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Ghai RR, Straily A, Wineland N, Calogero J, Stobierski MG, Signs K, Blievernicht M, Torres-Mendoza Y, Waltenburg MA, Condrey JA, Blankenship HM, Riner D, Barr N, Schalow M, Goodrich J, Collins C, Ahmad A, Metz JM, Herzegh O, Straka K, Arsnoe DM, Duffiney AG, Shriner SA, Kainulainen MH, Carpenter A, Whitehill F, Wendling NM, Stoddard RA, Retchless AC, Uehara A, Tao Y, Li Y, Zhang J, Tong S, Barton Behravesh C. Epidemiologic and Genomic Evidence for Zoonotic Transmission of SARS-CoV-2 among People and Animals on a Michigan Mink Farm, United States, 2020. Viruses 2023; 15:2436. [PMID: 38140677 PMCID: PMC10747742 DOI: 10.3390/v15122436] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Farmed mink are one of few animals in which infection with SARS-CoV-2 has resulted in sustained transmission among a population and spillback from mink to people. In September 2020, mink on a Michigan farm exhibited increased morbidity and mortality rates due to confirmed SARS-CoV-2 infection. We conducted an epidemiologic investigation to identify the source of initial mink exposure, assess the degree of spread within the facility's overall mink population, and evaluate the risk of further viral spread on the farm and in surrounding wildlife habitats. Three farm employees reported symptoms consistent with COVID-19 the same day that increased mortality rates were observed among the mink herd. One of these individuals, and another asymptomatic employee, tested positive for SARS-CoV-2 by real-time reverse transcription PCR (RT-qPCR) 9 days later. All but one mink sampled on the farm were positive for SARS-CoV-2 based on nucleic acid detection from at least one oral, nasal, or rectal swab tested by RT-qPCR (99%). Sequence analysis showed high degrees of similarity between sequences from mink and the two positive farm employees. Epidemiologic and genomic data, including the presence of F486L and N501T mutations believed to arise through mink adaptation, support the hypothesis that the two employees with SARS-CoV-2 nucleic acid detection contracted COVID-19 from mink. However, the specific source of virus introduction onto the farm was not identified. Three companion animals living with mink farm employees and 31 wild animals of six species sampled in the surrounding area were negative for SARS-CoV-2 by RT-qPCR. Results from this investigation support the necessity of a One Health approach to manage the zoonotic spread of SARS-CoV-2 and underscores the critical need for multifaceted public health approaches to prevent the introduction and spread of respiratory viruses on mink farms.
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Affiliation(s)
- Ria R. Ghai
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Anne Straily
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Nora Wineland
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | - Jennifer Calogero
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | | | - Kimberly Signs
- Michigan Department of Health and Human Services, Lansing, MI 48909, USA
| | - Melissa Blievernicht
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | | | | | - Jillian A. Condrey
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | | | - Diana Riner
- Michigan Department of Health and Human Services, Lansing, MI 48909, USA
| | - Nancy Barr
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | - Michele Schalow
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | - Jarold Goodrich
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | - Cheryl Collins
- Michigan Department of Agriculture and Rural Development, Lansing, MI 48933, USA
| | - Ausaf Ahmad
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - John Michael Metz
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Owen Herzegh
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Kelly Straka
- Michigan Department of Natural Resources, Lansing, MI 48909, USA
| | - Dustin M. Arsnoe
- U.S. Department of Agriculture Animal and Plant Health Inspection Service, Washington, DC 20250, USA
| | - Anthony G. Duffiney
- U.S. Department of Agriculture Animal and Plant Health Inspection Service, Washington, DC 20250, USA
| | - Susan A. Shriner
- U.S. Department of Agriculture Animal and Plant Health Inspection Service, Washington, DC 20250, USA
| | | | - Ann Carpenter
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Florence Whitehill
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Natalie M. Wendling
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Robyn A. Stoddard
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Adam C. Retchless
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Anna Uehara
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Ying Tao
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Yan Li
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Jing Zhang
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
| | - Suxiang Tong
- U.S. Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.R.G.)
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2
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Yao W, Li Y, Ma D, Hou X, Wang H, Tang X, Cheng D, Zhang H, Du C, Pan H, Li C, Lin H, Sun M, Ding Q, Wang Y, Gao J, Zhong G. Evolution of SARS-CoV-2 Spikes shapes their binding affinities to animal ACE2 orthologs. Microbiol Spectr 2023; 11:e0267623. [PMID: 37943512 PMCID: PMC10715038 DOI: 10.1128/spectrum.02676-23] [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: 07/10/2023] [Accepted: 10/08/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Spike-receptor interaction is a critical determinant for the host range of coronaviruses. In this study, we investigated the SARS-CoV-2 WHU01 strain and five WHO-designated SARS-CoV-2 variants of concern (VOCs), including Alpha, Beta, Gamma, Delta, and the early Omicron variant, for their Spike interactions with ACE2 proteins of 18 animal species. First, the receptor-binding domains (RBDs) of Alpha, Beta, Gamma, and Omicron were found to display progressive gain of affinity to mouse ACE2. More interestingly, these RBDs were also found with progressive loss of affinities to multiple ACE2 orthologs. The Omicron RBD showed decreased or complete loss of affinity to eight tested animal ACE2 orthologs, including that of some livestock animals (horse, donkey, and pig), pet animals (dog and cat), and wild animals (pangolin, American pika, and Rhinolophus sinicus bat). These findings shed light on potential host range shift of SARS-CoV-2 VOCs, especially that of the Omicron variant.
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Affiliation(s)
- Weitong Yao
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
- Hubei JiangXia Laboratory, Wuhan, Hubei, China
| | - Yujun Li
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Danting Ma
- Shenzhen Bay Laboratory, Shenzhen, China
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Xudong Hou
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Haimin Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Xiaojuan Tang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Dechun Cheng
- Shenzhen Bay Laboratory, Shenzhen, China
- Heilongjiang Academy of Medical Sciences, Harbin, China
| | - He Zhang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Chengzhi Du
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Hong Pan
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Chao Li
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Hua Lin
- Biomedical Research Center of South China, Fujian Normal University, Fuzhou, China
| | - Mengsi Sun
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Qiang Ding
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | | | - Jiali Gao
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Guocai Zhong
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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3
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Hansen LG, Larsen LE, Rasmussen TB, Miar Y, Lassuniére R, Jørgensen CS, Ryt-Hansen P. Investigation of the SARS-CoV-2 post-vaccination antibody response in Canadian farmed mink. Vaccine 2023; 41:7387-7394. [PMID: 37932134 DOI: 10.1016/j.vaccine.2023.10.073] [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: 08/10/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023]
Abstract
Currently, SARS-CoV-2 have been detected in farmed mink in 13 different countries. Due to the high susceptibility and transmissibility among mink, great concerns of mink serving as a reservoir to generate novel variants with unknown virulence and antigenic properties arose. These concerns have consequently resulted in entire mink productions being culled and banned. This study investigates the post-vaccination antibody response in the Canadian farmed mink vaccinated with a commercial Index spike protein-based vaccine, approved for use in cats, and compares the antibody response to that observed post infection in Danish farmed mink. Blood samples were obtained from 50 mink at the Canadian Centre for Fur Animal Research (CCFAR), Dalhousie University (Truro, Canada). The sera were initially analyzed for antibodies by enzyme-linked immunosorbent assay (ELISA), and selected sera was subsequently tested in a virus neutralization tests. The levels of neutralizing antibodies were evaluated for an ancestral D614G strain and a recent circulating SARS-CoV-2 variant of concern (Omicron BA.4). The results revealed that the vaccine induced a strong antibody response in mink by reaching antibody titer levels of up to 1:12800 in the ELISA. Moreover, high levels of neutralizing antibodies were obtained, and despite the great level of genetic differences between the ancestral and Omicron BA.4 strains, the vaccinated mink showed high levels of cross-reacting neutralizing antibodies. Interestingly, the antibody levels towards SARS-CoV-2 in the Canadian vaccinated mink were significantly higher than observed in recently SARS-CoV-2 infected Danish mink and equal to anamnestic responses following re-infection. In conclusion, the vaccine used in the Canadian farmed mink was able to induce a strong and broad-reacting antibody response in mink, which could limit the spread of SARS-CoV-2 in farmed mink and thereby reduce the risk of mink serving as a SARS-CoV-2 reservoir for human infections.
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Affiliation(s)
- Line Gram Hansen
- Dpt. of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, DK-1870 Frederiksberg C, Denmark.
| | - Lars Erik Larsen
- Dpt. of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, DK-1870 Frederiksberg C, Denmark.
| | | | - Younes Miar
- Haley Institute of Animal Science and Aquaculture 100-A, Dalhousie University, Faculty of Agriculture, 58 Sipu Awti, Truro, NS, Canada.
| | - Ria Lassuniére
- Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark.
| | | | - Pia Ryt-Hansen
- Dpt. of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, DK-1870 Frederiksberg C, Denmark.
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4
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Peka M, Balatsky V. Analysis of RBD-ACE2 interactions in livestock species as a factor in the spread of SARS-CoV-2 among animals. Vet Anim Sci 2023; 21:100303. [PMID: 37521409 PMCID: PMC10372456 DOI: 10.1016/j.vas.2023.100303] [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] [Indexed: 08/01/2023] Open
Abstract
The high mutation rate of SARS-CoV-2, which has led to the emergence of a number of virus variants, creates risks of transmission from humans to animal species and the emergence of new animal reservoirs of COVID-19. This study aimed to identify animal species among livestock susceptible to infection and develop an approach that would be possible to use for assessing the hazards caused by new SARS-CoV-2 variants for animals. Bioinformatic analysis was used to evaluate the ability of receptor-binding domains (RBDs) of different SARS-CoV-2 variants to interact with ACE2 receptors of livestock species. The results indicated that the stability of RBD-ACE2 complexes depends on both amino acid residues in the ACE2 sequences of animal species and on mutations in the RBDs of SARS-CoV-2 variants, with the residues in the interface of the RBD-ACE2 complex being the most important. All studied SARS-CoV-2 variants had high affinity for ferret and American mink receptors, while the affinity for horse, donkey, and bird species' receptors significantly increased in the highly mutated Omicron variant. Hazards that future SARS-CoV-2 variants may acquire specificity to new animal species remain high given the mutability of the virus. The continued use and expansion of the bioinformatic approach presented in this study may be relevant for monitoring transmission risks and preventing the emergence of new reservoirs of COVID-19 among animals.
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Affiliation(s)
- Mykyta Peka
- V. N. Karazin Kharkiv National University, 4 Svobody Sq, Kharkiv, 61022, Ukraine
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013, Ukraine
| | - Viktor Balatsky
- V. N. Karazin Kharkiv National University, 4 Svobody Sq, Kharkiv, 61022, Ukraine
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013, Ukraine
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5
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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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6
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Kleinerman G, Gross S, Topol S, Ariel E, Volokh G, Melloul S, Mergy SE, Malamud Y, Gilboa S, Gal Y, Weiss L, Richt JA, Decaro N, Eskandar S, Arieli Y, Gingis E, Sachter Y, Chaim L. Low serological rate of SARS-CoV-2 in cats from military bases in Israel. Comp Immunol Microbiol Infect Dis 2022; 90-91:101905. [PMID: 36356507 PMCID: PMC9632235 DOI: 10.1016/j.cimid.2022.101905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 11/05/2022]
Abstract
Domestic cats are susceptible to SARS-CoV-2 infection and can transmit the virus to other felines. A high number of COVID-19 human cases within the military personnel and a high density of stray cats living close to soldiers raised the need to perform active animal surveillance. We validated a novel quantitative serological microarray for use in cats, that enables simultaneous detection of IgG and IgM responses; in addition, molecular genetic SARS-CoV-2 detection was performed. Three out of 131 cats analyzed, showed IgG antibodies against SARS-CoV-2 RBD and S2P (2.3 %). None of cats were positive for SARS-CoV-2 RNA by RT-PCR. SARS-CoV-2 infection rate in soldiers ranged from 4.7 % to 16 % (average rate=8.9 %). Further investigations on a larger cohort are necessary, in the light of the emerging new viral variants in other animal species and in humans.
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Affiliation(s)
- Gabriela Kleinerman
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel.
| | - Saar Gross
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel
| | - Shira Topol
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel
| | - Ella Ariel
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel
| | - Gerry Volokh
- Emek HaMaayanot Regional Veterinary Service, Emek Beit She'an 11710, Israel
| | - Sivan Melloul
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel
| | - Shani Etty Mergy
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel
| | - Yaakov Malamud
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel
| | - Sagi Gilboa
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel
| | - Yoav Gal
- Chemical, Biological, Radiological and Nucleal Defense Diviosion, Israeli Ministry of Defense, HaKiria, Tel Aviv 61909, Israel
| | - Libby Weiss
- Chemical, Biological, Radiological and Nucleal Defense Diviosion, Israeli Ministry of Defense, HaKiria, Tel Aviv 61909, Israel
| | - Juergen A Richt
- Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Nicola Decaro
- Department of VeterinaryMedicine, University of Bari, 70010 Valenzano, Bari, Italy
| | - Shadi Eskandar
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel
| | - Yarden Arieli
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel
| | - Efrat Gingis
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel
| | - Yacov Sachter
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel
| | - Lavie Chaim
- Preventive medicine branch, Medical Corps, Israel Defense Forces, Tel Hashomer Camp, 5510802, Qriat Ono, Israel
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7
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Sánchez-Morales L, Sánchez-Vizcaíno JM, Pérez-Sancho M, Domínguez L, Barroso-Arévalo S. The Omicron (B.1.1.529) SARS-CoV-2 variant of concern also affects companion animals. Front Vet Sci 2022; 9:940710. [PMID: 36032286 PMCID: PMC9411866 DOI: 10.3389/fvets.2022.940710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/27/2022] [Indexed: 12/02/2022] Open
Abstract
The emergence of the Omicron variant (B.1. 1.529) has brought with it an increase in the incidence of SARS-CoV-2 disease. However, there is hardly any data on its incidence in companion animals. We have detected the presence of this new variant in domestic animals (dogs and cats) living with infected owners in Spain. None of the RT-qPCR positive animals (10.13%) presented any clinical signs and the viral loads detected were low. In addition, the shedding of viral RNA lasted a short period of time in the positive animals. Infection with this variant of concern (VOC) was confirmed by RT-qPCR and sequencing. These outcomes suggest a lower virulence of this variant in infected cats and dogs. They also demonstrate the transmission from infected humans to domestic animals and highlight the importance of active surveillance as well as genomic research to detect the presence of VOCs or mutations associated with animal hosts.
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Affiliation(s)
- Lidia Sánchez-Morales
- VISAVET Health Surveillance Centre, 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 Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - Marta Pérez-Sancho
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - Sandra Barroso-Arévalo
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
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8
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Tai JH, Sun HY, Tseng YC, Li G, Chang SY, Yeh SH, Chen PJ, Chaw SM, Wang HY. Contrasting patterns in the early stage of SARS-CoV-2 evolution between humans and minks. Mol Biol Evol 2022; 39:6658056. [PMID: 35934827 PMCID: PMC9384665 DOI: 10.1093/molbev/msac156] [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] [Indexed: 11/13/2022] Open
Abstract
One of the unique features of SARS-CoV-2 is its apparent neutral evolution during the early pandemic (before February 2020). This contrasts with the preceding SARS-CoV epidemics, where viruses evolved adaptively. SARS-CoV-2 may exhibit a unique or adaptive feature which deviates from other coronaviruses. Alternatively, the virus may have been cryptically circulating in humans for a sufficient time to have acquired adaptive changes before the onset of the current pandemic. To test the scenarios above, we analyzed the SARS-CoV-2 sequences from minks (Neovision vision) and parental humans. In the early phase of the mink epidemic (April to May 2020), nonsynonymous to synonymous mutation ratio per site in the spike protein is 2.93, indicating a selection process favoring adaptive amino acid changes. Mutations in the spike protein were concentrated within its receptor binding domain and receptor binding motif. An excess of high frequency derived variants produced by genetic hitchhiking was found during the middle (June to July 2020) and late phase I (August to September 2020) of the mink epidemic. In contrast, the site frequency spectra of early SARS-CoV-2 in humans only show an excess of low frequency mutations, consistent with the recent outbreak of the virus. Strong positive selection in the mink SARS-CoV-2 implies the virus may not be pre-adapted to a wide range of hosts and illustrates how a virus evolves to establish a continuous infection in a new host. Therefore, the lack of positive selection signal during the early pandemic in humans deserves further investigation.
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Affiliation(s)
- Jui Hung Tai
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Hsiao Yu Sun
- Taipei Municipal Zhongshan Girls High School, Taipei 10490, Taiwan
| | - Yi Cheng Tseng
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Guanghao Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sui Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Shiou Hwei Yeh
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Pei Jer Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan.,Department of Microbiology, College of Medicine, National Taiwan University, Taipei 10617, Taiwan.,Hepatitis Research Center, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei 10002, Taiwan.,Department of Internal Medicine, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei 10002, Taiwan.,Department of Medical Research, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei 10002, Taiwan
| | - Shu Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hurng Yi Wang
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan.,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan.,Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 10002, Taiwan
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9
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Yan K, Dumenil T, Tang B, Le TT, Bishop CR, Suhrbier A, Rawle DJ. Evolution of ACE2-independent SARS-CoV-2 infection and mouse adaption after passage in cells expressing human and mouse ACE2. Virus Evol 2022; 8:veac063. [PMID: 35919871 PMCID: PMC9338707 DOI: 10.1093/ve/veac063] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/11/2022] [Accepted: 07/20/2022] [Indexed: 11/28/2022] Open
Abstract
Human ACE2 Human angiotensin converting enzyme 2 (hACE2) is the key cell attachment and entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with the original SARS-CoV-2 isolates unable to use mouse ACE2 (mACE2). Herein we describe the emergence of a SARS-CoV-2 strain capable of ACE2-independent infection and the evolution of mouse-adapted (MA) SARS-CoV-2 by in vitro serial passaging of virus in co-cultures of cell lines expressing hACE2 and mACE2. MA viruses evolved with up to five amino acid changes in the spike protein, all of which have been seen in human isolates. MA viruses replicated to high titers in C57BL/6J mouse lungs and nasal turbinates and caused characteristic lung histopathology. One MA virus also evolved to replicate efficiently in several ACE2-negative cell lines across several species, including clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) ACE2 knockout cells. An E484D substitution is likely involved in ACE2-independent entry and has appeared in only ≈0.003 per cent of human isolates globally, suggesting that it provided no significant selection advantage in humans. ACE2-independent entry reveals a SARS-CoV-2 infection mechanism that has potential implications for disease pathogenesis, evolution, tropism, and perhaps also intervention development.
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Affiliation(s)
- Kexin Yan
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
| | - Troy Dumenil
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
| | - Bing Tang
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
| | - Thuy T Le
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
| | - Cameron R Bishop
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
| | - Andreas Suhrbier
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
- Australian Infectious Disease Research Centre, GVN Center of Excellence, Brisbane, 300 Herston Road, Herston, 4029 and The University of Queensland, St Lucia, 4072, Australia
| | - Daniel J Rawle
- Infection and Inflammation Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, 4029, Queensland, Australia
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10
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Yoon E, Kim D, Jeon H, Kwon Y, Jang Y, Kim S, Hwang KY. Severe acute respiratory syndrome coronavirus 2 variants-Possibility of universal vaccine design: A review. Comput Struct Biotechnol J 2022; 20:3533-3544. [PMID: 35765543 PMCID: PMC9221512 DOI: 10.1016/j.csbj.2022.06.043] [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: 03/28/2022] [Accepted: 06/18/2022] [Indexed: 11/28/2022] Open
Abstract
Both novel and conventional vaccination strategies have been implemented worldwide since the onset of coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite various medical advances in the treatment and prevention of the spread of this contagious disease, it remains a major public health threat with a high mortality rate. As several lethal SARS-CoV-2 variants continue to emerge, the development of several vaccines and medicines, each with certain advantages and disadvantages, is underway. Additionally, many modalities are at various stages of research and development or clinical trials. Here, we summarize emerging SARS-CoV-2 variants, including delta, omicron, and "stealth omicron," as well as available oral drugs for COVID-19. We also discuss possible antigen candidates other than the receptor-binding domain protein for the development of a universal COVID-19 vaccine. The present review will serve as a helpful resource for future vaccine and drug development to combat COVID-19.
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Key Words
- ACE2, angiotensin-converting enzyme 2
- Antigen
- COVID-19
- COVID-19, coronavirus disease 2019
- Coronavirus
- FDA, Food and Drug Administration
- FP, fusion peptide
- HE, hemagglutinin-esterase
- HIV, human immunodeficiency virus
- HR1, heptad repeat 1
- HR2, heptad repeat 2
- Oral drug
- RBD, receptor binding domain
- Receptor-binding domain
- S1-CTD, S1 C-terminal domain
- S1-NTD, S1 N-terminal domain
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- TMPRSS2, transmembrane protease serine 2
- Universal vaccine
- mAbs, monoclonal antibodies
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Affiliation(s)
- Eunhye Yoon
- Division of Biotechnology, College of Life Sciences and Biotechnology, Seoul 02841, South Korea
| | - Dahyun Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Seoul 02841, South Korea
| | - Hyeeun Jeon
- Division of Biotechnology, College of Life Sciences and Biotechnology, Seoul 02841, South Korea
| | - Yejin Kwon
- Division of Biotechnology, College of Life Sciences and Biotechnology, Seoul 02841, South Korea
| | - Yejin Jang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Seoul 02841, South Korea
| | - Sulhee Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Seoul 02841, South Korea
- Institute of Bioresource, Korea University, Seoul 02841, South Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Seoul 02841, South Korea
- Institute of Bioresource, Korea University, Seoul 02841, South Korea
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11
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Barua A, Grot N, Plawski A. The basis of mink susceptibility to SARS-CoV-2 infection. J Appl Genet 2022; 63:543-555. [PMID: 35396646 PMCID: PMC8993591 DOI: 10.1007/s13353-022-00689-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
Abstract
Of all known airborne diseases in the twenty-first century, coronavirus disease 19 (COVID-19) has the highest infection and death rate. Over the past few decades, animal origin viral diseases, notably those of bats-linked, have increased many folds in humans with cross-species transmissions noted and the ongoing COVID-19 pandemic has emphasized the importance of understanding the evolution of natural hosts in response to viral pathogens. Cross-species transmissions are possible due to the possession of the angiotensin-converting enzyme 2 (ACE2) receptor in animals. ACE2 recognition by SARS-CoV-2 is a critical determinant of the host range, interspecies transmission, and viral pathogenesis. Thus, the phenomenon of breaking the cross-species barrier is mainly associated with mutations in the receptor-binding domain (RBD) of the spike (S) protein that interacts with ACE2. In this review, we raise the issue of cross-species transmission based on sequence alignment of S protein. Based on previous reports and our observations, we can conclude that the occurrence of one of two mutations D614G or Y453F is sufficient for infection of minks by SARS-CoV-2 from humans. Unfortunately, D614G is observed in the world’s most common line of virus B.1.1.7 and the latest SARS-CoV-2 variants B.1.617.1, B.1.617.2, and B.1.617.3 too.
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Affiliation(s)
- Avishak Barua
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-631, Poznań, Poland
| | - Natalia Grot
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland
| | - Andrzej Plawski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland. .,Department of General and Endocrine Surgery and Gastroenterological Oncology, Poznań University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznań, Poland.
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12
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Clayton E, Ackerley J, Aelmans M, Ali N, Ashcroft Z, Ashton C, Barker R, Budryte V, Burrows C, Cai S, Callaghan A, Carberry J, Chatwin R, Davies I, Farlow C, Gamblin S, Iacobut A, Lambe A, Lynch F, Mihalache D, Mokbel A, Potamsetty S, Qadir Z, Soden J, Sun X, Vasile A, Wheeler O, Rohaim MA, Munir M. Structural Bases of Zoonotic and Zooanthroponotic Transmission of SARS-CoV-2. Viruses 2022; 14:418. [PMID: 35216011 PMCID: PMC8875863 DOI: 10.3390/v14020418] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/25/2022] [Accepted: 02/07/2022] [Indexed: 01/27/2023] Open
Abstract
The emergence of multiple variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the importance of possible animal-to-human (zoonotic) and human-to-animal (zooanthroponotic) transmission and potential spread within animal species. A range of animal species have been verified for SARS-CoV-2 susceptibility, either in vitro or in vivo. However, the molecular bases of such a broad host spectrum for the SARS-CoV-2 remains elusive. Here, we structurally and genetically analysed the interaction between the spike protein, with a particular focus on receptor binding domains (RBDs), of SARS-CoV-2 and its receptor angiotensin-converting enzyme 2 (ACE2) for all conceivably susceptible groups of animals to gauge the structural bases of the SARS-CoV-2 host spectrum. We describe our findings in the context of existing animal infection-based models to provide a foundation on the possible virus persistence in animals and their implications in the future eradication of COVID-19.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK; (E.C.); (J.A.); (M.A.); (N.A.); (Z.A.); (C.A.); (R.B.); (V.B.); (C.B.); (S.C.); (A.C.); (J.C.); (R.C.); (I.D.); (C.F.); (S.G.); (A.I.); (A.L.); (F.L.); (D.M.); (A.M.); (S.P.); (Z.Q.); (J.S.); (X.S.); (A.V.); (O.W.); (M.A.R.)
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13
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Zhou J, Peacock TP, Brown JC, Goldhill DH, Elrefaey AME, Penrice-Randal R, Cowton VM, De Lorenzo G, Furnon W, Harvey WT, Kugathasan R, Frise R, Baillon L, Lassaunière R, Thakur N, Gallo G, Goldswain H, Donovan-Banfield I, Dong X, Randle NP, Sweeney F, Glynn MC, Quantrill JL, McKay PF, Patel AH, Palmarini M, Hiscox JA, Bailey D, Barclay WS. Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Cell Rep 2022; 38:110344. [PMID: 35093235 PMCID: PMC8768428 DOI: 10.1016/j.celrep.2022.110344] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/11/2021] [Accepted: 01/14/2022] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 has a broad mammalian species tropism infecting humans, cats, dogs, and farmed mink. Since the start of the 2019 pandemic, several reverse zoonotic outbreaks of SARS-CoV-2 have occurred in mink, one of which reinfected humans and caused a cluster of infections in Denmark. Here we investigate the molecular basis of mink and ferret adaptation and demonstrate the spike mutations Y453F, F486L, and N501T all specifically adapt SARS-CoV-2 to use mustelid ACE2. Furthermore, we risk assess these mutations and conclude mink-adapted viruses are unlikely to pose an increased threat to humans, as Y453F attenuates the virus replication in human cells and all three mink adaptations have minimal antigenic impact. Finally, we show that certain SARS-CoV-2 variants emerging from circulation in humans may naturally have a greater propensity to infect mustelid hosts and therefore these species should continue to be surveyed for reverse zoonotic infections.
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Affiliation(s)
- Jie Zhou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jonathan C Brown
- Department of Infectious Disease, Imperial College London, London, UK
| | - Daniel H Goldhill
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laury Baillon
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ria Lassaunière
- Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Nazia Thakur
- The Pirbright Institute, Woking, Surrey, UK; The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Hannah Goldswain
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - I'ah Donovan-Banfield
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Nadine P Randle
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Fiachra Sweeney
- Department of Infectious Disease, Imperial College London, London, UK
| | - Martha C Glynn
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Paul F McKay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK; Infectious Diseases Horizontal Technology Centre (ID HTC), A(∗)STAR, Singapore, Singapore
| | | | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK.
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14
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Badiola JJ, Otero A, Sevilla E, Marín B, García Martínez M, Betancor M, Sola D, Pérez Lázaro S, Lozada J, Velez C, Chiner-Oms Á, Comas I, Cancino-Muñoz I, Monleón E, Monzón M, Acín C, Bolea R, Moreno B. SARS-CoV-2 Outbreak on a Spanish Mink Farm: Epidemiological, Molecular, and Pathological Studies. Front Vet Sci 2022; 8:805004. [PMID: 35127883 PMCID: PMC8814420 DOI: 10.3389/fvets.2021.805004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/21/2021] [Indexed: 01/29/2023] Open
Abstract
Farmed minks have been reported to be highly susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and may represent a risk to humans. In this study, we describe the first outbreak of SARS-CoV-2 occurred on a mink farm in Spain, between June and July 2020, involving 92,700 animals. The outbreak started shortly after some farm workers became seropositive for SARS-CoV-2. Minks showed no clinical signs compatible with SARS-CoV-2 infection throughout the outbreak. Samples from 98 minks were collected for histopathological, serological, and molecular studies. Twenty out of 98 (20.4%) minks were positive by RT-qPCR and 82 out 92 (89%) seroconverted. This finding may reflect a rapid spread of the virus at the farm with most of the animals overcoming the infection. Additionally, SARS-CoV-2 was detected by RT-qPCR in 30% of brain samples from positive minks. Sequencing analysis showed that the mink sequences were not closely related with the other mink SARS-CoV-2 sequences available, and that this mink outbreak has its probable origin in one of the genetic variants that were prevalent in Spain during the first COVID-19 epidemic wave. Histological studies revealed bronchointerstitial pneumonia in some animals. Immunostaining of viral nucleocapsid was also observed in nasal turbinate tissue. Farmed minks could therefore constitute an important SARS-CoV-2 reservoir, contributing to virus spread among minks and humans. Consequently, continuous surveillance of mink farms is needed.
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Affiliation(s)
- Juan José Badiola
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
| | - Alicia Otero
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
- *Correspondence: Alicia Otero
| | - Eloisa Sevilla
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
| | - Belén Marín
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
| | - Mirta García Martínez
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
| | - Marina Betancor
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
| | - Diego Sola
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
| | - Sonia Pérez Lázaro
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
| | - Jenny Lozada
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
| | - Carolina Velez
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Pampa, General Pico, Argentina
| | - Álvaro Chiner-Oms
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Cientìficas (IBV-CSIC), CIBER in Epidemiology and Public Health, Valencia, Spain
| | - Irving Cancino-Muñoz
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
| | - Eva Monleón
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
| | - Marta Monzón
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
| | - Cristina Acín
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
| | - Rosa Bolea
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
| | - Bernardino Moreno
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), Instituto de Investigación Sanitaria de Aragón (IISA), Zaragoza, Spain
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15
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Dolskiy AA, Gudymo AS, Taranov OS, Grishchenko IV, Shitik EM, Prokopov DY, Soldatov VO, Sobolevskaya EV, Bodnev SA, Danilchenko NV, Moiseeva AA, Torzhkova PY, Bulanovich YA, Onhonova GS, Ivleva EK, Kubekina MV, Belykh AE, Tregubchak TV, Ryzhikov AB, Gavrilova EV, Maksyutov RA, Deykin AV, Yudkin DV. The Tissue Distribution of SARS-CoV-2 in Transgenic Mice With Inducible Ubiquitous Expression of hACE2. Front Mol Biosci 2022; 8:821506. [PMID: 35118120 PMCID: PMC8804232 DOI: 10.3389/fmolb.2021.821506] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/15/2021] [Indexed: 12/15/2022] Open
Abstract
The novel coronavirus disease COVID-19 has become one of the most socially significant infections. One of the main models for COVID-19 pathogenesis study and anti-COVID-19 drug development is laboratory animals sensitive to the virus. Herein, we report SARS-CoV-2 infection in novel transgenic mice conditionally expressing human ACE2 (hACE2), with a focus on viral distribution after intranasal inoculation. Transgenic mice carrying hACE2 under the floxed STOP cassette [(hACE2-LoxP(STOP)] were mated with two types of Cre-ERT2 strains (UBC-Cre and Rosa-Cre). The resulting offspring with temporal control of transgene expression were treated with tamoxifen to induce the removal of the floxed STOP cassette, which prevented hACE2 expression. Before and after intranasal inoculation, the mice were weighed and clinically examined. On Days 5 and 10, the mice were sacrificed for isolation of internal organs and the further assessment of SARS-CoV-2 distribution. Intranasal SARS-CoV-2 inoculation in hACE2-LoxP(STOP)×UBC-Cre offspring resulted in weight loss and death in 6 out of 8 mice. Immunostaining and focus formation assays revealed the most significant viral load in the lung, brain, heart and intestine samples. In contrast, hACE2-LoxP(STOP) × Rosa-Cre offspring easily tolerated the infection, and SARS-CoV-2 was detected only in the brain and lungs, whereas other studied tissues had null or negligible levels of the virus. Histological examination revealed severe alterations in the lungs, and mild changes were observed in the brain tissues. Notably, no changes were observed in mice without tamoxifen treatment. Thus, this novel murine model with the Cre-dependent activation of hACE2 provides a useful and safe tool for COVID-19 studies.
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Affiliation(s)
- Alexander A. Dolskiy
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
- *Correspondence: Alexander A. Dolskiy,
| | - Andrey S. Gudymo
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Oleg S. Taranov
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Irina V. Grishchenko
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Ekaterina M. Shitik
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Dmitry Yu Prokopov
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Vladislav O. Soldatov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Genome Editing for Veterinary and Biomedicine, Belgorod State National Research University, Belgorod, Russia
| | - Elvira V. Sobolevskaya
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Sergey A. Bodnev
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Natalia V. Danilchenko
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Anastasia A. Moiseeva
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Polina Y. Torzhkova
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Yulia A. Bulanovich
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Galina S. Onhonova
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Elena K. Ivleva
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Marina V. Kubekina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey E. Belykh
- Research Institute of General Pathology, Kursk State Medical University, Kursk, Russia
| | - Tatiana V. Tregubchak
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Alexander B. Ryzhikov
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Elena V. Gavrilova
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Rinat A. Maksyutov
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
| | - Alexey V. Deykin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Genome Editing for Veterinary and Biomedicine, Belgorod State National Research University, Belgorod, Russia
| | - Dmitry V. Yudkin
- State Research Center of Virology and Biotechnology “Vector”, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program on the Development of Genetic Technologies, Koltsovo, Russia
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16
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Alkhatib M, Svicher V, Salpini R, Ambrosio FA, Bellocchi MC, Carioti L, Piermatteo L, Scutari R, Costa G, Artese A, Alcaro S, Shafer R, Ceccherini-Silberstein F. SARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021. Microbiol Spectr 2021; 9:e0109621. [PMID: 34787497 PMCID: PMC8597642 DOI: 10.1128/spectrum.01096-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/21/2021] [Indexed: 12/13/2022] Open
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic caused by it, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been undergoing a genetic diversification leading to the emergence of new variants. Nevertheless, a clear definition of the genetic signatures underlying the circulating variants is still missing. Here, we provide a comprehensive insight into mutational profiles characterizing each SARS-CoV-2 variant, focusing on spike mutations known to modulate viral infectivity and/or antigenicity. We focused on variants and on specific relevant mutations reported by GISAID, Nextstrain, Outbreak.info, Pango, and Stanford database websites that were associated with any clinical/diagnostic impact, according to published manuscripts. Furthermore, 1,223,338 full-length high-quality SARS-CoV-2 genome sequences were retrieved from GISAID and used to accurately define the specific mutational patterns in each variant. Finally, mutations were mapped on the three-dimensional structure of the SARS-CoV-2 spike protein to assess their localization in the different spike domains. Overall, this review sheds light and assists in defining the genetic signatures characterizing the currently circulating variants and their clinical relevance. IMPORTANCE Since the emergence of SARS-CoV-2, several recurrent mutations, particularly in the spike protein, arose during human-to-human transmission or spillover events between humans and animals, generating distinct worrisome variants of concern (VOCs) or of interest (VOIs), designated as such due to their clinical and diagnostic impacts. Characterizing these variants and their related mutations is important in tracking SAR-CoV-2 evolution and understanding the efficacy of vaccines and therapeutics based on monoclonal antibodies, convalescent-phase sera, and direct antivirals. Our study provides a comprehensive survey of the mutational profiles characterizing the important SARS-CoV-2 variants, focusing on spike mutations and highlighting other protein mutations.
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Affiliation(s)
- Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Valentina Svicher
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Romina Salpini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Francesca Alessandra Ambrosio
- Dipartimento di Scienze della Salute, Campus S. Venuta, Università degli Studi “Magna Graecia” di Catanzaro, Catanzaro, Italy
| | | | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Lorenzo Piermatteo
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Rossana Scutari
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Campus S. Venuta, Università degli Studi “Magna Graecia” di Catanzaro, Catanzaro, Italy
- Net4Science Academic Spin-Off, Campus S. Venuta, Università Magna Græcia di Catanzaro, Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus S. Venuta, Università degli Studi “Magna Graecia” di Catanzaro, Catanzaro, Italy
- Net4Science Academic Spin-Off, Campus S. Venuta, Università Magna Græcia di Catanzaro, Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus S. Venuta, Università degli Studi “Magna Graecia” di Catanzaro, Catanzaro, Italy
- Net4Science Academic Spin-Off, Campus S. Venuta, Università Magna Græcia di Catanzaro, Catanzaro, Italy
| | - Robert Shafer
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
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17
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Sharun K, Dhama K, Pawde AM, Gortázar C, Tiwari R, Bonilla-Aldana DK, Rodriguez-Morales AJ, de la Fuente J, Michalak I, Attia YA. SARS-CoV-2 in animals: potential for unknown reservoir hosts and public health implications. Vet Q 2021; 41:181-201. [PMID: 33892621 PMCID: PMC8128218 DOI: 10.1080/01652176.2021.1921311] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/29/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, previously 2019-nCoV) is suspected of having originated in 2019 in China from a coronavirus infected bat of the genus Rhinolophus. Following the initial emergence, possibly facilitated by a mammalian bridge host, SARS-CoV-2 is currently transmitted across the globe via efficient human-to-human transmission. Results obtained from experimental studies indicate that animal species such as cats, ferrets, raccoon dogs, cynomolgus macaques, rhesus macaques, white-tailed deer, rabbits, Egyptian fruit bats, and Syrian hamsters are susceptible to SARS-CoV-2 infection, and that cat-to-cat and ferret-to-ferret transmission can take place via contact and air. However, natural infections of SARS-CoV-2 have been reported only in pet dogs and cats, tigers, lions, snow leopards, pumas, and gorillas at zoos, and farmed mink and ferrets. Even though human-to-animal spillover has been reported at several instances, SARS-CoV-2 transmission from animals-to-humans has only been reported from mink-to-humans in mink farms. Following the rapid transmission of SARS-CoV-2 within the mink population, a new mink-associated SARS-CoV-2 variant emerged that was identified in both humans and mink. The increasing reports of SARS-CoV-2 in carnivores indicate the higher susceptibility of animal species belonging to this order. The sporadic reports of SARS-CoV-2 infection in domestic and wild animal species require further investigation to determine if SARS-CoV-2 or related Betacoronaviruses can get established in kept, feral or wild animal populations, which may eventually act as viral reservoirs. This review analyzes the current evidence of SARS-CoV-2 natural infection in domestic and wild animal species and their possible implications on public health.
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Affiliation(s)
- Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Abhijit M. Pawde
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Christian Gortázar
- SaBio IREC Instituto de Investigación en Recursos Cinegéticos (CSIC-Universidad de Castilla-La Mancha), Ciudad Real, Spain
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, India
| | - D. Katterine Bonilla-Aldana
- Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigacion BIOECOS, Fundacion Universitaria Autonoma de las Americas, Pereira, Colombia
- Faculty of Health Sciences, Public Health and Infection Research Group, Universidad Tecnologica de Pereira, Pereira, Colombia
| | - Alfonso J. Rodriguez-Morales
- Faculty of Health Sciences, Public Health and Infection Research Group, Universidad Tecnologica de Pereira, Pereira, Colombia
- Faculty of Medicine, Grupo de Investigacion Biomedicina, Fundacion Universitaria Autonoma de las Americas, Pereira, Colombia
- Latin American Network of Coronavirus Disease 2019-COVID-19 Research (LANCOVID-19), Pereira, Colombia
- School of Medicine, Universidad Privada Franz Tamayo, (UNIFRANZ), Cochabamba, Bolivia
| | - José de la Fuente
- SaBio IREC Instituto de Investigación en Recursos Cinegéticos (CSIC-Universidad de Castilla-La Mancha), Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Izabela Michalak
- Faculty of Chemistry, Department of Advanced Material Technologies, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Youssef A. Attia
- Faculty of Environmental Sciences, Department of Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
- The Strategic Center to Kingdom Vision Realization, King Abdulaziz University, Jeddah, Saudi Arabia
- Faculty of Agriculture, Animal and Poultry Production Department, Damanhour University, Damanhour, Egypt
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18
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Terrier O, Si-Tahar M, Ducatez M, Chevalier C, Pizzorno A, Le Goffic R, Crépin T, Simon G, Naffakh N. Influenza viruses and coronaviruses: Knowns, unknowns, and common research challenges. PLoS Pathog 2021; 17:e1010106. [PMID: 34969061 PMCID: PMC8718010 DOI: 10.1371/journal.ppat.1010106] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The development of safe and effective vaccines in a record time after the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a remarkable achievement, partly based on the experience gained from multiple viral outbreaks in the past decades. However, the Coronavirus Disease 2019 (COVID-19) crisis also revealed weaknesses in the global pandemic response and large gaps that remain in our knowledge of the biology of coronaviruses (CoVs) and influenza viruses, the 2 major respiratory viruses with pandemic potential. Here, we review current knowns and unknowns of influenza viruses and CoVs, and we highlight common research challenges they pose in 3 areas: the mechanisms of viral emergence and adaptation to humans, the physiological and molecular determinants of disease severity, and the development of control strategies. We outline multidisciplinary approaches and technological innovations that need to be harnessed in order to improve preparedeness to the next pandemic.
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Affiliation(s)
- Olivier Terrier
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Mustapha Si-Tahar
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- Inserm U1100, Research Center for Respiratory Diseases (CEPR), Université de Tours, Tours, France
| | - Mariette Ducatez
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- IHAP, UMR1225, Université de Toulouse, ENVT, INRAE, Toulouse, France
| | - Christophe Chevalier
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- Université Paris-Saclay, UVSQ, INRAE, VIM, Equipe Virus Influenza, Jouy-en-Josas, France
| | - Andrés Pizzorno
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Ronan Le Goffic
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- Université Paris-Saclay, UVSQ, INRAE, VIM, Equipe Virus Influenza, Jouy-en-Josas, France
| | - Thibaut Crépin
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Gaëlle Simon
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- Swine Virology Immunology Unit, Ploufragan-Plouzané-Niort Laboratory, ANSES, Ploufragan, France
| | - Nadia Naffakh
- CNRS GDR2073 ResaFlu, Groupement de Recherche sur les Virus Influenza, France
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
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19
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Evolutionary and Phenotypic Characterization of Two Spike Mutations in European Lineage 20E of SARS-CoV-2. mBio 2021; 12:e0231521. [PMID: 34781748 PMCID: PMC8593680 DOI: 10.1128/mbio.02315-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We have detected two mutations in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at amino acid positions 1163 and 1167 that appeared independently in multiple transmission clusters and different genetic backgrounds. Furthermore, both mutations appeared together in a cluster of 1,627 sequences belonging to clade 20E. This cluster is characterized by 12 additional single nucleotide polymorphisms but no deletions. The available structural information on the S protein in the pre- and postfusion conformations predicts that both mutations confer rigidity, which could potentially decrease viral fitness. Accordingly, we observed reduced infectivity of this spike genotype relative to the ancestral 20E sequence in vitro, and the levels of viral RNA in nasopharyngeal swabs were not significantly higher. Furthermore, the mutations did not impact thermal stability or antibody neutralization by sera from vaccinated individuals but moderately reduce neutralization by convalescent-phase sera from the early stages of the pandemic. Despite multiple successful appearances of the two spike mutations during the first year of SARS-CoV-2 evolution, the genotype with both mutations was displaced upon the expansion of the 20I (Alpha) variant. The midterm fate of the genotype investigated was consistent with the lack of advantage observed in the clinical and experimental data.
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20
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Van Cleemput J, van Snippenberg W, Lambrechts L, Dendooven A, D'Onofrio V, Couck L, Trypsteen W, Vanrusselt J, Theuns S, Vereecke N, van den Bosch TPP, Lammens M, Driessen A, Achten R, Bracke KR, Van den Broeck W, Von der Thüsen J, Nauwynck H, Van Dorpe J, Gerlo S, Maes P, Cox J, Vandekerckhove L. Organ-specific genome diversity of replication-competent SARS-CoV-2. Nat Commun 2021; 12:6612. [PMID: 34785663 PMCID: PMC8595628 DOI: 10.1038/s41467-021-26884-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/25/2021] [Indexed: 12/26/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is not always confined to the respiratory system, as it impacts people on a broad clinical spectrum from asymptomatic to severe systemic manifestations resulting in death. Further, accumulation of intra-host single nucleotide variants during prolonged SARS-CoV-2 infection may lead to emergence of variants of concern (VOCs). Still, information on virus infectivity and intra-host evolution across organs is sparse. We report a detailed virological analysis of thirteen postmortem coronavirus disease 2019 (COVID-19) cases that provides proof of viremia and presence of replication-competent SARS-CoV-2 in extrapulmonary organs of immunocompromised patients, including heart, kidney, liver, and spleen (NCT04366882). In parallel, we identify organ-specific SARS-CoV-2 genome diversity and mutations of concern N501Y, T1027I, and Y453F, while the patient had died long before reported emergence of VOCs. These mutations appear in multiple organs and replicate in Vero E6 cells, highlighting their infectivity. Finally, we show two stages of fatal disease evolution based on disease duration and viral loads in lungs and plasma. Our results provide insights about the pathogenesis and intra-host evolution of SARS-CoV-2 and show that COVID-19 treatment and hygiene measures need to be tailored to specific needs of immunocompromised patients, even when respiratory symptoms cease.
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Affiliation(s)
- Jolien Van Cleemput
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium.
| | - Willem van Snippenberg
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Amélie Dendooven
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent, Belgium
- Department of Pathology, Antwerp University Hospital, Edegem, Belgium
- Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Valentino D'Onofrio
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
- Department of Infectious Diseases and Immunity, Jessa Hospital, Hasselt, Belgium
| | - Liesbeth Couck
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Jan Vanrusselt
- Department of Radiology, Jessa hospital, Hasselt, Belgium
| | - Sebastiaan Theuns
- PathoSense BV, Lier, Belgium
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Nick Vereecke
- PathoSense BV, Lier, Belgium
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | | | - Martin Lammens
- Department of Pathology, Antwerp University Hospital, Edegem, Belgium
- Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Ann Driessen
- Department of Pathology, Antwerp University Hospital, Edegem, Belgium
- Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Ruth Achten
- Department of Pathology, Antwerp University Hospital, Edegem, Belgium
- Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
- Department of Pathology, Jessa hospital, Hasselt, Belgium
| | - Ken R Bracke
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Wim Van den Broeck
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | | | - Hans Nauwynck
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sarah Gerlo
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Janneke Cox
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
- Department of Infectious Diseases and Immunity, Jessa Hospital, Hasselt, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium.
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21
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SARS-CoV-2 evolution in animals suggests mechanisms for rapid variant selection. Proc Natl Acad Sci U S A 2021; 118:2105253118. [PMID: 34716263 PMCID: PMC8612357 DOI: 10.1073/pnas.2105253118] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/15/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 spillback from humans into domestic and wild animals has been well documented, and an accumulating number of studies illustrate that human-to-animal transmission is widespread in cats, mink, deer, and other species. Experimental inoculations of cats, mink, and ferrets have perpetuated transmission cycles. We sequenced full genomes of Vero cell-expanded SARS-CoV-2 inoculum and viruses recovered from cats (n = 6), dogs (n = 3), hamsters (n = 3), and a ferret (n = 1) following experimental exposure. Five nonsynonymous changes relative to the USA-WA1/2020 prototype strain were near fixation in the stock used for inoculation but had reverted to wild-type sequences at these sites in dogs, cats, and hamsters within 1- to 3-d postexposure. A total of 14 emergent variants (six in nonstructural genes, six in spike, and one each in orf8 and nucleocapsid) were detected in viruses recovered from animals. This included substitutions in spike residues H69, N501, and D614, which also vary in human lineages of concern. Even though a live virus was not cultured from dogs, substitutions in replicase genes were detected in amplified sequences. The rapid selection of SARS-CoV-2 variants in vitro and in vivo reveals residues with functional significance during host switching. These observations also illustrate the potential for spillback from animal hosts to accelerate the evolution of new viral lineages, findings of particular concern for dogs and cats living in households with COVID-19 patients. More generally, this glimpse into viral host switching reveals the unrealized rapidity and plasticity of viral evolution in experimental animal model systems.
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22
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Meekins DA, Gaudreault NN, Richt JA. Natural and Experimental SARS-CoV-2 Infection in Domestic and Wild Animals. Viruses 2021; 13:1993. [PMID: 34696423 PMCID: PMC8540328 DOI: 10.3390/v13101993] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 is the etiological agent responsible for the ongoing COVID-19 pandemic, which continues to spread with devastating effects on global health and socioeconomics. The susceptibility of domestic and wild animal species to infection is a critical facet of SARS-CoV-2 ecology, since reverse zoonotic spillover events resulting in SARS-CoV-2 outbreaks in animal populations could result in the establishment of new virus reservoirs. Adaptive mutations in the virus to new animal species could also complicate ongoing mitigation strategies to combat SARS-CoV-2. In addition, animal species susceptible to SARS-CoV-2 infection are essential as standardized preclinical models for the development and efficacy testing of vaccines and therapeutics. In this review, we summarize the current findings regarding the susceptibility of different domestic and wild animal species to experimental SARS-CoV-2 infection and provide detailed descriptions of the clinical disease and transmissibility in these animals. In addition, we outline the documented natural infections in animals that have occurred at the human-animal interface. A comprehensive understanding of animal susceptibility to SARS-CoV-2 is crucial to inform public health, veterinary, and agricultural systems, and to guide environmental policies.
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Affiliation(s)
- David A. Meekins
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (D.A.M.); (N.N.G.)
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (D.A.M.); (N.N.G.)
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (D.A.M.); (N.N.G.)
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502, USA
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23
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El-Sayed A, Abdel-Daim MM, Kamel M. Zoonotic and anthropozoonotic potential of COVID-19 and its implications for public health. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:52599-52609. [PMID: 34523089 PMCID: PMC8439532 DOI: 10.1007/s11356-021-16415-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 09/05/2021] [Indexed: 05/07/2023]
Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Mohamed M Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah, 21442, Saudi Arabia
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
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24
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Günl F, Mecate-Zambrano A, Rehländer S, Hinse S, Ludwig S, Brunotte L. Shooting at a Moving Target-Effectiveness and Emerging Challenges for SARS-CoV-2 Vaccine Development. Vaccines (Basel) 2021; 9:1052. [PMID: 34696160 PMCID: PMC8540924 DOI: 10.3390/vaccines9101052] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/06/2023] Open
Abstract
Since late 2019 the newly emerged pandemic SARS-CoV-2, the causative agent of COVID-19, has hit the world with recurring waves of infections necessitating the global implementation of non-pharmaceutical interventions, including strict social distancing rules, the wearing of masks and the isolation of infected individuals in order to restrict virus transmissions and prevent the breakdown of our healthcare systems. These measures are not only challenging on an economic level but also have a strong impact on social lifestyles. Using traditional and novel technologies, highly efficient vaccines against SARS-CoV-2 were developed and underwent rapid clinical evaluation and approval to accelerate the immunization of the world population, aiming to end the pandemic and return to normality. However, the emergence of virus variants with improved transmission, enhanced fitness and partial immune escape from the first generation of vaccines poses new challenges, which are currently being addressed by scientists and pharmaceutical companies all over the world. In this ongoing pandemic, the evaluation of SARS-CoV-2 vaccines underlies diverse unpredictable dynamics, posed by the first broad application of the mRNA vaccine technology and their compliance, the occurrence of unexpected side effects and the rapid emergence of variations in the viral antigen. However, despite these hurdles, we conclude that the available SARS-CoV-2 vaccines are very safe and efficiently protect from severe COVID-19 and are thereby the most powerful tools to prevent further harm to our healthcare systems, economics and individual lives. This review summarizes the unprecedented pathways of vaccine development and approval during the ongoing SARS-CoV-2 pandemic. We focus on the real-world effectiveness and unexpected positive and negative side effects of the available vaccines and summarize the timeline of the applied adaptations to the recommended vaccination strategies in the light of emerging virus variants. Finally, we highlight upcoming strategies to improve the next generations of SARS-CoV-2 vaccines.
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Affiliation(s)
- Franziska Günl
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Angeles Mecate-Zambrano
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
| | - Selina Rehländer
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Saskia Hinse
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Stephan Ludwig
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
| | - Linda Brunotte
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
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25
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Choi H, Chatterjee P, Hwang M, Lichtfouse E, Sharma VK, Jinadatha C. The viral phoenix: enhanced infectivity and immunity evasion of SARS-CoV-2 variants. ENVIRONMENTAL CHEMISTRY LETTERS 2021; 20:1539-1544. [PMID: 34522191 PMCID: PMC8428212 DOI: 10.1007/s10311-021-01318-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
SARS-CoV-2 pandemic continues with emergence of new variants of concerns. These variants are fueling the third and fourth waves of pandemic across many nations. Here we describe the new emerging variants of SARS-CoV-2 and why they have enhanced infectivity and possess the ability to evade immunity.
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Affiliation(s)
- Hosoon Choi
- Central Texas Veterans Health Care System, 1901 Veterans Memorial Drive, Temple, TX USA
| | - Piyali Chatterjee
- Central Texas Veterans Health Care System, 1901 Veterans Memorial Drive, Temple, TX USA
| | - Munok Hwang
- Central Texas Veterans Health Care System, 1901 Veterans Memorial Drive, Temple, TX USA
| | - Eric Lichtfouse
- Aix-Marseille University, CNRS, IRD, INRAE, CEREGE, Aix en Provence, 13100 France
| | - Virender K. Sharma
- Program of the Environment and Sustainability, Department of Environmental and Occupational Health, School of Public Health, Texas A&M University, College Station, TX 77843 USA
| | - Chetan Jinadatha
- Central Texas Veterans Health Care System, 1901 Veterans Memorial Drive, Temple, TX USA
- College of Medicine, Texas A&M University, College Station, TX 77842-3012 USA
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26
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Ghorbani A, Samarfard S, Eskandarzade N, Afsharifar A, Eskandari MH, Niazi A, Izadpanah K, Karbanowicz TP. Comparative phylogenetic analysis of SARS-CoV-2 spike protein-possibility effect on virus spillover. Brief Bioinform 2021; 22:bbab144. [PMID: 33885726 PMCID: PMC8083239 DOI: 10.1093/bib/bbab144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/18/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 has developed into a dramatic pandemic with tremendous global impact. The receptor-binding motif (RBM) region of the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), binds to host angiotensin-converting enzyme 2 (ACE2) receptors for infection. As ACE2 receptors are highly conserved within vertebrate species, SARS-CoV-2 can infect significant animal species as well as human populations. An analysis of SARS-CoV-2 genotypes isolated from human and significant animal species was conducted to compare and identify mutation and adaptation patterns across different animal species. The phylogenetic data revealed seven distinct phylogenetic clades with no significant relationship between the clades and geographical locations. A high rate of variation within SARS-CoV-2 mink isolates implies that mink populations were infected before human populations. Positions of most single-nucleotide polymorphisms (SNPs) within the spike (S) protein of SARS-CoV-2 genotypes from the different hosts are mostly accumulated in the RBM region and highlight the pronounced accumulation of variants with mutations in the RBM region in comparison with other variants. These SNPs play a crucial role in viral transmission and pathogenicity and are keys in identifying other animal species as potential intermediate hosts of SARS-CoV-2. The possible roles in the emergence of new viral strains and the possible implications of these changes, in compromising vaccine effectiveness, deserve urgent considerations.
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Affiliation(s)
- Abozar Ghorbani
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Samira Samarfard
- Queensland Biosciences Precinct, The University of Queensland, St Lucia 4072, Queensland, Australia
- Department of Primary Industries and Regional Development, DPIRD Diagnostic Laboratory Services, South Perth, WA, Australia
| | - Neda Eskandarzade
- Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Alireza Afsharifar
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Mohammad Hadi Eskandari
- Department of Food Science and Technology, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
| | | | - Thomas P Karbanowicz
- Queensland Biosciences Precinct, The University of Queensland, St Lucia 4072, Queensland, Australia
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27
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Chaintoutis SC, Thomou Z, Mouchtaropoulou E, Tsiolas G, Chassalevris T, Stylianaki I, Lagou M, Michailidou S, Moutou E, Koenen JJH, Dijkshoorn JW, Paraskevis D, Poutahidis T, Siarkou VI, Sypsa V, Argiriou A, Fortomaris P, Dovas CI. Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. PLoS Pathog 2021; 17:e1009883. [PMID: 34492088 PMCID: PMC8448373 DOI: 10.1371/journal.ppat.1009883] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/17/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 infection outbreaks in minks have serious implications associated with animal health and welfare, and public health. In two naturally infected mink farms (A and B) located in Greece, we investigated the outbreaks and assessed parameters associated with virus transmission, immunity, pathology, and environmental contamination. Symptoms ranged from anorexia and mild depression to respiratory signs of varying intensity. Although the farms were at different breeding stages, mortality was similarly high (8.4% and 10.0%). The viral strains belonged to lineages B.1.1.218 and B.1.1.305, possessing the mink-specific S-Y453F substitution. Lung histopathology identified necrosis of smooth muscle and connective tissue elements of vascular walls, and vasculitis as the main early key events of the acute SARS-CoV-2-induced broncho-interstitial pneumonia. Molecular investigation in two dead minks indicated a consistently higher (0.3-1.3 log10 RNA copies/g) viral load in organs of the male mink compared to the female. In farm A, the infected farmers were responsible for the significant initial infection of 229 out of 1,000 handled minks, suggesting a very efficient human-to-mink transmission. Subsequent infections across the sheds wherein animals were being housed occurred due to airborne transmission. Based on a R0 of 2.90 and a growth rate equal to 0.293, the generation time was estimated to be 3.6 days, indicative of the massive SARS-CoV-2 dispersal among minks. After the end of the outbreaks, a similar percentage of animals were immune in the two farms (93.0% and 93.3%), preventing further virus transmission whereas, viral RNA was detected in samples collected from shed surfaces and air. Consequently, strict biosecurity is imperative during the occurrence of clinical signs. Environmental viral load monitoring, in conjunction with NGS should be adopted in mink farm surveillance. The minimum proportion of minks that need to be immunized to avoid outbreaks in farms was calculated at 65.5%, which is important for future vaccination campaigns.
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Affiliation(s)
- Serafeim C. Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Zoi Thomou
- Pecon Hellas PC, Dispilio, Kastoria, Greece
| | | | - George Tsiolas
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, Greece
| | - Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioanna Stylianaki
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Lagou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Michailidou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | | | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Theofilos Poutahidis
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Victoria I. Siarkou
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Vana Sypsa
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, Greece
- Department of Food Science and Nutrition, University of the Aegean, Myrina, Greece
| | - Paschalis Fortomaris
- Laboratory of Animal Husbandry, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysostomos I. Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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28
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Borges V, Isidro J, Cunha M, Cochicho D, Martins L, Banha L, Figueiredo M, Rebelo L, Trindade MC, Duarte S, Vieira L, Alves MJ, Costa I, Guiomar R, Santos M, Cortê-Real R, Dias A, Póvoas D, Cabo J, Figueiredo C, Manata MJ, Maltez F, Gomes da Silva M, Gomes JP. Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. mSphere 2021; 6:e0024421. [PMID: 34319130 PMCID: PMC8386466 DOI: 10.1128/msphere.00244-21] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/14/2021] [Indexed: 12/31/2022] Open
Abstract
Recent studies have shown that persistent SARS-CoV-2 infections in immunocompromised patients can trigger the accumulation of an unusual high number of mutations with potential relevance at both biological and epidemiological levels. Here, we report a case of an immunocompromised patient (non-Hodgkin lymphoma patient under immunosuppressive therapy) with a persistent SARS-CoV-2 infection (marked by intermittent positivity) over at least 6 months. Viral genome sequencing was performed at days 1, 164, and 171 to evaluate SARS-CoV-2 evolution. Among the 15 single-nucleotide polymorphisms (SNPs) (11 leading to amino acid alterations) and 3 deletions accumulated during this long-term infection, four amino acid changes (V3G, S50L, N87S, and A222V) and two deletions (18-30del and 141-144del) occurred in the virus Spike protein. Although no convalescent plasma therapy was administered, some of the detected mutations have been independently reported in other chronically infected individuals, which supports a scenario of convergent adaptive evolution. This study shows that it is of the utmost relevance to monitor the SARS-CoV-2 evolution in immunocompromised individuals, not only to identify novel potentially adaptive mutations, but also to mitigate the risk of introducing "hyper-evolved" variants in the community. IMPORTANCE Tracking the within-patient evolution of SARS-CoV-2 is key to understanding how this pandemic virus shapes its genome toward immune evasion and survival. In the present study, by monitoring a long-term COVID-19 immunocompromised patient, we observed the concurrent emergence of mutations potentially associated with immune evasion and/or enhanced transmission, mostly targeting the SARS-CoV-2 key host-interacting protein and antigen. These findings show that the frequent oscillation in the immune status in immunocompromised individuals can trigger an accelerated virus evolution, thus consolidating this study model as an accelerated pathway to better understand SARS-CoV-2 adaptive traits and anticipate the emergence of variants of concern.
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Affiliation(s)
- Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Mário Cunha
- Clinical Pathology–Virology Lab, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal
| | - Daniela Cochicho
- Clinical Pathology–Virology Lab, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal
| | - Luís Martins
- Clinical Pathology–Virology Lab, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal
| | - Luís Banha
- Clinical Pathology–Virology Lab, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal
| | - Margarida Figueiredo
- Clinical Pathology–Virology Lab, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal
| | - Leonor Rebelo
- Clinical Pathology–Virology Lab, Instituto Português de Oncologia de Lisboa, Lisbon, Portugal
| | - Maria Céu Trindade
- Serviço de Hematologia, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Maria João Alves
- Centre for Vectors and Infectious Diseases Research, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Inês Costa
- National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Raquel Guiomar
- National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Madalena Santos
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica do CHULC, Lisbon, Portugal
| | - Rita Cortê-Real
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica do CHULC, Lisbon, Portugal
| | - André Dias
- Serviço de Doenças Infecciosas do Hospital de Curry Cabral-CHULC, Lisbon, Portugal
| | - Diana Póvoas
- Serviço de Doenças Infecciosas do Hospital de Curry Cabral-CHULC, Lisbon, Portugal
| | - João Cabo
- Serviço de Doenças Infecciosas do Hospital de Curry Cabral-CHULC, Lisbon, Portugal
| | - Carlos Figueiredo
- Serviço de Doenças Infecciosas do Hospital de Curry Cabral-CHULC, Lisbon, Portugal
| | - Maria José Manata
- Serviço de Doenças Infecciosas do Hospital de Curry Cabral-CHULC, Lisbon, Portugal
| | - Fernando Maltez
- Serviço de Doenças Infecciosas do Hospital de Curry Cabral-CHULC, Lisbon, Portugal
| | - Maria Gomes da Silva
- Serviço de Hematologia, Instituto Português de Oncologia de Lisboa Francisco Gentil, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
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29
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Salleh MZ, Derrick JP, Deris ZZ. Structural Evaluation of the Spike Glycoprotein Variants on SARS-CoV-2 Transmission and Immune Evasion. Int J Mol Sci 2021; 22:7425. [PMID: 34299045 PMCID: PMC8306177 DOI: 10.3390/ijms22147425] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents significant social, economic and political challenges worldwide. SARS-CoV-2 has caused over 3.5 million deaths since late 2019. Mutations in the spike (S) glycoprotein are of particular concern because it harbours the domain which recognises the angiotensin-converting enzyme 2 (ACE2) receptor and is the target for neutralising antibodies. Mutations in the S protein may induce alterations in the surface spike structures, changing the conformational B-cell epitopes and leading to a potential reduction in vaccine efficacy. Here, we summarise how the more important variants of SARS-CoV-2, which include cluster 5, lineages B.1.1.7 (Alpha variant), B.1.351 (Beta), P.1 (B.1.1.28/Gamma), B.1.427/B.1.429 (Epsilon), B.1.526 (Iota) and B.1.617.2 (Delta) confer mutations in their respective spike proteins which enhance viral fitness by improving binding affinity to the ACE2 receptor and lead to an increase in infectivity and transmission. We further discuss how these spike protein mutations provide resistance against immune responses, either acquired naturally or induced by vaccination. This information will be valuable in guiding the development of vaccines and other therapeutics for protection against the ongoing coronavirus disease 2019 (COVID-19) pandemic.
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Affiliation(s)
- Mohd Zulkifli Salleh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Malaysia;
| | - Jeremy P. Derrick
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester M13 9PL, UK;
| | - Zakuan Zainy Deris
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Malaysia;
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30
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Goraichuk IV, Arefiev V, Stegniy BT, Gerilovych AP. Zoonotic and Reverse Zoonotic Transmissibility of SARS-CoV-2. Virus Res 2021; 302:198473. [PMID: 34118360 PMCID: PMC8188804 DOI: 10.1016/j.virusres.2021.198473] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/17/2022]
Abstract
The Coronavirus Disease 2019 (COVID-19) is the first known pandemic caused by a coronavirus. Its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), appears to be capable of infecting different mammalian species. Recent detections of this virus in pet, zoo, wild, and farm animals have compelled inquiry regarding the zoonotic (animal-to-human) and reverse zoonotic (human-to-animal) transmissibility of SARS-CoV-2 with the potential of COVID-19 pandemic evolving into a panzootic. It is important to monitor the global spread of disease and to assess the significance of genomic changes to support prevention and control efforts during a pandemic. An understanding of the SARS-CoV-2 epidemiology provides opportunities to prevent the risk of repeated re-infection of humans and requires a robust One Health-based investigation. This review paper describes the known properties and the existing gaps in scientific knowledge about the zoonotic and reverse zoonotic transmissibility of the novel virus SARS-CoV-2 and the COVID-19 disease it causes.
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Affiliation(s)
- Iryna V Goraichuk
- National Scientific Center "Institute of Experimental and Clinical Veterinary Medicine", 83 Pushkinska street, Kharkiv, 61023, Ukraine.
| | - Vasiliy Arefiev
- National Scientific Center "Institute of Experimental and Clinical Veterinary Medicine", 83 Pushkinska street, Kharkiv, 61023, Ukraine.
| | - Borys T Stegniy
- National Scientific Center "Institute of Experimental and Clinical Veterinary Medicine", 83 Pushkinska street, Kharkiv, 61023, Ukraine.
| | - Anton P Gerilovych
- National Scientific Center "Institute of Experimental and Clinical Veterinary Medicine", 83 Pushkinska street, Kharkiv, 61023, Ukraine.
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31
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Liu H, Yuan M, Huang D, Bangaru S, Zhao F, Lee CCD, Peng L, Barman S, Zhu X, Nemazee D, Burton DR, van Gils MJ, Sanders RW, Kornau HC, Reincke SM, Prüss H, Kreye J, Wu NC, Ward AB, Wilson IA. A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection. Cell Host Microbe 2021; 29:806-818.e6. [PMID: 33894127 PMCID: PMC8049401 DOI: 10.1016/j.chom.2021.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 12/15/2022]
Abstract
Coronaviruses have caused several human epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Prophylactic vaccines and therapeutic antibodies have already shown striking effectiveness against COVID-19. Nevertheless, concerns remain about antigenic drift in SARS-CoV-2 as well as threats from other sarbecoviruses. Cross-neutralizing antibodies to SARS-related viruses provide opportunities to address such concerns. Here, we report on crystal structures of a cross-neutralizing antibody, CV38-142, in complex with the receptor-binding domains from SARS-CoV-2 and SARS-CoV. Recognition of the N343 glycosylation site and water-mediated interactions facilitate cross-reactivity of CV38-142 to SARS-related viruses, allowing the antibody to accommodate antigenic variation in these viruses. CV38-142 synergizes with other cross-neutralizing antibodies, notably COVA1-16, to enhance neutralization of SARS-CoV and SARS-CoV-2, including circulating variants of concern B.1.1.7 and B.1.351. Overall, this study provides valuable information for vaccine and therapeutic design to address current and future antigenic drift in SARS-CoV-2 and to protect against zoonotic SARS-related coronaviruses.
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Affiliation(s)
- Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sandhya Bangaru
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fangzhu Zhao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shawn Barman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Hans-Christian Kornau
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - S Momsen Reincke
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Helmholtz Innovation Lab BaoBab, Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Helmholtz Innovation Lab BaoBab, Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Helmholtz Innovation Lab BaoBab, Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany; Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Mashe T, Takawira FT, Gumbo H, Juru A, Nyagupe C, Maeka KK, Mtapuri-Zinyowera S, Gudza-Mugabe M, de Oliveira Martins L, O'Grady J, Kingsley RA, Page AJ, Simbi R. Surveillance of SARS-CoV-2 in Zimbabwe shows dominance of variants of concern. THE LANCET. MICROBE 2021; 2:e177. [PMID: 33723535 PMCID: PMC7946415 DOI: 10.1016/s2666-5247(21)00061-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
| | | | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Agnes Juru
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Charles Nyagupe
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Kenneth K Maeka
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | | | | | | | | | | | | | - Raiva Simbi
- Ministry of Health and Child Care, Harare, Zimbabwe
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Davis MF, Innes GK. The Cat's in the Bag: Despite Limited Cat-to-Cat Severe Acute Respiratory Syndrome Coronavirus 2 Transmission, One Health Surveillance Efforts Are Needed. J Infect Dis 2021; 223:1309-1312. [PMID: 33605418 PMCID: PMC7928724 DOI: 10.1093/infdis/jiab106] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 01/01/2023] Open
Affiliation(s)
- Meghan F Davis
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.,Department of Molecular and Comparative Pathobiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Gabriel K Innes
- Department of Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
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34
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Peacock TP, Penrice-Randal R, Hiscox JA, Barclay WS. SARS-CoV-2 one year on: evidence for ongoing viral adaptation. J Gen Virol 2021; 102:001584. [PMID: 33855951 PMCID: PMC8290271 DOI: 10.1099/jgv.0.001584] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/16/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral 'genetic drift' or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wendy S. Barclay
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
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35
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Goncalves Cabecinhas AR, Roloff T, Stange M, Bertelli C, Huber M, Ramette A, Chen C, Nadeau S, Gerth Y, Yerly S, Opota O, Pillonel T, Schuster T, Metzger CMJA, Sieber J, Bel M, Wohlwend N, Baumann C, Koch MC, Bittel P, Leuzinger K, Brunner M, Suter-Riniker F, Berlinger L, Søgaard KK, Beckmann C, Noppen C, Redondo M, Steffen I, Seth-Smith HMB, Mari A, Lienhard R, Risch M, Nolte O, Eckerle I, Martinetti Lucchini G, Hodcroft EB, Neher RA, Stadler T, Hirsch HH, Leib SL, Risch L, Kaiser L, Trkola A, Greub G, Egli A. SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Microorganisms 2021; 9:677. [PMID: 33806013 PMCID: PMC8064472 DOI: 10.3390/microorganisms9040677] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological and microbiological definitions. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 13,387 VoCs have been identified since the detection of the first Swiss case in October 2020, with 4194 being B.1.1.7, 172 B.1.351, and 7 P.1. The remaining 9014 cases of VoCs have been described without further lineage specification. Overall, all diagnostic centers reported a rapid increase of the percentage of detected VOCs, with a range of 6 to 46% between 25 to 31 of January 2021 increasing towards 41 to 82% between 22 to 28 of February. A total of 739 N501Y positive genomes were analysed and show a broad range of introduction events to Switzerland. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.
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Affiliation(s)
- Ana Rita Goncalves Cabecinhas
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland; (A.R.G.C.); (S.Y.); (I.E.); (L.K.)
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
| | - Madlen Stange
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (O.O.); (T.P.); (G.G.)
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (M.H.); (A.T.)
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; (C.C.); (S.N.)
| | - Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; (C.C.); (S.N.)
| | - Yannick Gerth
- Center for Laboratory Medicine, 9001 Saint Gall, Switzerland; (Y.G.); (O.N.)
| | - Sabine Yerly
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland; (A.R.G.C.); (S.Y.); (I.E.); (L.K.)
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (O.O.); (T.P.); (G.G.)
| | - Trestan Pillonel
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (O.O.); (T.P.); (G.G.)
| | - Tobias Schuster
- Federal Office of Public Health FOPH, 3097 Berne, Switzerland; (T.S.); (M.B.)
| | - Cesar M. J. A. Metzger
- Spiez Laboratory, Federal Office for Civil Protection FOCP, 3700 Spiez, Switzerland; (C.M.J.A.M.); (J.S.)
| | - Jonas Sieber
- Spiez Laboratory, Federal Office for Civil Protection FOCP, 3700 Spiez, Switzerland; (C.M.J.A.M.); (J.S.)
| | - Michael Bel
- Federal Office of Public Health FOPH, 3097 Berne, Switzerland; (T.S.); (M.B.)
| | - Nadia Wohlwend
- Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland; (N.W.); (M.R.); (L.R.)
| | - Christian Baumann
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Michel C. Koch
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Karoline Leuzinger
- Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland; (K.L.); (H.H.H.)
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Myrta Brunner
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
| | - Franziska Suter-Riniker
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | | | - Kirstine K. Søgaard
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland
| | | | - Christoph Noppen
- Viollier AG, 4123 Allschwil, Switzerland; (C.B.); (C.N.); (M.R.)
| | - Maurice Redondo
- Viollier AG, 4123 Allschwil, Switzerland; (C.B.); (C.N.); (M.R.)
| | | | - Helena M. B. Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
| | - Alfredo Mari
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
| | - Reto Lienhard
- ADMED Microbiology, 2300 La Chaux-de-Fonds, Switzerland;
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland;
| | - Martin Risch
- Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland; (N.W.); (M.R.); (L.R.)
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland;
| | - Oliver Nolte
- Center for Laboratory Medicine, 9001 Saint Gall, Switzerland; (Y.G.); (O.N.)
| | - Isabella Eckerle
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland; (A.R.G.C.); (S.Y.); (I.E.); (L.K.)
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Gladys Martinetti Lucchini
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland;
- EOC Microbiological Laboratory, 6500 Bellinzona, Switzerland
| | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland;
| | - Richard A. Neher
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Tanja Stadler
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; (C.C.); (S.N.)
| | - Hans H. Hirsch
- Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland; (K.L.); (H.H.H.)
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4031 Basel, Switzerland
| | - Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Lorenz Risch
- Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland; (N.W.); (M.R.); (L.R.)
- Faculty of Medical Sciences, Private University of the Principality of Liechtenstein, 9495 Triesen, Liechtenstein
- Centre of Laboratory Medicine, University Institute of Clinical Chemistry, University of Bern, 3010 Bern, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland; (A.R.G.C.); (S.Y.); (I.E.); (L.K.)
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (M.H.); (A.T.)
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (O.O.); (T.P.); (G.G.)
| | - Adrian Egli
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland;
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36
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Rees-Spear C, Muir L, Griffith SA, Heaney J, Aldon Y, Snitselaar JL, Thomas P, Graham C, Seow J, Lee N, Rosa A, Roustan C, Houlihan CF, Sanders RW, Gupta RK, Cherepanov P, Stauss HJ, Nastouli E, Doores KJ, van Gils MJ, McCoy LE. The effect of spike mutations on SARS-CoV-2 neutralization. Cell Rep 2021; 34:108890. [PMID: 33713594 DOI: 10.1101/2021.01.15.426849] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/17/2021] [Accepted: 03/01/2021] [Indexed: 05/18/2023] Open
Abstract
Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines show protective efficacy, which is most likely mediated by neutralizing antibodies recognizing the viral entry protein, spike. Because new SARS-CoV-2 variants are emerging rapidly, as exemplified by the B.1.1.7, B.1.351, and P.1 lineages, it is critical to understand whether antibody responses induced by infection with the original SARS-CoV-2 virus or current vaccines remain effective. In this study, we evaluate neutralization of a series of mutated spike pseudotypes based on divergence from SARS-CoV and then compare neutralization of the B.1.1.7 spike pseudotype and individual mutations. Spike-specific monoclonal antibody neutralization is reduced dramatically; in contrast, polyclonal antibodies from individuals infected in early 2020 remain active against most mutated spike pseudotypes, but potency is reduced in a minority of samples. This work highlights that changes in SARS-CoV-2 spike can alter neutralization sensitivity and underlines the need for effective real-time monitoring of emerging mutations and their effect on vaccine efficacy.
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Affiliation(s)
- Chloe Rees-Spear
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Luke Muir
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Sarah A Griffith
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Judith Heaney
- Advanced Pathogens Diagnostic Unit, Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London W1T 4EU, UK
| | - Yoann Aldon
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Jonne L Snitselaar
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Peter Thomas
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Carl Graham
- School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Jeffrey Seow
- School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Nayung Lee
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | | | | | - Catherine F Houlihan
- Advanced Pathogens Diagnostic Unit, Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London W1T 4EU, UK; Research Department of Infection, Division of Infection and Immunity, University College London, London WC1 6BT, UK
| | - Rogier W Sanders
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK
| | | | - Hans J Stauss
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Eleni Nastouli
- Advanced Pathogens Diagnostic Unit, Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London W1T 4EU, UK; The Francis Crick Institute, London NW1 1AT, UK; Great Ormond Street Institute for Child Health, Infection, Immunity and Inflammation, University College London, London WC1N 1EH, UK
| | - Katie J Doores
- School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Marit J van Gils
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Laura E McCoy
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK.
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37
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Rees-Spear C, Muir L, Griffith SA, Heaney J, Aldon Y, Snitselaar JL, Thomas P, Graham C, Seow J, Lee N, Rosa A, Roustan C, Houlihan CF, Sanders RW, Gupta RK, Cherepanov P, Stauss HJ, Nastouli E, Doores KJ, van Gils MJ, McCoy LE. The effect of spike mutations on SARS-CoV-2 neutralization. Cell Rep 2021; 34:108890. [PMID: 33713594 PMCID: PMC7936541 DOI: 10.1016/j.celrep.2021.108890] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/17/2021] [Accepted: 03/01/2021] [Indexed: 01/08/2023] Open
Abstract
Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines show protective efficacy, which is most likely mediated by neutralizing antibodies recognizing the viral entry protein, spike. Because new SARS-CoV-2 variants are emerging rapidly, as exemplified by the B.1.1.7, B.1.351, and P.1 lineages, it is critical to understand whether antibody responses induced by infection with the original SARS-CoV-2 virus or current vaccines remain effective. In this study, we evaluate neutralization of a series of mutated spike pseudotypes based on divergence from SARS-CoV and then compare neutralization of the B.1.1.7 spike pseudotype and individual mutations. Spike-specific monoclonal antibody neutralization is reduced dramatically; in contrast, polyclonal antibodies from individuals infected in early 2020 remain active against most mutated spike pseudotypes, but potency is reduced in a minority of samples. This work highlights that changes in SARS-CoV-2 spike can alter neutralization sensitivity and underlines the need for effective real-time monitoring of emerging mutations and their effect on vaccine efficacy.
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Affiliation(s)
- Chloe Rees-Spear
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Luke Muir
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Sarah A Griffith
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Judith Heaney
- Advanced Pathogens Diagnostic Unit, Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London W1T 4EU, UK
| | - Yoann Aldon
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Jonne L Snitselaar
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Peter Thomas
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Carl Graham
- School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Jeffrey Seow
- School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Nayung Lee
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | | | | | - Catherine F Houlihan
- Advanced Pathogens Diagnostic Unit, Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London W1T 4EU, UK; Research Department of Infection, Division of Infection and Immunity, University College London, London WC1 6BT, UK
| | - Rogier W Sanders
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge CB2 0AW, UK
| | | | - Hans J Stauss
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Eleni Nastouli
- Advanced Pathogens Diagnostic Unit, Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London W1T 4EU, UK; The Francis Crick Institute, London NW1 1AT, UK; Great Ormond Street Institute for Child Health, Infection, Immunity and Inflammation, University College London, London WC1N 1EH, UK
| | - Katie J Doores
- School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Marit J van Gils
- Amsterdam University Medical Centers, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Laura E McCoy
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK.
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38
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Bashor L, Gagne RB, Bosco-Lauth A, Bowen R, Stenglein M, VandeWoude S. SARS-CoV-2 evolution in animals suggests mechanisms for rapid variant selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.05.434135. [PMID: 33758844 PMCID: PMC7987003 DOI: 10.1101/2021.03.05.434135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2 spillback from humans into domestic and wild animals has been well-documented. We compared variants of cell culture-expanded SARS-CoV-2 inoculum and virus recovered from four species following experimental exposure. Five nonsynonymous changes in nsp12, S, N and M genes were near fixation in the inoculum, but reverted to wild-type sequences in RNA recovered from dogs, cats and hamsters within 1-3 days post-exposure. Fourteen emergent variants were detected in viruses recovered from animals, including substitutions at spike positions H69, N501, and D614, which also vary in human lineages of concern. The rapidity of in vitro and in vivo SARS-CoV-2 selection reveals residues with functional significance during host-switching, illustrating the potential for spillback reservoir hosts to accelerate evolution, and demonstrating plasticity of viral adaptation in animal models. ONE-SENTENCE SUMMARY SARS-CoV-2 variants rapidly arise in non-human hosts, revealing viral evolution and potential risk for human reinfection.
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Affiliation(s)
- Laura Bashor
- Department of Microbiology, Immunology, and Pathology, Colorado State University; Fort Collins, CO, 80523, USA
| | - Roderick B. Gagne
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine; Kennett Square, PA, 19348, USA
| | - Angela Bosco-Lauth
- Department of Biomedical Sciences, Colorado State University; Fort Collins, CO, 80523, USA
| | - Richard Bowen
- Department of Biomedical Sciences, Colorado State University; Fort Collins, CO, 80523, USA
| | - Mark Stenglein
- Department of Microbiology, Immunology, and Pathology, Colorado State University; Fort Collins, CO, 80523, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University; Fort Collins, CO, 80523, USA
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Boklund A, Gortázar C, Pasquali P, Roberts H, Nielsen SS, Stahl K, Stegeman A, Baldinelli F, Broglia A, Van Der Stede Y, Adlhoch C, Alm E, Melidou A, Mirinaviciute G. Monitoring of SARS-CoV-2 infection in mustelids. EFSA J 2021; 19:e06459. [PMID: 33717355 PMCID: PMC7926496 DOI: 10.2903/j.efsa.2021.6459] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
American mink and ferret are highly susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but no information is available for other mustelid species. SARS-CoV-2 spreads very efficiently within mink farms once introduced, by direct and indirect contact, high within-farm animal density increases the chance for transmission. Between-farm spread is likely to occur once SARS-CoV-2 is introduced, short distance between SARS-CoV-2 positive farms is a risk factor. As of 29 January 2021, SARS-CoV-2 virus has been reported in 400 mink farms in eight countries in the European Union. In most cases, the likely introduction of SARS-CoV-2 infection into farms was infected humans. Human health can be at risk by mink-related variant viruses, which can establish circulation in the community, but so far these have not shown to be more transmissible or causing more severe impact compared with other circulating SARS-CoV-2. Concerning animal health risk posed by SARS-CoV-2 infection the animal species that may be included in monitoring plans are American mink, ferrets, cats, raccoon dogs, white-tailed deer and Rhinolophidae bats. All mink farms should be considered at risk of infection; therefore, the monitoring objective should be early detection. This includes passive monitoring (in place in the whole territory of all countries where animals susceptible to SARS-CoV-2 are bred) but also active monitoring by regular testing. First, frequent testing of farm personnel and all people in contact with the animals is recommended. Furthermore randomly selected animals (dead or sick animals should be included) should be tested using reverse transcriptase-polymerase chain reaction (RT-PCR), ideally at weekly intervals (i.e. design prevalence approximately 5% in each epidemiological unit, to be assessed case by case). Suspected animals (dead or with clinical signs and a minimum five animals) should be tested for confirmation of SARS-CoV-2 infection. Positive samples from each farm should be sequenced to monitor virus evolution and results publicly shared.
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Liu H, Yuan M, Huang D, Bangaru S, Lee CCD, Peng L, Zhu X, Nemazee D, van Gils MJ, Sanders RW, Kornau HC, Reincke SM, Prüss H, Kreye J, Wu NC, Ward AB, Wilson IA. A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.11.430866. [PMID: 33594361 PMCID: PMC7885913 DOI: 10.1101/2021.02.11.430866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Coronaviruses have caused several epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Some prophylactic vaccines and therapeutic antibodies have already showed striking effectiveness against COVID-19. Nevertheless, concerns remain about antigenic drift in SARS-CoV-2 as well as threats from other sarbecoviruses. Cross-neutralizing antibodies to SARS-related viruses provide opportunities to address such concerns. Here, we report on crystal structures of a cross-neutralizing antibody CV38-142 in complex with the receptor binding domains from SARS-CoV-2 and SARS-CoV. Our structural findings provide mechanistic insights into how this antibody can accommodate antigenic variation in these viruses. CV38-142 synergizes with other cross-neutralizing antibodies, in particular COVA1-16, to enhance neutralization of SARS-CoV-2 and SARS-CoV. Overall, this study provides valuable information for vaccine and therapeutic design to address current and future antigenic drift in SARS-CoV-2 and to protect against zoonotic coronaviruses.
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Affiliation(s)
- Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology and Infection Prevention, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sandhya Bangaru
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D. Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology and Infection Prevention, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology and Infection Prevention, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Hans-Christian Kornau
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - S. Momsen Reincke
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
- Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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Updated insight into COVID-19 disease and health management to combat the pandemic. ENVIRONMENTAL AND HEALTH MANAGEMENT OF NOVEL CORONAVIRUS DISEASE (COVID-19 ) 2021. [PMCID: PMC8237642 DOI: 10.1016/b978-0-323-85780-2.00017-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 disease in humans and is the responsible viral agent for the currently ongoing pandemic. Early cases of COVID-19 were reported from Wuhan, Hubei province of China, the likely birthplace of this outbreak. Currently, over 92 million people in the globe are actively battling this virus, and over 2 million individuals have already succumbed to the disease. The high human-to-human transmission capacity of the virus is among the primary causes for such a rapid global spread of COVID-19. In humans, it causes acute to severe respiratory distress in the form of pneumonia. The presentation of clinical features of the disease ranges from mild in healthy adults to severe among individuals with weakened or immunocompromised immune systems and the elderly. Thus, increasing patient cases of COVID-19 warrants a growing demand for medical attention that is eventually overburdening our health care systems. Rapid detection of COVID-19 in suspected individuals and isolation are among the crucial intervention norms in health management strategies to control the COVID-19 pandemic, in addition to strict observance of public hygienic practices such as reduced public gathering, use of facial masks, and practicing of social distancing. This chapter provides an overview of the epidemiology of COVID-19 and the current classical health management strategies and issues to tackle this pandemic. It particularly highlights the role of standard as well as novel biomolecular diagnostic techniques as a tool for successful implementation of such public safety measures issued by medical policy makers and the governing bodies.
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