tetano
Editor, Senior Moderator
J Med Virol
. 2022 Dec 2.
doi: 10.1002/jmv.28366. Online ahead of print.
Molecular evolution of SARS-CoV-2 from December 2019 to August 2022
Jonas Michel Wolf[SUP] 1 [/SUP], Lucas Michel Wolf[SUP] 2 [/SUP], Graziele Lima Bello[SUP] 3 [/SUP], Juçara Gasparetto Maccari[SUP] 4 [/SUP], Luiz Antonio Nasi[SUP] 5 [/SUP]
Affiliations
Abstract
Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning worldwide, presenting more than 590 million coronavirus disease 2019 cases and 6,4 million deaths. The emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide during the pandemic.
Aim: The present study review and summarizes the temporal spreading and molecular evolution of SARS-CoV-2 clades and variants worldwide. The evaluation of these data is important for understanding the evolutionary histories of SARS-CoV-2 lineages, allowing us to identify the origins of each lineage of this virus responsible for one of the biggest pandemics in history.
Method: A total of 2,897 SARS-CoV-2 whole-genome sequences (WGSs) with available information from the country and sampling date (Dec/2019 - Aug/2022), were obtained and were evaluated by Bayesian approach.
Results: The results demonstrated that the SARS-CoV-2 the time to the most recent common ancestor (tMRCA) in Asia was 2019-12-26 [Highest Posterior Density 95% (HPD95%): 2019-12-18; 2019-12-29), in Oceania 2020-01-24 (HPD95%: 2020-01-15; 2020-01-30), in Africa 2020-02-27 (HPD95%: 2020-02-21; 2020-03-04), in Europe 2020-02-27 (HPD95%: 2020-02-20; 2020-03-06), in North America 2020-03-12 (HPD95%: 2020-03-05; 2020-03-18) and in South America 2020-03-15 (HPD95%: 2020-03-09; 2020-03-28). Between Dec 2019 and June 2020, 11 clades were detected [20I (Alpha) and 19A, 19B, 20B, 20C, 20A, 20D, 20E (EU1), 20F, 20H (Beta)]. From July to Dec 2020 four clades were identified [20J (Gamma, V3), 21C (Epsilon), 21D (Eta), and 21G (Lambda)]. Between Jan and June 2021, three clades of the delta variant were detected (21A, 21I, and 21J). Between July and Dec 2021, two variants were detected, delta (21A, 21I, and 21J) and omicron (21K, 21L, 22B, and 22C). Between Jan and June 2022, the delta (21I and 21J) and omicron (21K, 21L, and 22A) variants were detected. Finally, between July and Aug 2022 three clades of omicron were detected (22B, 22C, and 22D). Clade 19A was first detected in the SARS-CoV-2 pandemic (Wuhan strain) with origin in 2019-12-16 (HPD95%: 2019-12-15; 2019-12-25); 20I (Alpha) in 2020-11-24 (HPD95%: 2020-11-15; 2021-12-02); 20H (Beta) in 2020-11-25 (HPD95%: 2020-11-13; 2020-11-29); 20J (Gamma) was 2020-12-21 (HPD95%: 2020-11-05; 2021-01-15); 21A (Delta) in 2020-09-20 (HPD95%: 2020-05-17; 2021-02-03); 21J (Delta) in 2021-02-26 (2020-11-02; 2021-04-24); 21M (Omicron) in 2021-01-25 (HPD95%: 2020-09-16; 2021-08-08); 21K (Omicron) in 2021-07-30 (HPD95%: 2021-05-30; 2021-10-19); 21L (Omicron) in 2021-10-03 (HPD95%: 2021-04-16; 2021-12-23); 22B (Omicron) in 2022-01-25 (HPD95%: 2022-01-10; 2022-02-05); 21L in 2021-12-20 (HPD95%: 2021-05-16; 2021-12-31). Currently, the omicron variant predominates worldwide, with the 21L clade branching into three (22A, 22B, and 22C). Phylogeographic data showed that Alpha variant originated in the UK, Beta in South Africa, Gamma in Brazil, Delta in India, Omicron in South Africa, Mu in Colombia, Epsilon in the USA, and Lambda in Peru.
Conclusion: The COVID-19 pandemic has had a significant impact on global health worldwide and the present study provides an overview of the molecular evolution of SARS-CoV-2 lineage clades (from the Wuhan strain to the currently circulating lineages of the omicron). This article is protected by copyright. All rights reserved.
Keywords: Bayesian; COVID-19; SARS-CoV-2; molecular evolution.
. 2022 Dec 2.
doi: 10.1002/jmv.28366. Online ahead of print.
Molecular evolution of SARS-CoV-2 from December 2019 to August 2022
Jonas Michel Wolf[SUP] 1 [/SUP], Lucas Michel Wolf[SUP] 2 [/SUP], Graziele Lima Bello[SUP] 3 [/SUP], Juçara Gasparetto Maccari[SUP] 4 [/SUP], Luiz Antonio Nasi[SUP] 5 [/SUP]
Affiliations
- PMID: 36458547
- DOI: 10.1002/jmv.28366
Abstract
Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning worldwide, presenting more than 590 million coronavirus disease 2019 cases and 6,4 million deaths. The emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide during the pandemic.
Aim: The present study review and summarizes the temporal spreading and molecular evolution of SARS-CoV-2 clades and variants worldwide. The evaluation of these data is important for understanding the evolutionary histories of SARS-CoV-2 lineages, allowing us to identify the origins of each lineage of this virus responsible for one of the biggest pandemics in history.
Method: A total of 2,897 SARS-CoV-2 whole-genome sequences (WGSs) with available information from the country and sampling date (Dec/2019 - Aug/2022), were obtained and were evaluated by Bayesian approach.
Results: The results demonstrated that the SARS-CoV-2 the time to the most recent common ancestor (tMRCA) in Asia was 2019-12-26 [Highest Posterior Density 95% (HPD95%): 2019-12-18; 2019-12-29), in Oceania 2020-01-24 (HPD95%: 2020-01-15; 2020-01-30), in Africa 2020-02-27 (HPD95%: 2020-02-21; 2020-03-04), in Europe 2020-02-27 (HPD95%: 2020-02-20; 2020-03-06), in North America 2020-03-12 (HPD95%: 2020-03-05; 2020-03-18) and in South America 2020-03-15 (HPD95%: 2020-03-09; 2020-03-28). Between Dec 2019 and June 2020, 11 clades were detected [20I (Alpha) and 19A, 19B, 20B, 20C, 20A, 20D, 20E (EU1), 20F, 20H (Beta)]. From July to Dec 2020 four clades were identified [20J (Gamma, V3), 21C (Epsilon), 21D (Eta), and 21G (Lambda)]. Between Jan and June 2021, three clades of the delta variant were detected (21A, 21I, and 21J). Between July and Dec 2021, two variants were detected, delta (21A, 21I, and 21J) and omicron (21K, 21L, 22B, and 22C). Between Jan and June 2022, the delta (21I and 21J) and omicron (21K, 21L, and 22A) variants were detected. Finally, between July and Aug 2022 three clades of omicron were detected (22B, 22C, and 22D). Clade 19A was first detected in the SARS-CoV-2 pandemic (Wuhan strain) with origin in 2019-12-16 (HPD95%: 2019-12-15; 2019-12-25); 20I (Alpha) in 2020-11-24 (HPD95%: 2020-11-15; 2021-12-02); 20H (Beta) in 2020-11-25 (HPD95%: 2020-11-13; 2020-11-29); 20J (Gamma) was 2020-12-21 (HPD95%: 2020-11-05; 2021-01-15); 21A (Delta) in 2020-09-20 (HPD95%: 2020-05-17; 2021-02-03); 21J (Delta) in 2021-02-26 (2020-11-02; 2021-04-24); 21M (Omicron) in 2021-01-25 (HPD95%: 2020-09-16; 2021-08-08); 21K (Omicron) in 2021-07-30 (HPD95%: 2021-05-30; 2021-10-19); 21L (Omicron) in 2021-10-03 (HPD95%: 2021-04-16; 2021-12-23); 22B (Omicron) in 2022-01-25 (HPD95%: 2022-01-10; 2022-02-05); 21L in 2021-12-20 (HPD95%: 2021-05-16; 2021-12-31). Currently, the omicron variant predominates worldwide, with the 21L clade branching into three (22A, 22B, and 22C). Phylogeographic data showed that Alpha variant originated in the UK, Beta in South Africa, Gamma in Brazil, Delta in India, Omicron in South Africa, Mu in Colombia, Epsilon in the USA, and Lambda in Peru.
Conclusion: The COVID-19 pandemic has had a significant impact on global health worldwide and the present study provides an overview of the molecular evolution of SARS-CoV-2 lineage clades (from the Wuhan strain to the currently circulating lineages of the omicron). This article is protected by copyright. All rights reserved.
Keywords: Bayesian; COVID-19; SARS-CoV-2; molecular evolution.