.2022.1080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/18/2022] [Indexed: 11/12/2022] Open
Abstract
The ecology and life history of wild animals influences their potential to harbour infectious disease. This observation has motivated studies identifying empirical relationships between traits of wild animals and historical patterns of spillover and emergence into humans. Although these studies have identified compelling broad-scale patterns, they are generally agnostic with respect to underlying mechanisms. Here, we develop mathematical models that couple reservoir population ecology with viral epidemiology and evolution to clarify existing verbal arguments and pinpoint the conditions that favour spillover and emergence. Our results support the idea that average lifespan influences the likelihood of an animal serving as a reservoir for human infectious disease. At the same time, however, our results show that the magnitude of this effect is sensitive to the rate of viral mutation. Our results also demonstrate that viral pathogens causing persistent infections or a transient immune response within the reservoir are more likely to fuel emergence. Genetically explicit stochastic simulations enrich these mathematical results by identifying relationships between the genetic basis of transmission and the risk of spillover and emergence. Together, our results clarify the scope of applicability for existing hypotheses and refine our understanding of emergence risk.
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Affiliation(s)
- Scott L. Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Andrew J. Basinski
- Institute for Interdisciplinary Data Science, University of Idaho, Moscow, ID 83844, USA
| | - Courtney Schreiner
- Bioinformatics and Computational Biology, University of Idaho, Moscow, ID 83844, USA
| | - Alexander Whitlock
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Christopher H. Remien
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID 83844, USA
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41
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Boeger WA, Brooks DR, Trivellone V, Agosta SJ, Hoberg EP. Ecological super-spreaders drive host-range oscillations: Omicron and risk space for emerging infectious disease. Transbound Emerg Dis 2022; 69:e1280-e1288. [PMID: 35411706 PMCID: PMC9115439 DOI: 10.1111/tbed.14557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/16/2022] [Accepted: 04/07/2022] [Indexed: 11/28/2022]
Abstract
The unusual genetic diversity of the Omicron strain has led to speculation about its origin. The mathematical modelling platform developed for the Stockholm Paradigm (SP) indicates strongly that it has retro-colonized humans from an unidentified nonhuman mammal, likely originally infected by humans. The relationship between Omicron and all other SARS-CoV-2 variants indicates oscillations among hosts, a core part of the SP. Such oscillations result from the emergence of novel variants following colonization of new hosts, replenishing and expanding the risk space for disease emergence. The SP predicts that pathogens colonize new hosts using pre-existing capacities. Those events are thus predictable to a certain extent. Novel variants emerge after a colonization and are not predictable. This makes it imperative to take proactive measures for anticipating emerging infectious diseases (EID) and mitigating their impact. The SP suggests a policy protocol, DAMA, to accomplish this goal. DAMA comprises: DOCUMENT to detect pathogens before they emerge in new places or colonize new hosts; ASSESS to determine risk; MONITOR to detect changes in pathogen populations that increase the risk of outbreaks and ACT to prevent outbreaks when possible and minimize their impact when they occur.
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Affiliation(s)
- Walter A. Boeger
- Biological InteractionsUniversidade Federal do ParanáCuritibaBrazil
| | - Daniel R. Brooks
- Eötvös Loránd Research NetworkCentre for Ecological ResearchInstitute of EvolutionBudapestHungary
- Stellenbosch Institute for Advanced StudyStellenboschSouth Africa
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Valeria Trivellone
- Illinois Natural History SurveyPrairie Research InstituteUniversity of Illinois at Urbana‐ChampaignChampaignIllinoisUSA
| | - Salvatore J. Agosta
- Stellenbosch Institute for Advanced StudyStellenboschSouth Africa
- Center for Environmental StudiesVCU Life SciencesVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Eric P. Hoberg
- Department of Pathobiological SciencesSchool of Veterinary MedicineUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- Museum of Southwestern BiologyDepartment of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
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42
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Reply to Chandra: Severe Acute Respiratory Syndrome-Coronavirus-2 variant analysis reveals within-host selection of intra-host single nucleotide variants. Proc Natl Acad Sci U S A 2022; 119:e2206919119. [PMID: 35914184 PMCID: PMC9407363 DOI: 10.1073/pnas.2206919119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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43
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Data analysis of viral complementary DNA/RNA sequences for low-frequency intrahost-single nucleotide variants in COVID-19. Proc Natl Acad Sci U S A 2022; 119:e2205269119. [PMID: 35914186 PMCID: PMC9407639 DOI: 10.1073/pnas.2205269119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Bosco-Lauth AM, Porter SM, Fox KA, Wood ME, Neubaum D, Quilici M. Experimental Infection of Brazilian Free-Tailed Bats (Tadarida brasiliensis) with Two Strains of SARS-CoV-2. Viruses 2022; 14:v14081809. [PMID: 36016431 PMCID: PMC9412320 DOI: 10.3390/v14081809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/07/2022] [Accepted: 08/16/2022] [Indexed: 12/02/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is presumed to have originated from wildlife and shares homology with other bat coronaviruses. Determining the susceptibility of North American bat species to SARS-CoV-2 is of utmost importance for making decisions regarding wildlife management, public health, and conservation. In this study, Brazilian free-tailed bats (Tadarida brasiliensis) were experimentally infected with two strains of SARS-CoV-2 (parental WA01 and Delta variant), evaluated for clinical disease, sampled for viral shedding and antibody production, and analyzed for pathology. None of the bats (n = 18) developed clinical disease associated with infection, shed infectious virus, or developed histopathological lesions associated with SARS-CoV-2 infection. All bats had low levels of viral RNA in oral swabs, six bats had low levels of viral RNA present in the lungs during acute infection, and one of the four bats that were maintained until 28 days post-infection developed a neutralizing antibody response. These findings suggest that Brazilian free-tailed bats are permissive to infection by SARS-CoV-2, but they are unlikely to contribute to environmental maintenance or transmission.
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Affiliation(s)
- Angela M. Bosco-Lauth
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Correspondence:
| | - Stephanie M. Porter
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO 80523, USA
| | - Karen A. Fox
- Colorado Parks and Wildlife, Fort Collins, CO 80523, USA
| | - Mary E. Wood
- Colorado Parks and Wildlife, Fort Collins, CO 80523, USA
| | - Daniel Neubaum
- Colorado Parks and Wildlife, Fort Collins, CO 80523, USA
| | - Marissa Quilici
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
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45
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Gu H, Quadeer AA, Krishnan P, Ng DY, Chang LD, Liu GY, Cheng SS, Lam TT, Peiris M, McKay MR, Poon LL. Within-host diversity of SARS-CoV-2 lineages and effect of vaccination. RESEARCH SQUARE 2022:rs.3.rs-1927944. [PMID: 35982671 PMCID: PMC9387541 DOI: 10.21203/rs.3.rs-1927944/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Viral and host factors can shape SARS-CoV-2 within-host viral diversity and virus evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here we analysed deep sequencing data from 2,146 SARS-CoV-2 samples with different viral lineages to describe the patterns of within-host diversity in different conditions, including vaccine-breakthrough infections. Variant of Concern (VOC) Alpha, Delta, and Omicron samples were found to have higher within-host nucleotide diversity while being under weaker purifying selection at full genome level compared to non-VOC SARS-CoV-2 viruses. Breakthrough Delta and Omicron infections in Comirnaty and CoronaVac vaccinated individuals appeared to have higher within-host purifying selection at the full-genome and/or Spike gene levels. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 evolution. Our findings suggest that vaccination does not increase SARS-CoV-2 protein sequence space and may not facilitate emergence of more viral variants.
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Affiliation(s)
- Haogao Gu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ahmed Abdul Quadeer
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Daisy Y.M. Ng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lydia D.J Chang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Gigi Y.Z. Liu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Samuel S.M. Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tommy T.Y. Lam
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science and Technology Park, Hong Kong, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Matthew R. McKay
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Electrical and Electronic Engineering, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Leo L.M. Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong, China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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46
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Gontu A, Marlin EA, Ramasamy S, Neerukonda S, Anil G, Morgan J, Quraishi M, Chen C, Boorla VS, Nissly RH, Jakka P, Chothe SK, Ravichandran A, Kodali N, Amirthalingam S, LaBella L, Kelly K, Natesan P, Minns AM, Rossi RM, Werner JR, Hovingh E, Lindner SE, Tewari D, Kapur V, Vandegrift KJ, Maranas CD, Surendran Nair M, Kuchipudi SV. Development and Validation of Indirect Enzyme-Linked Immunosorbent Assays for Detecting Antibodies to SARS-CoV-2 in Cattle, Swine, and Chicken. Viruses 2022; 14:v14071358. [PMID: 35891340 PMCID: PMC9317974 DOI: 10.3390/v14071358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
Multiple domestic and wild animal species are susceptible to SARS-CoV-2 infection. Cattle and swine are susceptible to experimental SARS-CoV-2 infection. The unchecked transmission of SARS-CoV-2 in animal hosts could lead to virus adaptation and the emergence of novel variants. In addition, the spillover and subsequent adaptation of SARS-CoV-2 in livestock could significantly impact food security as well as animal and public health. Therefore, it is essential to monitor livestock species for SARS-CoV-2 spillover. We developed and optimized species-specific indirect ELISAs (iELISAs) to detect anti-SARS-CoV-2 antibodies in cattle, swine, and chickens using the spike protein receptor-binding domain (RBD) antigen. Serum samples collected prior to the COVID-19 pandemic were used to determine the cut-off threshold. RBD hyperimmunized sera from cattle (n = 3), swine (n = 6), and chicken (n = 3) were used as the positive controls. The iELISAs were evaluated compared to a live virus neutralization test using cattle (n = 150), swine (n = 150), and chicken (n = 150) serum samples collected during the COVID-19 pandemic. The iELISAs for cattle, swine, and chicken were found to have 100% sensitivity and specificity. These tools facilitate the surveillance that is necessary to quickly identify spillovers into the three most important agricultural species worldwide.
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Affiliation(s)
- Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
| | - Erika A. Marlin
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Clinical & Diagnostic Assay Development Group, Pfizer, Pearl River, NY 10965, USA
| | - Santhamani Ramasamy
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | | | - Gayatri Anil
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Jasmine Morgan
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Meysoon Quraishi
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Chen Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (C.C.); (V.S.B.); (C.D.M.)
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (C.C.); (V.S.B.); (C.D.M.)
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
| | - Padmaja Jakka
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
| | - Shubhada K. Chothe
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Abirami Ravichandran
- Department of Integrative and Biomedical Physiology, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Nishitha Kodali
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
| | - Saranya Amirthalingam
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
| | - Lindsey LaBella
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Kathleen Kelly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
| | - Pazhanivel Natesan
- Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600007, India;
| | - Allen M. Minns
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Randall M. Rossi
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
| | - Jacob R. Werner
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Ernest Hovingh
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Scott E. Lindner
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Deepanker Tewari
- Pennsylvania Department of Agriculture, Pennsylvania Veterinary Laboratory, Harrisburg, PA 17110, USA;
| | - Vivek Kapur
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA;
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kurt J. Vandegrift
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (C.C.); (V.S.B.); (C.D.M.)
| | - Meera Surendran Nair
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
- Correspondence: (M.S.N.); (S.V.K.)
| | - Suresh V. Kuchipudi
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (M.S.N.); (S.V.K.)
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47
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A simulation of geographic distribution for the emergence of consequential SARS-CoV-2 variant lineages. Sci Rep 2022; 12:9999. [PMID: 35705624 PMCID: PMC9199467 DOI: 10.1038/s41598-022-14308-5] [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: 12/06/2021] [Accepted: 06/06/2022] [Indexed: 11/08/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has been facilitated by the intermittent emergence of consequential variant strains. This study evaluated the geographic disproportionality in the detection of consequential variant lineages across countries. As of November 2021, a total of 40 potentially consequential SARS-CoV-2 variant lineages have been identified. One-hundred repeated simulations that randomly produced consequential variants from overall COVID-19 cases worldwide were performed to evaluate the presence of geographical disproportion in the occurrence of consequential variant outbreaks. Both the total number of reported COVID-19 cases and the number of reported genome sequences in each country showed weak positive correlations with the number of detected consequential lineages in each country. The simulations suggest the presence of geographical disproportion in the occurrence of consequential variant outbreaks. Based on the random occurrence of consequential variants among COVID-19 cases, identified consequential variants occurred more often than expected in the United Kingdom and Africa, whereas they occurred less in other European countries and the Middle East. Simulations of the occurrence of consequential variants by assuming a random occurrence among all COVID-19 cases suggested the presence of biogeographic disproportion. Further studies enrolling unevaluated crucial biogeographical factors are needed to determine the factors underlying the suggested disproportionality.
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48
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Doliff R, Martens P. Cats and SARS-CoV-2: A Scoping Review. Animals (Basel) 2022; 12:1413. [PMID: 35681877 PMCID: PMC9179433 DOI: 10.3390/ani12111413] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 11/22/2022] Open
Abstract
Since the beginning of the COVID-19 pandemic, various animal species were found to be susceptible to SARS-CoV-2 infection. The close contact that exists between humans and cats warrants special attention to the role of this species. Therefore, a scoping review was performed to obtain a comprehensive overview of the existing literature, and to map key concepts, types of research, and possible gaps in the research. A systematic search of the databases PubMed, Google Scholar, and Scopus and the preprint servers medRxiv and bioRxiv was performed. After a two-step screening process, 27 peer-reviewed articles, 8 scientific communication items, and 2 unpublished pre-prints were included. The main themes discussed were susceptibility to SARS-CoV-2, induced immunity, prevalence of infection, manifestation of infection, interspecies transmission between humans and cats, and lastly, intraspecies transmission between cats. The main gaps in the research identified were a lack of large-scale studies, underrepresentation of stray, feral, and shelter cat populations, lack of investigation into cat-to-cat transmissions under non-experimental conditions, and the relation of cats to other animal species regarding SARS-CoV-2. Overall, cats seemingly play a limited role in the spread of SARS-CoV-2. While cats are susceptible to the virus and reverse zoonotic transmission from humans to cats happens regularly, there is currently no evidence of SARS-CoV-2 circulation among cats.
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Affiliation(s)
| | - Pim Martens
- University College Venlo, Maastricht University, Nassaustraat 36, 5911 BV Venlo, The Netherlands;
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49
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Gudowska-Sawczuk M, Mroczko B. The Role of Nuclear Factor Kappa B (NF-κB) in Development and Treatment of COVID-19: Review. Int J Mol Sci 2022; 23:ijms23095283. [PMID: 35563673 PMCID: PMC9101079 DOI: 10.3390/ijms23095283] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 01/27/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 19 (COVID-19), a disease that has affected more than 500 million people worldwide since the end of 2019. Due to its high complications and death rates, there is still a need to find the best therapy for SARS-CoV-2 infection. The dysregulation of the inflammatory response in COVID-19 plays a very important role in disease progression. It has been observed that abnormal activity of Nuclear Factor kappa B (NF-κB) is directly associated with, inter alia, increased synthesis of proinflammatory factors. Therefore, this review paper focuses on the functions of NF-κB in the development of SARS-CoV-2 infection and potential application of NF-κB inhibitors in COVID-19 immunotherapy. A comprehensive literature search was performed using the MEDLINE/PubMed database. In the current review, it is highlighted that NF-κB plays important functions in the modulation of an adaptive inflammatory response, including inducing the expression of proinflammatory genes. Increased activation of NF-κB in SARS-CoV-2 infection was observed. The association between NF-κB activation and the expression of SARS-CoV-2 structural and non-structural proteins were also reported. It was observed that modulation of NF-κB using, e.g., traditional Chinese medicine or glucocorticosteroids resulted in decreased synthesis of proinflammatory factors caused by SARS-CoV-2 infection. This review summarizes the role of NF-κB in COVID-19 and describes its potential immunotherapeutic target in treatment of SARS-CoV-2 infection. However, indisputably more studies involving patients with a severe course of COVID-19 are sorely needed.
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Affiliation(s)
- Monika Gudowska-Sawczuk
- Department of Biochemical Diagnostics, Medical University of Bialystok, 15-269 Bialystok, Poland;
- Correspondence: ; Tel.: +48-85-831-8703
| | - Barbara Mroczko
- Department of Biochemical Diagnostics, Medical University of Bialystok, 15-269 Bialystok, Poland;
- Department of Neurodegeneration Diagnostics, Medical University of Bialystok, 15-269 Bialystok, Poland
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50
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Martins M, Boggiatto PM, Buckley A, Cassmann ED, Falkenberg S, Caserta LC, Fernandes MHV, Kanipe C, Lager K, Palmer MV, Diel DG. From Deer-to-Deer: SARS-CoV-2 is efficiently transmitted and presents broad tissue tropism and replication sites in white-tailed deer. PLoS Pathog 2022; 18:e1010197. [PMID: 35312736 PMCID: PMC8970504 DOI: 10.1371/journal.ppat.1010197] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/31/2022] [Accepted: 03/10/2022] [Indexed: 01/09/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) in humans, has a broad host range, and is able to infect domestic and wild animal species. Notably, white-tailed deer (WTD, Odocoileus virginianus), the most widely distributed cervid species in the Americas, were shown to be highly susceptible to SARS-CoV-2 in challenge studies and reported natural infection/exposure rates approaching 30-40% in free-ranging WTD in the U.S. Thus, understanding the infection and transmission dynamics of SARS-CoV-2 in WTD is critical to prevent future zoonotic transmission to humans, at the human-WTD interface during hunting or venison farming, and for implementation of effective disease control measures. Here, we demonstrated that following intranasal inoculation with SARS-CoV-2 B.1 lineage, WTD fawns (~8-month-old) shed infectious virus up to day 5 post-inoculation (pi), with high viral loads shed in nasal and oral secretions. This resulted in efficient deer-to-deer transmission on day 3 pi. Consistent a with lack of infectious SARS-CoV-2 shedding after day 5 pi, no transmission was observed to contact animals added on days 6 and 9 pi. We have also investigated the tropism and sites of SARS-CoV-2 replication in adult WTD (3-4 years of age). Infectious virus was detected up to day 6 pi in nasal secretions, and from various respiratory-, lymphoid-, and central nervous system tissues, indicating broad tissue tropism and multiple sites of virus replication. The study provides important insights on the infection and transmission dynamics of SARS-CoV-2 in WTD, a wild animal species that is highly susceptible to infection and with the potential to become a reservoir for the virus in the field.
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Affiliation(s)
- Mathias Martins
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Paola M. Boggiatto
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, Iowa, United States of America
| | - Alexandra Buckley
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, Iowa, United States of America
| | - Eric D. Cassmann
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, Iowa, United States of America
| | - Shollie Falkenberg
- Ruminant Disease and Immunology Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, Iowa, United States of America
| | - Leonardo C. Caserta
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Maureen H. V. Fernandes
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Carly Kanipe
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, Iowa, United States of America
| | - Kelly Lager
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, Iowa, United States of America
| | - Mitchell V. Palmer
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, Iowa, United States of America
| | - Diego G. Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
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