» Articles » PMID: 36700580

Clinical and Epidemiological Aspects of Delta and Gamma SARS-CoV-2 Variant of Concern from the Western Brazilian Amazon

Abstract

Background: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has become a major concern contributing to increased morbidity and mortality worldwide.

Objectives: Here we describe the replacement of the Gamma variant of concern (VOC) with Delta in the western Brazilian Amazon.

Methods: In this study, we analysed 540 SARS-CoV-2 positive samples determined by qualitative real-time RT-PCR selected in the state of Rondônia between June and December 2021. The positive cohort was sequenced through next-generation sequencing (NGS) and each sample was quantified using real-time RT-qPCR, the whole genome sequence was obtained, SARS-CoV-2 lineages were classified using the system Pango and the maximum likelihood (ML) method was used to conduct phylogenetic analyses.

Findings: A total of 540 high-quality genomes were obtained, where the Delta VOC showed the highest prevalence making up 72%, with strain AY.43 being the most abundant, while the Gamma VOC was present in 28%, where the P.1 strain was the most frequent. In this study population, only 32.96% (178/540) had completed the vaccination schedule.

Main Conclusions: This study highlighted the presence of Gamma and Delta variants of SARS-CoV-2 in RO. Furthermore, we observed the replacement of the Gamma VOC with the Delta VOC and its lineages.

Citing Articles

SARS-CoV-2 Infection Among Children in Rondônia, Western Brazilian Amazon: SARS-CoV-2 Among Children in Rondônia.

Mota Amaral G, Sgorlon G, Batista Ferreira V, Serrano Batista F, da Silva Soares Farias L, Barbagelata L Adv Virol. 2025; 2025:6655790.

PMID: 39995617 PMC: 11850067. DOI: 10.1155/av/6655790.


Haplotypic Distribution of SARS-CoV-2 Variants in Cases of Intradomiciliary Infection in the State of Rondônia, Western Amazon.

Teixeira K, Custodio M, Sgorlon G, Roca T, Queiroz J, Passos-Silva A Bioinform Biol Insights. 2024; 18:11779322241266354.

PMID: 39574519 PMC: 11580058. DOI: 10.1177/11779322241266354.


Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis.

Y Castro T, Piccoli B, Vieira A, Casarin B, Tessele L, Salvato R Microorganisms. 2023; 11(12).

PMID: 38138081 PMC: 10745878. DOI: 10.3390/microorganisms11122938.


The emergence of Omicron VOC and its rapid spread and persistence in the Western Amazon.

Sgorlon G, Roca T, Passos-Silva A, Queiroz J, Teixeira K, Araujo A PLoS One. 2023; 18(8):e0285742.

PMID: 37590264 PMC: 10434903. DOI: 10.1371/journal.pone.0285742.


SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia.

Sgorlon G, Roca T, Passos-Silva A, Custodio M, Queiroz J, da Silva A Bioinform Biol Insights. 2023; 17:11779322231186477.

PMID: 37461740 PMC: 10350575. DOI: 10.1177/11779322231186477.


References
1.
Campbell F, Archer B, Laurenson-Schafer H, Jinnai Y, Konings F, Batra N . Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021. Euro Surveill. 2021; 26(24). PMC: 8212592. DOI: 10.2807/1560-7917.ES.2021.26.24.2100509. View

2.
Yang W, Shaman J . COVID-19 pandemic dynamics in India, the SARS-CoV-2 Delta variant and implications for vaccination. J R Soc Interface. 2022; 19(191):20210900. PMC: 9169547. DOI: 10.1098/rsif.2021.0900. View

3.
Kumar S . Second wave of COVID-19: emergency situation in India. J Travel Med. 2021; 28(7). PMC: 8244620. DOI: 10.1093/jtm/taab082. View

4.
Harvey W, Carabelli A, Jackson B, Gupta R, Thomson E, Harrison E . SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021; 19(7):409-424. PMC: 8167834. DOI: 10.1038/s41579-021-00573-0. View

5.
Pan Y, Zhang D, Yang P, Poon L, Wang Q . Viral load of SARS-CoV-2 in clinical samples. Lancet Infect Dis. 2020; 20(4):411-412. PMC: 7128099. DOI: 10.1016/S1473-3099(20)30113-4. View