Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from sampl...
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| Veröffentlicht in: | International journal of environmental research and public health 2023-04, Vol.20 (8), p.5503 |
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| description | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from samples collected between March 2020 and mid-February 2022 in the Dominican Republic were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Phylogenetic relationships and evolution rates were analyzed using the maximum likelihood method and the Bayesian Markov chain Monte Carlo (MCMC) approach. The genotyping details (lineages) were obtained using the Pangolin web application. In addition, the web tools Coronapp, and Genome Detective Viral Tools, among others, were used to monitor epidemiological characteristics. Our results show that the most frequent non-synonymous mutation over the study period was D614G. Of the 1149 samples, 870 (75.74%) were classified into 8 relevant variants according to Pangolin/Scorpio. The first Variants Being Monitored (VBM) were detected in December 2020. Meanwhile, in 2021, the variants of concern Delta and Omicron were identified. The mean mutation rate was estimated to be 1.5523 × 10
(95% HPD: 1.2358 × 10
, 1.8635 × 10
) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. A better understanding of viral evolution and genomic surveillance data will help to inform strategies to mitigate the impact on public health. |
| doi_str_mv | 10.3390/ijerph20085503 |
| format | Article |
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(95% HPD: 1.2358 × 10
, 1.8635 × 10
) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. A better understanding of viral evolution and genomic surveillance data will help to inform strategies to mitigate the impact on public health.</description><identifier>ISSN: 1660-4601</identifier><identifier>ISSN: 1661-7827</identifier><identifier>EISSN: 1660-4601</identifier><identifier>DOI: 10.3390/ijerph20085503</identifier><identifier>PMID: 37107785</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Animals ; Applications programs ; Bayes Theorem ; Bayesian analysis ; Coronaviruses ; COVID-19 ; COVID-19 - epidemiology ; Disease transmission ; Dominican Republic - epidemiology ; Epidemiology ; Evolution ; Genomes ; Genomics ; Genotyping ; Health aspects ; Humans ; Markov chains ; Maximum likelihood method ; Mutation ; Mutation rates ; Nucleotides ; Pandemics ; Pangolins ; Phylogenetics ; Phylogeny ; Proteins ; Public health ; RNA viruses ; SARS-CoV-2 - genetics ; Severe acute respiratory syndrome ; Severe acute respiratory syndrome coronavirus 2 ; Software packages ; Surveillance ; Viruses ; World health</subject><ispartof>International journal of environmental research and public health, 2023-04, Vol.20 (8), p.5503</ispartof><rights>COPYRIGHT 2023 MDPI AG</rights><rights>2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 by the authors. 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4013-1043363fea289e15dcec3d3ceed8c7221a1712bfb638ba10681210d3fac4d6143</citedby><cites>FETCH-LOGICAL-c4013-1043363fea289e15dcec3d3ceed8c7221a1712bfb638ba10681210d3fac4d6143</cites><orcidid>0000-0002-3676-0357 ; 0000-0003-4810-0871</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10138544/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10138544/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27923,27924,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37107785$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Paulino-Ramírez, Robert</creatorcontrib><creatorcontrib>López, Pablo</creatorcontrib><creatorcontrib>Mueses, Sayira</creatorcontrib><creatorcontrib>Cuevas, Paula</creatorcontrib><creatorcontrib>Jabier, Maridania</creatorcontrib><creatorcontrib>Rivera-Amill, Vanessa</creatorcontrib><title>Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage</title><title>International journal of environmental research and public health</title><addtitle>Int J Environ Res Public Health</addtitle><description>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from samples collected between March 2020 and mid-February 2022 in the Dominican Republic were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Phylogenetic relationships and evolution rates were analyzed using the maximum likelihood method and the Bayesian Markov chain Monte Carlo (MCMC) approach. The genotyping details (lineages) were obtained using the Pangolin web application. In addition, the web tools Coronapp, and Genome Detective Viral Tools, among others, were used to monitor epidemiological characteristics. Our results show that the most frequent non-synonymous mutation over the study period was D614G. Of the 1149 samples, 870 (75.74%) were classified into 8 relevant variants according to Pangolin/Scorpio. The first Variants Being Monitored (VBM) were detected in December 2020. Meanwhile, in 2021, the variants of concern Delta and Omicron were identified. The mean mutation rate was estimated to be 1.5523 × 10
(95% HPD: 1.2358 × 10
, 1.8635 × 10
) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. 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In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from samples collected between March 2020 and mid-February 2022 in the Dominican Republic were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Phylogenetic relationships and evolution rates were analyzed using the maximum likelihood method and the Bayesian Markov chain Monte Carlo (MCMC) approach. The genotyping details (lineages) were obtained using the Pangolin web application. In addition, the web tools Coronapp, and Genome Detective Viral Tools, among others, were used to monitor epidemiological characteristics. Our results show that the most frequent non-synonymous mutation over the study period was D614G. Of the 1149 samples, 870 (75.74%) were classified into 8 relevant variants according to Pangolin/Scorpio. The first Variants Being Monitored (VBM) were detected in December 2020. Meanwhile, in 2021, the variants of concern Delta and Omicron were identified. The mean mutation rate was estimated to be 1.5523 × 10
(95% HPD: 1.2358 × 10
, 1.8635 × 10
) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. A better understanding of viral evolution and genomic surveillance data will help to inform strategies to mitigate the impact on public health.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>37107785</pmid><doi>10.3390/ijerph20085503</doi><orcidid>https://orcid.org/0000-0002-3676-0357</orcidid><orcidid>https://orcid.org/0000-0003-4810-0871</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Applications programs Bayes Theorem Bayesian analysis Coronaviruses COVID-19 COVID-19 - epidemiology Disease transmission Dominican Republic - epidemiology Epidemiology Evolution Genomes Genomics Genotyping Health aspects Humans Markov chains Maximum likelihood method Mutation Mutation rates Nucleotides Pandemics Pangolins Phylogenetics Phylogeny Proteins Public health RNA viruses SARS-CoV-2 - genetics Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Software packages Surveillance Viruses World health |
| title | Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage |
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