Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon.

IF 2.5 4区 医学 Q2 PARASITOLOGY Memorias do Instituto Oswaldo Cruz Pub Date : 2023-01-01 DOI:10.1590/0074-02760220155
Gabriella Sgorlon, Jackson Alves da Silva Queiroz, Tárcio Peixoto Roca, Ana Maisa Passos da Silva, Nadson Willian Felipe Gasparelo, Karolaine Santos Teixeira, Andreia Souza da Nóbrega Oliveira, Aline Linhares Ferreira de Melo Mendonça, Adriana Cristina Salvador Maia, Soraya Dos Santos Pereira, Flávia Serrano Batista, Juan Miguel Villalobos Salcedo, Rita de Cassia Pontello Rampazzo, Paola Cristina Resende, Marilda Mendonça Siqueira, Felipe Gomes Naveca, Deusilene Vieira
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引用次数: 4

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.

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来自巴西亚马逊西部的令人关注的Delta和Gamma SARS-CoV-2变体的临床和流行病学方面。
背景:严重急性呼吸综合征冠状病毒2 (SARS-CoV-2)变体的出现已成为导致全球发病率和死亡率增加的主要问题。目的:在这里,我们描述了在巴西西部亚马逊地区用Delta替代关注的伽马变体(VOC)。方法:对2021年6月至12月在Rondônia采集的540份定性实时RT-PCR检测的SARS-CoV-2阳性样本进行分析。采用新一代测序(NGS)对阳性队列进行测序,每个样本采用实时RT-qPCR定量,获得全基因组序列,采用Pango系统对SARS-CoV-2谱系进行分类,采用最大似然(ML)法进行系统发育分析。结果:共获得540个高质量基因组,其中δ型VOC含量最高,占72%,其中AY.43菌株含量最多;Gamma型VOC含量为28%,其中P.1菌株含量最多。在本研究人群中,只有32.96%(178/540)完成了疫苗接种计划。主要结论:本研究强调了RO中存在SARS-CoV-2的Gamma和Delta变体。此外,我们观察到伽马挥发性有机化合物被Delta挥发性有机化合物及其谱系所取代。
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来源期刊
CiteScore
5.00
自引率
3.60%
发文量
91
审稿时长
3-8 weeks
期刊介绍: Memórias do Instituto Oswaldo Cruz is a journal specialized in microbes & their vectors causing human infections. This means that we accept manuscripts covering multidisciplinary approaches and findings in the basic aspects of infectious diseases, e.g. basic in research in prokariotes, eukaryotes, and/or virus. Articles must clearly show what is the main question to be answered, the hypothesis raised, and the contribution given by the study. Priority is given to manuscripts reporting novel mechanisms and general findings concerning the biology of human infectious prokariotes, eukariotes or virus. Papers reporting innovative methods for diagnostics or that advance the basic research with these infectious agents are also welcome. It is important to mention what we do not publish: veterinary infectious agents research, taxonomic analysis and re-description of species, epidemiological studies or surveys or case reports and data re-analysis. Manuscripts that fall in these cases or that are considered of low priority by the journal editorial board, will be returned to the author(s) for submission to another journal.
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