Teixeira Karolaine Santos, Custódio Márlon Grégori Flores, Sgorlon Gabriella, Roca Tárcio Peixoto, Queiroz Jackson Alves da Silva, Passos-Silva Ana Maisa, Ribeiro Jessiane, Vieira Deusilene
Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia-FIOCRUZ/RO, Porto Velho, Brazil.
Instituto Nacional de Epidemiologia da Amazônia Ocidental-INCT EpiAmO, Porto Velho, Brazil.
Bioinform Biol Insights. 2024 Nov 21;18:11779322241266354. doi: 10.1177/11779322241266354. eCollection 2024.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a high transmissibility profile which favors the accumulation of mutations along its genome, providing the emergence of new variants. In this context, haplotype studies have allowed mapping specific regions and combining approaches and tracking phylogenetic changes. During the COVID-19 pandemic, it was notorious that home environments favored the circulation of SARS-CoV-2, in this study we evaluated 1,407 individuals positive for SARS-CoV-2, in which we located 53 families in the period from June 2021 to February 2023. The epidemiological data were collected in E-SUS notifica and SIVEP-gripe. Then, the genetic material was extracted using the commercial kit and the viral load was evaluated and the viral genomes were sequenced using the Illumina MiSeq methodology. In addition, the circulation of 3 variants and their respective subvariants was detected. The delta variant represented the highest number of cases with 45%, the Omicron variant 43% and the lowest number with 11% of cases the Gamma variants. There were cases of families infected by different subvariants, thus showing different sources of infection. The haplotype network showed a distribution divided into 6 large clusters that were established according to the genetic characteristics observed by the algorithm and 224 Parsimony informative sites were found. In addition, 92% of subjects were symptomatic and 8% asymptomatic. The secondary attack rate of this study was 8.32%. Therefore, we can infer that the home environment favors the spread of SARS-CoV-2, so it is of paramount importance to carry out genomic surveillance in specific groups such as intradomiciliary ones.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）具有高传播性，这有利于其基因组沿线积累突变，从而产生新的变体。在此背景下，单倍型研究有助于绘制特定区域、结合方法并追踪系统发育变化。在新冠疫情期间，家庭环境有利于SARS-CoV-2传播是众所周知的。在本研究中，我们评估了1407名SARS-CoV-2呈阳性的个体，在2021年6月至2023年2月期间找到了53个家庭。流行病学数据收集于电子健康记录系统（E-SUS）通知和流感监测信息系统（SIVEP-gripe）。然后，使用商业试剂盒提取遗传物质，评估病毒载量，并使用Illumina MiSeq方法对病毒基因组进行测序。此外，检测到3种变体及其各自亚变体的传播情况。德尔塔变体的病例数最多，占45%，奥密克戎变体占43%，伽马变体的病例数最少，占11%。存在家庭感染不同亚变体的情况，从而显示出不同的感染源。单倍型网络显示分布分为6个大簇，这些簇是根据算法观察到的遗传特征建立的，共发现224个简约信息位点。此外，92%的受试者有症状，8%无症状。本研究的继发感染率为8.32%。因此，我们可以推断家庭环境有利于SARS-CoV-2传播，所以在特定群体（如家庭内部群体）中开展基因组监测至关重要。
