Comparison of Ion Torrent,Illumina,and Nanopore platforms for sequencing SARS-CoV-2 JN.1 lineage variants from Dalian,China
Xingying Lang1
Yue Wang1
Mingchun Luan1
Zhijian Bo1
Huan Wang1
Xue Teng1
Xuehong Meng2
Shumin Niu3
Xiaoman Cui1
Nan Xia3
1.Dalian Center for Disease Control and Prevention,Dalian,China2.Thermo Fisher Scientific,Beijing,China3.National Clinical Research Center for Laboratory Medicine,Department of Laboratory Medicine,The First Hospital of China Medical University,Shenyang,China
摘要：Objectives Dominant strains of SARS-CoV-2 have been replaced by SARS-CoV-2 JN.1 lineage variants,which have spread widely in a short period of time.However,an accurate detection method and the reason for rapid spread have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 SARS-CoV-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 moni-toring 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.
机标关键词：sars-cov-2illuminachinafromcomparisondalianlineagenanopore
论文发表日期：2024-12-30
在线出版日期：2025-08-15（本平台首次上网日期，不代表文献的发表时间）
页数：14( 63-76 )
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