Linosefa Linosefa, Hasmiwati Hasmiwati, Jamsari Jamsari, Putra Andani Eka
Department of Microbiology, Faculty of Medicine, Universitas Andalas, Padang, Indonesia.
Center for Infectious Disease Diagnostic and Research (PDRPI), Faculty of Medicine, Universitas Andalas, Padang, Indonesia.
Heliyon. 2024 Jul 9;10(14):e34365. doi: 10.1016/j.heliyon.2024.e34365. eCollection 2024 Jul 30.
The Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) has been undergoing evolutionary changes to improve its ability to thrive within human hosts, leading to the emergence of specific variants associated with subsequent waves of the coronavirus diseases 2019 (COVID-19) pandemic. Indonesia has grappled with the effects of this pandemic and subsequent waves affecting various regions, including West Sumatra. Although located outside Java island epicenter, West Sumatra experienced significant COVID-19 transmission, especially during the third wave in early 2022.
This study aimed to investigate the genetic evolution and epidemiological dynamics of SARS-CoV-2 variants in West Sumatra throughout the three pandemic waves.
We conducted a genotyping study retrospectively using 278 COVID-19 patient samples from 2020 to 2022. The Real-Time Quantitative Reverse Transcription PCR (RT-qPCR) was used for screening, and whole-genome sequence analysis was conducted through the Illumina MiSeq instrument.
The analysis revealed distinct patterns in the prevalence of viral lineages across the waves. The initial wave was predominated by clade 20A (77,4 %) especially lineage B.1.466.2 (50 %). The second wave was marked by a significant emergence of the Delta variant (72,5 %), particularly lineage AY.23 (81,1 %), originating from India, with subsequent local evolution leading to the formation of distinct clusters. We found that about 96,7 % of the third wave variant was dominated by Omicron variants, especially the generation of lineages BA.1 and BA.2, demonstrating widespread global dissemination and local variant development. Phylogenetic analysis indicated a close relatedness of West Sumatra variants to those from Malaysia and other parts of Indonesia, highlighting regional transmission dynamics and potential sources of variant introductions.
This study has identified unique variant clusters within each wave, suggesting distinct evolutionary pathways and local adaptations. These findings provide valuable insights into the genomic landscape of SARS-CoV-2 in West Sumatra and emphasize the crucial role of ongoing genomic surveillance in tracking viral changes and guiding public health measures.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）一直在发生进化变化，以提高其在人类宿主中繁衍的能力，导致出现了与2019冠状病毒病（COVID-19）大流行后续浪潮相关的特定变体。印度尼西亚一直在应对这一大流行及其影响各地区（包括西苏门答腊）的后续浪潮。尽管西苏门答腊位于爪哇岛疫情中心之外，但该地区经历了显著的COVID-19传播，尤其是在2022年初的第三波疫情期间。
本研究旨在调查西苏门答腊在整个三波大流行期间SARS-CoV-2变体的遗传进化和流行病学动态。
我们回顾性地使用了2020年至2022年期间278份COVID-19患者样本进行基因分型研究。采用实时定量逆转录聚合酶链反应（RT-qPCR）进行筛查，并通过Illumina MiSeq仪器进行全基因组序列分析。
分析揭示了各波次中病毒谱系流行情况的不同模式。第一波以20A分支（77.4%）为主，尤其是B.1.466.2谱系（50%）。第二波的显著特征是Delta变体（72.5%）大量出现，尤其是源自印度的AY.23谱系（81.1%），随后在当地进化形成了不同的簇。我们发现，第三波变体中约96.7%由奥密克戎变体主导，尤其是BA.1和BA.2谱系的产生，这表明其在全球广泛传播并在当地发生变体演变。系统发育分析表明，西苏门答腊的变体与马来西亚和印度尼西亚其他地区的变体密切相关，突出了区域传播动态以及变体引入的潜在来源。
本研究在每一波次中都识别出了独特的变体簇，表明存在不同的进化途径和局部适应性。这些发现为西苏门答腊SARS-CoV-2的基因组格局提供了有价值的见解，并强调了持续进行基因组监测在追踪病毒变化和指导公共卫生措施方面的关键作用。
