Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil.
Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil.
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DOI：
10.3389/fpubh.2023.1195779
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发表时间：
2023
影响因子：
5.2
通讯作者：
Simionatto, Simone
中科院分区：
文献类型：
--
作者：
de Oliveira, Lais Albuquerque;de Rezende, Izabela Mauricio;Navarini, Vinicius Joao;Marchioro, Silvana Beutinger;Torres, Alex Jose Leite;Croda, Julio;Croda, Mariana Garcia;Goncalves, Crhistinne Cavalheiro Maymone;Xavier, Joilson;de Castro, Emerson;Lima, Mauricio;Iani, Felipe;Adelino, Talita;Aburjaile, Flavia;Ferraz Demarchi, Luiz Henrique;Taira, Deborah Ledesma;Zardin, Marina Castilhos Souza Umaki;Fonseca, Vagner;Giovanetti, Marta;Andrews, Jason;Alcantara, Luiz Carlos Junior;Simionatto, Simone
新冠疫情对土著居民产生了重大影响。了解这一人群中的病毒动态对于制定有针对性的保护措施至关重要。
对2020年5月至2021年11月期间从巴西南部马托格罗索州（MS）的一个土著地区收集的共204份新冠病毒阳性样本进行了检测。样本使用纳米孔测序平台进行全基因组测序。对临床、人口统计学和系统发育数据进行了分析。
我们发现新冠病毒的六个主要谱系在土著居民中共同传播，其中泽塔谱系最为流行（27.66%），其次是B.1.1（一种原始毒株）（20.21%）、伽马（14.36%）和德尔塔（13.83%）。其他谱系占总数的45.74%。我们的系统发育重建表明，不同的新冠病毒谱系多次传入马托格罗索州的土著村落。估计的土著居民死亡率为1.47%。就我们研究队列的族裔而言，64.82%属于瓜拉尼族，33.16%属于特雷纳族，男性患病率（53.43%）略高于女性。其他族裔占2.01%。我们还观察到，几乎所有患者（89.55%）都出现了与新冠相关的症状和体征，其中最常见的是咳嗽、发烧、喉咙痛和头痛。
我们的研究结果显示，随着时间的推移，发生了多次独立的新冠病毒传入事件，这可能是由于土著居民的流动性，因为这里研究的村落靠近马托格罗索州的城市地区。死亡率略低于所研究期间该州的估计值，我们认为这可能与评估的样本数量少、该人群中病例和死亡报告不足以及本研究可用的二手数据不一致有关。
在这项研究中，我们展示了多种新冠病毒变异株在这一人群中的传播情况，由于他们因社会经济和文化差异属于最脆弱的群体，应该对他们进行隔离和保护。我们强调需要持续进行基因组监测，以监测和预防新出现病毒的传播，并更好地了解这些人群中的病毒动态，从而能够采取针对性行动。
The COVID-19 pandemic had a major impact on indigenous populations. Understanding the viral dynamics within this population is essential to create targeted protection measures. A total of 204 SARS-CoV-2 positive samples collected between May 2020 and November 2021 from an indigenous area in Mato Grosso do Sul (MS), Midwestern Brazil, were screened. Samples were submitted to whole genome sequencing using the Nanopore sequencing platform. Clinical, demographic, and phylogenetic data were analyzed. We found the co-circulation of six main SARS-CoV-2 lineages in the indigenous population, with the Zeta lineage being the most prevalent (27.66%), followed by B.1.1 (an ancestral strain) (20.21%), Gamma (14.36%) and Delta (13.83%). Other lineages represent 45.74% of the total. Our phylogenetic reconstruction indicates that multiple introduction events of different SARS-CoV-2 lineages occurred in the indigenous villages in MS. The estimated indigenous population mortality rate was 1.47%. Regarding the ethnicity of our cohort, 64.82% belong to the Guarani ethnicity, while 33.16% belong to the Terena ethnicity, with a slightly higher prevalence of males (53.43%) among females. Other ethnicities represent 2.01%. We also observed that almost all patients (89.55%) presented signs and symptoms related to COVID-19, being the most prevalent cough, fever, sore throat, and headache. Our results revealed that multiple independent SARS-CoV-2 introduction events had occurred through time, probably due to indigenous mobility, since the villages studied here are close to urban areas in MS. The mortality rate was slightly below of the estimation for the state in the period studied, which we believe could be related to the small number of samples evaluated, the underreporting of cases and deaths among this population, and the inconsistency of secondary data available for this study. In this study, we showed the circulation of multiple SARS-CoV-2 variants in this population, which should be isolated and protected as they belong to the most fragile group due to their socioeconomic and cultural disparities. We reinforce the need for constant genomic surveillance to monitor and prevent the spread of new emerging viruses and to better understand the viral dynamics in these populations, making it possible to direct specific actions.
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影响因子：
4.5
作者：
Ayouni I;Maatoug J;Dhouib W;Zammit N;Fredj SB;Ghammam R;Ghannem H
通讯作者：
Ghannem H
影响因子：
4.4
作者：
Gabriela Soto-Cabezas, M.;Reyes, Mary F.;Soriano, Anderson N.;Velasquez Rodriguez, Jean Pierre;Ordonez Ibarguen, Luis;Martel, Kevin S.;Flores Jaime, Noemi;Munayco, Cesar, V
通讯作者：
Munayco, Cesar, V
影响因子：
5.3
作者：
Sagulenko P;Puller V;Neher RA
通讯作者：
Neher RA
影响因子：
3.7
作者：
Cardoso, Andrey Moreira;Resende, Paola Cristina;Siqueira, Marilda M.
通讯作者：
Siqueira, Marilda M.
影响因子：
3.9
作者：
Palamim CVC;Ortega MM;Marson FAL
通讯作者：
Marson FAL