摘要
COVID-19 has swept globally and Pakistan is no exception.To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1,2020.We identified a total of 347 mutated positions,31 of which were over-represented in Pakistan.Meanwhile,we found over 1000 intra-host single-nucleotide variants(iSNVs).Several of them occurred concurrently,indicating possible interactions among them or coevolution.Some of the high-frequency iSNVs in Pakistan were not observed in the global population,suggesting strong purifying selections.The genomic epidemiology revealed five distinctive spreading clusters.The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure,indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation(G8371T in ORF1ab)of this cluster.Furthermore,28 putative international introductions were identified,several of which are consistent with the epidemiological investigations.In all,this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan,which could aid ongoing and future viral surveillance and COVID-19 control.
基金
supported by grants from the National Key R&D Program of China(Grant Nos.2021YFC0863300,2020YFC0848900,and 2016YFE0206600)
the National Natural Science Foundation of China(Grant No.82161148009)
the Strategic Priority Research Program of Chinese Academy of Sciences,China(Grant Nos.XDA19090116 and XDB38060100)
the Open Biodiversity and Health Big Data Programme of International Union of Biological Sciences,International Partnership Program of Chinese Academy of Sciences(Grant No.153F11KYSB20160008)
the Professional Association of the Alliance of International Science Organizations(Grant No.ANSO-PA-2020-07)
the Youth Innovation Promotion Association of Chinese Academy of Sciences(Grant No.2017141)。
