Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Campus Monterrey, Eugenio Garza Sada 2501 Sur, Monterrey 64849, Mexico; School of Advance Engineering, University of Petroleum and Energy Studies, Dehradun, Uttarakhand 248007, India.
School of Advance Engineering, University of Petroleum and Energy Studies, Dehradun, Uttarakhand 248007, India; Department of Biological and Ecological Engineering, School of Engineering, Oregon State University, Corvallis, OR, USA.
Sci Total Environ. 2024 Nov 1;949:174756. doi: 10.1016/j.scitotenv.2024.174756. Epub 2024 Jul 14.
Tracking new variants of SARS-CoV-2 is vital for managing COVID-19 spread and allocating resources. Domestic antigen testing has created surveillance gaps that make it hard to identify new viral variants. We conducted whole genome sequencing of wastewater viral genes from major and minor treatment facilities in Dehradun from March 2022 onwards. Based on our analysis, the samples that achieved higher sequencing depth and covered >90 % of the viral genome uncovered a major variant pattern resembling the XAP recombinant lineage that is reported for the first time in the City of Dehradun, Uttrakhand and is the first ever records in India as on date. This novel XAP recombinant lineage had 9, 2, 30, 1, 2, 5, 1, 1, 1 aminoacid changes (total 54 mutations) in Orf1a, Orf1b, S, E, M, N, Orf3a, Orf6 and Orf8 regions of the gene respectively that shares 49 mutations common to the ancestral lineages BA.1* and BA.2*, with 6 unique mutations. Subsequent comparison and analysis of the clinical sequence data from the region post-detection of this rare and unusual variant showed no causalities infected with the newly detected XAP lineage. These findings are indicative of future alarming situation with plausible threats of fresh spur of Omicron variant led infections in the urban community.
追踪 SARS-CoV-2 的新变体对于管理 COVID-19 的传播和分配资源至关重要。国内抗原检测造成了监测空白，难以识别新的病毒变体。我们从 2022 年 3 月起对德拉敦主要和次要处理设施的废水病毒基因进行了全基因组测序。根据我们的分析，那些达到更高测序深度且覆盖 >90%病毒基因组的样本揭示了一种主要的变体模式，类似于 XAP 重组谱系，这是首次在北阿坎德邦德拉敦市报告，截至目前也是印度的首次记录。这种新型 XAP 重组谱系在基因的 Orf1a、Orf1b、S、E、M、N、Orf3a、Orf6 和 Orf8 区域分别有 9、2、30、1、2、5、1、1、1 个氨基酸变化（总计 54 个突变），与祖先谱系 BA.1和 BA.2共有 49 个突变，有 6 个独特的突变。随后对该罕见和不寻常变体检测后该地区的临床序列数据进行比较和分析，未发现与新检测到的 XAP 谱系有关的感染病例。这些发现预示着未来可能会出现令人担忧的情况，奥密克戎变体可能会导致城市社区出现新的感染高峰。
