Comparison of Ion Torrent,Illumina,and Nanopore platforms for sequencing SARS-CoV-2 JN.1 lineage variants from Dalian,China  

作　　者：Xingying Lang Yue Wang Mingchun Luan Zhijian Bo Huan Wang Xue Teng Xuehong Meng Shumin Niu Xiaoman Cui Nan Xia 

机构地区：[1]Dalian Center for Disease Control and Prevention,Dalian,China [2]National Clinical Research Center for Laboratory Medicine,Department of Laboratory Medicine,The First Hospital of China Medical University,Shenyang,China [3]Thermo Fisher Scientific,Beijing,China

出　　处：《感染控制(英文)》2024年第4期63-76,共14页

基　　金：supported by grants from the Dalian Science and Technology Innovation Fund(Grant No.2023JJ13SN040);the Dalian Medical Science Research Project(Grant No.2111033).

摘　　要：Objectives Dominant strains of SARS-CoV-2 have been replaced by SARS-CoV-2 JN.1 lineage variants,which have spread widely in a short period of time.However,an accurate detection method and the reason for rapid spread have not been clarified.Methods Ion Torrent,Illumina,and Nanopore platforms were used to sequence the whole genome of SARSCoV-2 from samples collected from positive cases in the Dalian Center for Disease Control from December 2023 to January 2024.Results The Ion Torrent and Illumina platforms failed to detect some of the variation sites,whereas the optimized Ion Torrent and Nanopore platforms detected all the sites.The Ion Torrent platform had higher sensitivity than the other two platforms and was more suitable for short-read length sequencing;however,the amplicon primers had to be optimized.The Illumina platform was also suitable for short-read length but prone to miss some variation sites.The Nanopore platform was more suitable for long-read length sequencing and had high compatibility for more variation sites.By comparing JN.1 lineage variants with BA.2.86,multiple specific variation sites were detected for the first time in the non-S protein region.Conclusions Timely optimized primers and supplement variation sites provide a more effective means for monitoring and controlling the prevalence of JN.1 lineage variants in advance.The discovery of specific variation sites may indicate the reasons for immune escape and rapid transmission.

关 键 词：SARS-CoV-2 JN.1 lineage variation Ion Torrent sequencing Illumina sequencing Nanopore sequencing 

分 类 号：F42[经济管理—产业经济]