Omicron Sub-Lineages (BA.1.1.529 + BA.*) Current Status in Ecuador

Carrazco-Montalvo, Andrés; Herrera-Yela, Andrés; Alarcón-Vallejo, Damaris; Gutiérrez-Pallo, Diana; Armendáriz‐Castillo, Isaac; Andrade-Molina, Derly; Muñoz-Mawyin, Karen; Fernández-Cadena, Juan Carlos; Morey-León, Gabriel; Usfq-Covid-Consortium,; Ovr-Inspi, Crn Influenza Y; Patiño, Leandro

doi:10.3390/v14061177

Cited by 12 publications

(8 citation statements)

References 23 publications

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“…Omicron's BA.1 lineage and its sub‐lineages corresponded to 42.8% of the sequenced genomes (145 genomes) in the present study (with emphasis on BA.1.14 and BA.1.14.1 sub‐lineages). The sub‐lineage BA.1.14 was widely reported in different parts of the world in the first half of 2021, being evidenced in about 82 countries with varied prevalence 26–28 . In Brazil, the distribution of these sub‐lineages remained constant throughout the first half of 2021, with the same trend in the number of sequenced genomes in the different geographic regions of the country 29,30 .…”

Section: Discussionmentioning

confidence: 93%

“…The new variant of SARS-CoV-2 quickly crossed international borders and by December 9, 2021, it had already been reported in 57 countries. 19,20 In Brazil, the Omicron variant was introduced in mid-December 2021, and by the end of [26][27][28] In Brazil, the distribution of these sublineages remained constant throughout the first half of 2021, with the same trend in the number of sequenced genomes in the different geographic regions of the country. 29,30 Study carried out between October 2021 and April 2022 with genomes from all over Brazil, showed the BA.1, BA.1.1 and BA.1.14.1 sub-lineages as the most prevalent and pointed out that Omicron was imported mainly by the state of São Paulo, which in turn dispersed the lineages to other states and regions of the country.…”

Section: Discussionmentioning

confidence: 99%

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Molecular epidemiology of SARS‐CoV‐2 variants in circulation in the state of Maranhão, Brazil

de Sousa,

Ferreira,

Lobato

et al. 2023

Journal of Medical Virology

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Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a coronavirus belonging to the beta CoV genus, responsible for SARS in humans, which became known as COVID‐19. The emergence of variants of this virus is related to the presence of cases of reinfection, reduced vaccine effectiveness and greater transmission of the virus. Objective: In this study, we evaluated the molecular epidemiology of SARS‐CoV‐2 lineages circulating in the state of Maranhão. This is a cross‐sectional and retrospective epidemiological study of genomic surveillance of SARS‐CoV‐2. The study comprised of 338 genomes sequenced by the Next Generation Sequencing technique on Illumina's Miseq equipment, submitted to Global Initiative on Sharing Avian Influenza Data, 190 (56.2%) are from samples of female and 148 (43.8%) from male patients. Sequencing performed covered samples of patients aged between 1 and 108 years, with emphasis on the age groups from 30 to 39 years with 15.0% of sequenced genomes and 20 to 29 years with 12.4%. As for the distribution of sequenced genomes by health macro‐regions, 285 (84.3%) are from cities in the northern macro‐region. We evidenced the circulation of 29 lineages and sub‐lineages, four of which belonging to the Delta variant (AY.43, AY.99.1, AY.99.2 and AY.101 responsible for 4.5% of the genomes) and the others belonging to the Omicron variant, with emphasis on: BA.1 and sub‐lineages (42.8%); BA.4, BA.5 and sub‐lineages (5.3% and 41.1%); the sub‐lineages DL.1 and BQ.1 (5% and 2%). A strong genomic surveillance system allows the study of the natural history of the disease, when there is a resurgence of SARS‐CoV‐2 cases.

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Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Molecular epidemiology of SARS‐CoV‐2 variants in circulation in the state of Maranhão, Brazil

de Sousa,

Ferreira,

Lobato

et al. 2023

Journal of Medical Virology

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“…The studies are ordered based on the earliest date in each study. Omicron Study Country Dates BA.1 BA.2 Omicron Delta (or other variant) Cedro-Tanda et al 38 Mexico November 16, 2021 – November 21, 2021 2% 98% December 13, 2021 – December 19, 2021 65% 35% December 27, 2021 – December 31, 2021 88% 12% Mella-Torres et al 75 Chile November 29, 2021 – January 24, 2022 B.1.1529 (534/588) 90.5% 9.1%(54/588) Alpha (B.1.1.7) 0.2% (1/588) Gamma (P.1) 0.2% (1/588) Carrazco-Montalvo et al 56 Ecuador December 12, 2021 – December 18, 2021 50% (33/66) 50% (33/66) De Souza et al 25 …”

Section: Resultsmentioning

confidence: 99%

“…In Brazil, the prevalence of the Omicron variant increased from 0.4% between December 2021–2022 (n = 241) 25 to 85% between February and March 2022 (n = 67) 64 while in Ecuador the prevalence was 50% in December 2021 (n = 66). 56 Only one study reported the prevalence of the Omicron variant in Chile as 90.8% between November 2021 and January 2022 ( Figure 3(a) ). Ranzani et al, 79 reported the increase in the prevalence of Omicron in Brazil from 1% (September – December 2021) to 100% (December 2021-April 2022).…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, Chile had a relatively similar level of prevalence during the periods, November 2021–January 2022 (90.8%). 75 In Ecuador, Carrazco-Montalvo et al 56 reported that in a cohort of 66 subjects infected with SARS-CoV-2, 50% were infected with Omicron and 50% were infected with the Delta variant between December 12, 2021 and December 18, 2021. Furthermore, they identified 12 sub-lineages of the Omicron variant circulating in Ecuador, each with different mutation numbers and worldwide origins.…”

Section: Discussionmentioning

confidence: 99%

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The relative prevalence of the Omicron variant within SARS-CoV-2 infected cohorts in different countries: A systematic review

Sarkar,

Omar,

Alshareef

et al. 2023

Human Vaccines & Immunotherapeutics

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The Omicron variant of SARS-CoV-2 was detected in October 2021 and exhibited high transmissibility, immune evasion, and reduced severity when compared to the earlier variants. The lesser vaccine effectiveness against Omicron and its reduced severity created vaccination hesitancy among the public. This review compiled data reporting the relative prevalence of Omicron as compared to the early variants to give an insight into the existing variants, which may shape the decisions regarding the targets of the newly developed vaccines. Complied data revealed more than 90% prevalence within the infected cohorts in some countries. The BA.1 subvariant predominated over the BA.2 during the early stages of the Omicron wave. Moreover, BA.4/BA.5 subvariants were detected in South Africa, USA and Italy between October 2021 and April 2022. It is therefore important to develop vaccines that protect against Omicron as well as the early variants, which are known to cause more severe complications.

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COVID‐19 in a common woolly monkey (Lagothrix lagothricha): First evidence of fatal outcome in a nonhuman primate after natural SARS‐CoV‐2 infection

Diaz,

Sáenz,

Cabrera

et al. 2024

American J Primatol

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Coronavirus disease 2019 (COVID‐19), caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), was declared a pandemic by the World Health Organization in March 2020. Since then, viral spread from humans to animals has occurred worldwide. Nonhuman primates (NHPs) have been found to be susceptible to reverse‐zoonosis transmission of SARS‐CoV‐2, but initial research suggested that platyrrhine primates are less susceptible than catarrhine primates. Here we report the natural SARS‐CoV‐2 infection of a common woolly monkey (Lagothrix lagothricha) from a wildlife rehabilitation center in Ecuador. The course of the disease, the eventual death of the specimen, and the pathological findings are described. Our results show the susceptibility of a new platyrrhine species to SARS‐CoV‐2 and provide evidence for the first time of a COVID‐19‐associated death in a naturally infected NHP. The putative route of transmission from humans, and implications for captive NHPs management, are also discussed. Given that common woolly monkeys are at risk of extinction in Ecuador, further understanding of the potential threat of SARS‐CoV‐2 to their health should be a conservation priority. A One Health approach is the best way to protect NHPs from a new virus in the same way that we would protect the human population.

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Omicron Sub-Lineages (BA.1.1.529 + BA.*) Current Status in Ecuador

Cited by 12 publications

References 23 publications

Molecular epidemiology of SARS‐CoV‐2 variants in circulation in the state of Maranhão, Brazil

Molecular epidemiology of SARS‐CoV‐2 variants in circulation in the state of Maranhão, Brazil

The relative prevalence of the Omicron variant within SARS-CoV-2 infected cohorts in different countries: A systematic review

COVID‐19 in a common woolly monkey (Lagothrix lagothricha): First evidence of fatal outcome in a nonhuman primate after natural SARS‐CoV‐2 infection

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