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Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam
A second cluster of COVID-19 cases imported from Europe occured in Vietnam from early March 2020. We describe 44 SARS-CoV-2 RT-PCR positive patients (cycle threshold value
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| Published in: | PloS one 2020-11, Vol.15 (11), p.e0242537-e0242537 |
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| creator | Nguyen, Tam Thi Pham, Thach Ngoc Van, Trang Dinh Nguyen, Trang Thu Nguyen, Diep Thi Ngoc Le, Hoa Nguyen Minh Eden, John-Sebastian Rockett, Rebecca J Nguyen, Thuong Thi Hong Vu, Bich Thi Ngoc Tran, Giang Van Le, Tan Van Dwyer, Dominic E van Doorn, H Rogier |
| description | A second cluster of COVID-19 cases imported from Europe occured in Vietnam from early March 2020. We describe 44 SARS-CoV-2 RT-PCR positive patients (cycle threshold value |
| doi_str_mv | 10.1371/journal.pone.0242537 |
| format | article |
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We describe 44 SARS-CoV-2 RT-PCR positive patients (cycle threshold value <30) admitted to the National Hospital for Tropical Diseases in Hanoi between March 6 and April 15 2020. Whole SARS-CoV-2 genomes from these patients were sequenced using Illumina Miseq and analysed for common genetic variants and relationships to local and globally circulating strains. Results showed that 32 cases were Vietnamese with a median age of 37 years (range 15-74 years), and 23 were male. Most cases were acquired outside Vietnam, mainly from the UK (n = 15), other European countries (n = 14), Russia (n = 6) and countries in Asia (n = 3). No cases had travelled from China. Forty-one cases had symptoms at admission, typically dry cough (n = 36), fever (n = 20), sore throat (n = 14) and diarrhoea (n = 12). Hospitalisation was long with a median of 25 days, most commonly from 20-29 days. All SARS-CoV-2 genomes were similar (92-100% sequence homology) to the reference sequence Wuhan_1 (NC_045512), and 32 strains belonged to the B.1.1 lineage. The three most common variants were linked, and included C3037T, C14408T (nsp12: P323L) and A23403G (S: D614G) mutations. This group of mutations often accompanied variant C241T (39/44 genomes) or GGG 28881..28883 AAC (33/44 genomes). The prevalence of the former reflected probable European origin of viruses, and the transition D614G was dominant in Vietnam. New variants were identified; however, none could be associated with disease severity.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0242537</identifier><identifier>PMID: 33201914</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adolescent ; Adult ; Aged ; Betacoronavirus - genetics ; Betacoronavirus - isolation & purification ; Biodiversity ; Biology and life sciences ; Computer and Information Sciences ; Coronavirus Infections - epidemiology ; Coronavirus Infections - virology ; Coronaviruses ; Cough ; COVID-19 ; Diagnosis ; Diarrhea ; Distribution ; Epidemiology ; Female ; Fever ; Genetic analysis ; Genetic aspects ; Genetic diversity ; Genetic variance ; Genetic Variation ; Genomes ; Homology ; Hospital patients ; Humans ; Male ; Medical research ; Medicine and health sciences ; Middle Aged ; Mutation ; Pandemics ; Patients ; People and Places ; Pharyngitis ; Pneumonia, Viral - epidemiology ; Pneumonia, Viral - virology ; Polymerase chain reaction ; Prevalence ; Research and Analysis Methods ; SARS-CoV-2 ; Severe acute respiratory syndrome ; Severe acute respiratory syndrome coronavirus 2 ; Signs and symptoms ; Statistics ; Travel-Related Illness ; Vietnam ; Viral diseases ; Viral research ; Viruses ; Young Adult</subject><ispartof>PloS one, 2020-11, Vol.15 (11), p.e0242537-e0242537</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Nguyen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2020 Nguyen et al 2020 Nguyen et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-2e8706842eaac69fc3689d749fd6ef97b68c480e4913a910a07caafc3f2f90473</citedby><cites>FETCH-LOGICAL-c692t-2e8706842eaac69fc3689d749fd6ef97b68c480e4913a910a07caafc3f2f90473</cites><orcidid>0000-0002-0282-7760 ; 0000-0003-1374-3551</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2461518646?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2461518646?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,38516,43895,44590,53791,53793,74412,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33201914$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Zhao, Richard Y.</contributor><creatorcontrib>Nguyen, Tam Thi</creatorcontrib><creatorcontrib>Pham, Thach Ngoc</creatorcontrib><creatorcontrib>Van, Trang Dinh</creatorcontrib><creatorcontrib>Nguyen, Trang Thu</creatorcontrib><creatorcontrib>Nguyen, Diep Thi Ngoc</creatorcontrib><creatorcontrib>Le, Hoa Nguyen Minh</creatorcontrib><creatorcontrib>Eden, John-Sebastian</creatorcontrib><creatorcontrib>Rockett, Rebecca J</creatorcontrib><creatorcontrib>Nguyen, Thuong Thi Hong</creatorcontrib><creatorcontrib>Vu, Bich Thi Ngoc</creatorcontrib><creatorcontrib>Tran, Giang Van</creatorcontrib><creatorcontrib>Le, Tan Van</creatorcontrib><creatorcontrib>Dwyer, Dominic E</creatorcontrib><creatorcontrib>van Doorn, H Rogier</creatorcontrib><creatorcontrib>OUCRU COVID-19 Research Group</creatorcontrib><creatorcontrib>on behalf of the OUCRU COVID-19 Research Group</creatorcontrib><title>Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>A second cluster of COVID-19 cases imported from Europe occured in Vietnam from early March 2020. We describe 44 SARS-CoV-2 RT-PCR positive patients (cycle threshold value <30) admitted to the National Hospital for Tropical Diseases in Hanoi between March 6 and April 15 2020. Whole SARS-CoV-2 genomes from these patients were sequenced using Illumina Miseq and analysed for common genetic variants and relationships to local and globally circulating strains. Results showed that 32 cases were Vietnamese with a median age of 37 years (range 15-74 years), and 23 were male. Most cases were acquired outside Vietnam, mainly from the UK (n = 15), other European countries (n = 14), Russia (n = 6) and countries in Asia (n = 3). No cases had travelled from China. Forty-one cases had symptoms at admission, typically dry cough (n = 36), fever (n = 20), sore throat (n = 14) and diarrhoea (n = 12). Hospitalisation was long with a median of 25 days, most commonly from 20-29 days. All SARS-CoV-2 genomes were similar (92-100% sequence homology) to the reference sequence Wuhan_1 (NC_045512), and 32 strains belonged to the B.1.1 lineage. The three most common variants were linked, and included C3037T, C14408T (nsp12: P323L) and A23403G (S: D614G) mutations. This group of mutations often accompanied variant C241T (39/44 genomes) or GGG 28881..28883 AAC (33/44 genomes). The prevalence of the former reflected probable European origin of viruses, and the transition D614G was dominant in Vietnam. New variants were identified; however, none could be associated with disease severity.</description><subject>Adolescent</subject><subject>Adult</subject><subject>Aged</subject><subject>Betacoronavirus - genetics</subject><subject>Betacoronavirus - isolation & purification</subject><subject>Biodiversity</subject><subject>Biology and life sciences</subject><subject>Computer and Information Sciences</subject><subject>Coronavirus Infections - epidemiology</subject><subject>Coronavirus Infections - virology</subject><subject>Coronaviruses</subject><subject>Cough</subject><subject>COVID-19</subject><subject>Diagnosis</subject><subject>Diarrhea</subject><subject>Distribution</subject><subject>Epidemiology</subject><subject>Female</subject><subject>Fever</subject><subject>Genetic analysis</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetic variance</subject><subject>Genetic Variation</subject><subject>Genomes</subject><subject>Homology</subject><subject>Hospital patients</subject><subject>Humans</subject><subject>Male</subject><subject>Medical research</subject><subject>Medicine and health sciences</subject><subject>Middle Aged</subject><subject>Mutation</subject><subject>Pandemics</subject><subject>Patients</subject><subject>People and Places</subject><subject>Pharyngitis</subject><subject>Pneumonia, Viral - epidemiology</subject><subject>Pneumonia, Viral - virology</subject><subject>Polymerase chain reaction</subject><subject>Prevalence</subject><subject>Research and Analysis Methods</subject><subject>SARS-CoV-2</subject><subject>Severe acute respiratory syndrome</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Signs and symptoms</subject><subject>Statistics</subject><subject>Travel-Related Illness</subject><subject>Vietnam</subject><subject>Viral diseases</subject><subject>Viral research</subject><subject>Viruses</subject><subject>Young Adult</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>COVID</sourceid><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNqNk9Fq2zAUhs3YWLtsbzA2w2BsUGeSLMv2zSBkWxsoBJott-JYlhMFR0oluaxvP3lxSzx6MXQhcfT9v3SOdKLoLUZTnOb4y850VkM7PRgtp4hQkqX5s-gclylJGEHp85P1WfTKuR1CWVow9jI6S1OCcInpeeQvpZZeibhWd9I65e9j08Sr2c0qmZt1QmLQdSxapZWA9iKWB1XLvTKt2fSBWGzBgvDSKhdMXK-dL9eLbwku4wN4JbV3sdLxFWijLuK1kl7D_nX0ooHWyTfDPIl-_fj-c36VXC8vF_PZdSJYSXxCZJEjVlAiAUKkESkryjqnZVMz2ZR5xQpBCyRpiVMoMQKUC4CANaQpEc3TSfT-6HtojeNDwRwnlOEMF4yyQCyORG1gxw9W7cHecwOK_w0Yu-FgQ2at5Bmtq7qpKsIaQauMVgwQlqKoMUCFQ2kn0dfhtK7ay1qE3C20I9PxjlZbvjF3PGc5pmURDD4NBtbcdtJ5vldOyLYFLU13vHeRFQzjgH74B306u4HaQEhA6caEc0VvymeMEsRQTvt7T5-gwuhfWoTf1agQHwk-jwSB8fK330DnHF-sbv6fXa7H7McTdiuh9Vtn2s4ro90YpEdQWOOclc1jkTHifXM8VIP3zcGH5giyd6cP9Ch66Ib0D-c1COU</recordid><startdate>20201117</startdate><enddate>20201117</enddate><creator>Nguyen, Tam Thi</creator><creator>Pham, Thach Ngoc</creator><creator>Van, Trang Dinh</creator><creator>Nguyen, Trang Thu</creator><creator>Nguyen, Diep Thi Ngoc</creator><creator>Le, Hoa Nguyen Minh</creator><creator>Eden, John-Sebastian</creator><creator>Rockett, Rebecca J</creator><creator>Nguyen, Thuong Thi Hong</creator><creator>Vu, Bich Thi Ngoc</creator><creator>Tran, Giang Van</creator><creator>Le, Tan Van</creator><creator>Dwyer, Dominic E</creator><creator>van Doorn, H Rogier</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>COVID</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-0282-7760</orcidid><orcidid>https://orcid.org/0000-0003-1374-3551</orcidid></search><sort><creationdate>20201117</creationdate><title>Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam</title><author>Nguyen, Tam Thi ; Pham, Thach Ngoc ; Van, Trang Dinh ; Nguyen, Trang Thu ; Nguyen, Diep Thi Ngoc ; Le, Hoa Nguyen Minh ; Eden, John-Sebastian ; Rockett, Rebecca J ; Nguyen, Thuong Thi Hong ; Vu, Bich Thi Ngoc ; Tran, Giang Van ; Le, Tan Van ; Dwyer, Dominic E ; van Doorn, H Rogier</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-2e8706842eaac69fc3689d749fd6ef97b68c480e4913a910a07caafc3f2f90473</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Adolescent</topic><topic>Adult</topic><topic>Aged</topic><topic>Betacoronavirus - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nguyen, Tam Thi</au><au>Pham, Thach Ngoc</au><au>Van, Trang Dinh</au><au>Nguyen, Trang Thu</au><au>Nguyen, Diep Thi Ngoc</au><au>Le, Hoa Nguyen Minh</au><au>Eden, John-Sebastian</au><au>Rockett, Rebecca J</au><au>Nguyen, Thuong Thi Hong</au><au>Vu, Bich Thi Ngoc</au><au>Tran, Giang Van</au><au>Le, Tan Van</au><au>Dwyer, Dominic E</au><au>van Doorn, H Rogier</au><au>Zhao, Richard Y.</au><aucorp>OUCRU COVID-19 Research Group</aucorp><aucorp>on behalf of the OUCRU COVID-19 Research Group</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2020-11-17</date><risdate>2020</risdate><volume>15</volume><issue>11</issue><spage>e0242537</spage><epage>e0242537</epage><pages>e0242537-e0242537</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>A second cluster of COVID-19 cases imported from Europe occured in Vietnam from early March 2020. We describe 44 SARS-CoV-2 RT-PCR positive patients (cycle threshold value <30) admitted to the National Hospital for Tropical Diseases in Hanoi between March 6 and April 15 2020. Whole SARS-CoV-2 genomes from these patients were sequenced using Illumina Miseq and analysed for common genetic variants and relationships to local and globally circulating strains. Results showed that 32 cases were Vietnamese with a median age of 37 years (range 15-74 years), and 23 were male. Most cases were acquired outside Vietnam, mainly from the UK (n = 15), other European countries (n = 14), Russia (n = 6) and countries in Asia (n = 3). No cases had travelled from China. Forty-one cases had symptoms at admission, typically dry cough (n = 36), fever (n = 20), sore throat (n = 14) and diarrhoea (n = 12). Hospitalisation was long with a median of 25 days, most commonly from 20-29 days. All SARS-CoV-2 genomes were similar (92-100% sequence homology) to the reference sequence Wuhan_1 (NC_045512), and 32 strains belonged to the B.1.1 lineage. The three most common variants were linked, and included C3037T, C14408T (nsp12: P323L) and A23403G (S: D614G) mutations. This group of mutations often accompanied variant C241T (39/44 genomes) or GGG 28881..28883 AAC (33/44 genomes). The prevalence of the former reflected probable European origin of viruses, and the transition D614G was dominant in Vietnam. New variants were identified; however, none could be associated with disease severity.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>33201914</pmid><doi>10.1371/journal.pone.0242537</doi><tpages>e0242537</tpages><orcidid>https://orcid.org/0000-0002-0282-7760</orcidid><orcidid>https://orcid.org/0000-0003-1374-3551</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2020-11, Vol.15 (11), p.e0242537-e0242537 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2461518646 |
| source | Publicly Available Content Database; PubMed Central; Coronavirus Research Database |
| subjects | Adolescent Adult Aged Betacoronavirus - genetics Betacoronavirus - isolation & purification Biodiversity Biology and life sciences Computer and Information Sciences Coronavirus Infections - epidemiology Coronavirus Infections - virology Coronaviruses Cough COVID-19 Diagnosis Diarrhea Distribution Epidemiology Female Fever Genetic analysis Genetic aspects Genetic diversity Genetic variance Genetic Variation Genomes Homology Hospital patients Humans Male Medical research Medicine and health sciences Middle Aged Mutation Pandemics Patients People and Places Pharyngitis Pneumonia, Viral - epidemiology Pneumonia, Viral - virology Polymerase chain reaction Prevalence Research and Analysis Methods SARS-CoV-2 Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Signs and symptoms Statistics Travel-Related Illness Vietnam Viral diseases Viral research Viruses Young Adult |
| title | Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam |
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