1
|
Araujo DB, Machado RRG, Amgarten DE, Malta FDM, de Araujo GG, Monteiro CO, Candido ED, Soares CP, de Menezes FG, Pires ACC, Santana RAF, Viana ADO, Dorlass E, Thomazelli L, Ferreira LCDS, Botosso VF, Carvalho CRG, Oliveira DBL, Pinho JRR, Durigon EL. SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network. Mem Inst Oswaldo Cruz 2020; 115:e200342. [PMID: 33111751 PMCID: PMC7586445 DOI: 10.1590/0074-02760200342] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/24/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed in Brazil in February 2020, the first cases were followed by an increase in the number of cases throughout the country, resulting in an important public health crisis that requires fast and coordinated responses. OBJECTIVES The objective of this work is to describe the isolation and propagation properties of SARS-CoV-2 isolates from the first confirmed cases of coronavirus disease 2019 (COVID-19) in Brazil. METHODS After diagnosis in patients that returned from Italy to the São Paulo city in late February by RT-PCR, SARS-CoV-2 isolates were obtained in cell cultures and characterised by full genome sequencing, electron microscopy and in vitro replication properties. FINDINGS The virus isolate was recovered from nasopharyngeal specimen, propagated in Vero cells (E6, CCL-81 and hSLAM), with clear cytopathic effects, and characterised by full genome sequencing, electron microscopy and in vitro replication properties. Virus stocks - viable (titre 2.11 × 106 TCID50/mL, titre 1.5 × 106 PFUs/mL) and inactivated from isolate SARS.CoV2/SP02.2020.HIAE.Br were prepared and set available to the public health authorities and the scientific community in Brazil and abroad. MAIN CONCLUSION We believe that the protocols for virus growth and studies here described and the distribution initiative may constitute a viable model for other developing countries, not only to help a rapid effective pandemic response, but also to facilitate and support basic scientific research.
Collapse
Affiliation(s)
- Danielle Bastos Araujo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil.,Hospital Israelita Albert Einstein, São Paulo, SP, Brasil
| | | | | | | | - Gabriel Guarany de Araujo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | - Cairo Oliveira Monteiro
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | - Erika Donizetti Candido
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | - Camila Pereira Soares
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | | | | | | | - Amanda de Oliveira Viana
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | - Erick Dorlass
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | - Luciano Thomazelli
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | | | - Viviane Fongaro Botosso
- Instituto Butantã, Centro de Inovação e Desenvolvimento, Laboratório de Virologia, São Paulo, SP, Brasil
| | | | - Danielle Bruna Leal Oliveira
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil.,Hospital Israelita Albert Einstein, São Paulo, SP, Brasil.,Instituto Butantã, Centro de Inovação e Desenvolvimento, Laboratório de Virologia, São Paulo, SP, Brasil
| | - João Renato Rebello Pinho
- Hospital Israelita Albert Einstein, São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, Laboratório de Medicina Laboratorial (LIM/03), São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, Laboratório de Gastroenterologia Clínica e Experimental (LIM/07), São Paulo, SP, Brasil
| | - Edison Luiz Durigon
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil.,Plataforma Científica Pasteur-USP, São Paulo, SP, Brasil
| |
Collapse
|
2
|
Su S, Wong G, Shi W, Liu J, Lai ACK, Zhou J, Liu W, Bi Y, Gao GF. Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses. Trends Microbiol 2016; 24:490-502. [PMID: 27012512 PMCID: PMC7125511 DOI: 10.1016/j.tim.2016.03.003] [Citation(s) in RCA: 1794] [Impact Index Per Article: 224.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/02/2016] [Accepted: 03/04/2016] [Indexed: 02/07/2023]
Abstract
Human coronaviruses (HCoVs) were first described in the 1960s for patients with the common cold. Since then, more HCoVs have been discovered, including those that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), two pathogens that, upon infection, can cause fatal respiratory disease in humans. It was recently discovered that dromedary camels in Saudi Arabia harbor three different HCoV species, including a dominant MERS HCoV lineage that was responsible for the outbreaks in the Middle East and South Korea during 2015. In this review we aim to compare and contrast the different HCoVs with regard to epidemiology and pathogenesis, in addition to the virus evolution and recombination events which have, on occasion, resulted in outbreaks amongst humans.
Collapse
Affiliation(s)
- Shuo Su
- Engineering Laboratory of Animal Immunity of Jiangsu Province, Institute of immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
| | - Gary Wong
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; CAS Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing, China
| | - Weifeng Shi
- Institute of Pathogen Biology, Taishan Medical College, Taian, China
| | - Jun Liu
- CAS Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | | | - Jiyong Zhou
- Engineering Laboratory of Animal Immunity of Jiangsu Province, Institute of immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; CAS Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing, China
| | - Yuhai Bi
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; CAS Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing, China.
| | - George F Gao
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; CAS Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Zhejiang University, Hangzhou, China; University of Chinese Academy of Sciences Medical School, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
3
|
Identification of new respiratory viruses in the new millennium. Viruses 2015; 7:996-1019. [PMID: 25757061 PMCID: PMC4379558 DOI: 10.3390/v7030996] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/23/2015] [Accepted: 02/26/2015] [Indexed: 12/13/2022] Open
Abstract
The rapid advancement of molecular tools in the past 15 years has allowed for the retrospective discovery of several new respiratory viruses as well as the characterization of novel emergent strains. The inability to characterize the etiological origins of respiratory conditions, particularly in children, led several researchers to pursue the discovery of the underlying etiology of disease. In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Human bocavirus, with its four separate lineages, discovered in 2005, has been linked to acute respiratory tract infections and gastrointestinal complications. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. This review will detail the most current clinical and epidemiological findings to all respiratory viruses discovered since 2001.
Collapse
|
4
|
Dominguez SR, Shrivastava S, Berglund A, Qian Z, Góes LGB, Halpin RA, Fedorova N, Ransier A, Weston PA, Durigon EL, Jerez JA, Robinson CC, Town CD, Holmes KV. Isolation, propagation, genome analysis and epidemiology of HKU1 betacoronaviruses. J Gen Virol 2014; 95:836-848. [PMID: 24394697 DOI: 10.1099/vir.0.059832-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
From 1 January 2009 to 31 May 2013, 15 287 respiratory specimens submitted to the Clinical Virology Laboratory at the Children's Hospital Colorado were tested for human coronavirus RNA by reverse transcription-PCR. Human coronaviruses HKU1, OC43, 229E and NL63 co-circulated during each of the respiratory seasons but with significant year-to-year variability, and cumulatively accounted for 7.4-15.6 % of all samples tested during the months of peak activity. A total of 79 (0.5 % prevalence) specimens were positive for human betacoronavirus HKU1 RNA. Genotypes HKU1 A and B were both isolated from clinical specimens and propagated on primary human tracheal-bronchial epithelial cells cultured at the air-liquid interface and were neutralized in vitro by human intravenous immunoglobulin and by polyclonal rabbit antibodies to the spike glycoprotein of HKU1. Phylogenetic analysis of the deduced amino acid sequences of seven full-length genomes of Colorado HKU1 viruses and the spike glycoproteins from four additional HKU1 viruses from Colorado and three from Brazil demonstrated remarkable conservation of these sequences with genotypes circulating in Hong Kong and France. Within genotype A, all but one of the Colorado HKU1 sequences formed a unique subclade defined by three amino acid substitutions (W197F, F613Y and S752F) in the spike glycoprotein and exhibited a unique signature in the acidic tandem repeat in the N-terminal region of the nsp3 subdomain. Elucidating the function of and mechanisms responsible for the formation of these varying tandem repeats will increase our understanding of the replication process and pathogenicity of HKU1 and potentially of other coronaviruses.
Collapse
Affiliation(s)
- Samuel R Dominguez
- Departments of Microbiology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA.,Departments of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Susmita Shrivastava
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Andrew Berglund
- Departments of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Zhaohui Qian
- Departments of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Luiz Gustavo Bentim Góes
- Interdisciplinary Graduate Program in Biotechnology, University of São Paulo, Av Prof. Lineu Prestes, 2415, ICB-III, Cidade Universitária, CEP: 05508-900, São Paulo, SP - Brazil.,J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Rebecca A Halpin
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Nadia Fedorova
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Amy Ransier
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Philip A Weston
- Departments of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Edison Luiz Durigon
- Interdisciplinary Graduate Program in Biotechnology, University of São Paulo, Av Prof. Lineu Prestes, 2415, ICB-III, Cidade Universitária, CEP: 05508-900, São Paulo, SP - Brazil.,J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - José Antonio Jerez
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av Prof. Lineu Prestes 1374, ICB-II, Cidade Universitária, CEP: 05580-900, São Paulo, SP - Brazil.,J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Christine C Robinson
- Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, Cidade Universitária, CEP: 05508-270, Sao Paulo, SP - Brazil
| | - Christopher D Town
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Kathryn V Holmes
- Departments of Microbiology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| |
Collapse
|
5
|
Lee W, Chung Y, Yoon HS, Kang C, Kim K. Prevalence and molecular epidemiology of human coronavirus HKU1 in patients with acute respiratory illness. J Med Virol 2013; 85:309-14. [PMID: 23161446 PMCID: PMC7166784 DOI: 10.1002/jmv.23465] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2012] [Indexed: 11/25/2022]
Abstract
In 2005, human coronavirus HKU1 (HCoV-HKU1) was isolated and identified from a 71-year-old man with pneumonia in Hong Kong. To identify and classify genotypes of HCoV-HKU1 in Korea, a sensitive, specific, and quantitative real-time polymerase chain reaction (PCR) assay was developed and analyzed the sequences of HCoV-HKU1 isolated in Korea. A total of 1,985 respiratory specimens taken from patients with acute respiratory illness were tested for HCoV-HKU1 from January 2007 to May 2008. The major clinical symptoms associated with HCoV-HKU1 infection were examined statistically and sequence variations of the RNA-dependent RNA polymerase (RdRp), spike, and nucleocapsid genes were also analyzed. Fifty cases (2.5%) HCoV-HKU1 were identified by real-time PCR and viral loads ranged from 6.7 × 10(4) to 1.6 × 10(9) copies/ml. The clinical symptoms of HCoV-HKU1 infection included rhinorrhea (72%), cough (64%), nasal congestion (56%), fever (32%), sputum (30%), sore throat (18%), chills (16%), postnasal discharge (14%), and tonsillar hypertrophy (10%). There was a seasonal distribution of HCoV-HKU1 infection, peaking in winter and spring. Both genotypes A and B were detected but no recombination between them was found. This is the first report on the identification and genotyping of HCoV-HKU1 as a causative agent of acute respiratory illness in Korea. The data suggest that at least two genotypes, A and B, of HCoV-HKU1 with scattered silent mutations were circulating in Korea from 2007 to 2008.
Collapse
Affiliation(s)
- Wan‐Ji Lee
- Division of Respiratory Viruses, Center for Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Chung‐buk‐do, Korea
| | - Yoon‐Seok Chung
- Division of AIDS, Center for Immunology and Pathology, National Institute of Health, Korea Centers for Disease Control and Prevention, Chung‐buk‐do, Korea
| | - Hee Sook Yoon
- Division of Respiratory Viruses, Center for Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Chung‐buk‐do, Korea
| | - Chun Kang
- Division of Influenza Virus, Center for Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Chung‐buk‐do, Korea
| | - Kisoon Kim
- Division of Respiratory Viruses, Center for Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Chung‐buk‐do, Korea
| |
Collapse
|