Analysis of SARS-CoV-2 infection transmission routes by whole-genome analysis using next-generation sequencing and haplotype network

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  • KAJIWARA Ryosuke
    Department of Clinical Laboratory Medicine, Kurume University Hospital
  • MIYAMOTO Naoki
    Department of Clinical Laboratory Medicine, Kurume University Hospital
  • TASHIRO Naotaka
    Department of Clinical Laboratory Medicine, Kurume University Hospital
  • OTSUBO Naohiro
    Department of Clinical Laboratory Medicine, Kurume University Hospital
  • ICHINOSE Yuka
    Department of Clinical Laboratory Medicine, Kurume University Hospital
  • HORITA Rie
    Department of Clinical Laboratory Medicine, Kurume University Hospital
  • KAWANO Hiroyuki
    Department of Clinical Laboratory Medicine, Kurume University Hospital
  • NAITO Yoshiki
    Department of Clinical Laboratory Medicine, Kurume University Hospital

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Other Title
  • 次世代シーケンサを用いた全ゲノム解析とハプロタイプネットワーク解析からみるSARS-CoV-2感染伝播経路の解析
  • ジセダイ シーケンサ オ モチイタ ゼン ゲノム カイセキ ト ハプロタイプネットワーク カイセキ カラ ミル SARS-CoV-2 カンセン デンパ ケイロ ノ カイセキ

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Abstract

<p>Purpose: Nosocomial clusters (NCs) of SARS-CoV-2 transmission are problematic because of the high infectivity of SARS-CoV-2. However, there have been few studies on the routes of infection transmission into hospitals using next-generation sequencing (NGS). In this study, whole-genome analysis using NGS, Pango lineage classification, and haplotype network analysis were conducted to analyze the transmission routes of the virus that caused NC infections. Methods: Whole-genome analysis using NGS was performed on 12 specimens from patients infected in an NC and 37 other specimens from those infected in the community (CM), which were selected from specimens that tested positive for SARS-CoV-2 by PCR analysis at Kurume University Hospital. Pango lineage classification and haplotype network analysis were performed on the obtained genome sequences to analyze the transmission routes in NC and CM. The data for Tokyo and Osaka were also obtained from GISAID to analyze the routes of infection in the cities. Results: In the Pango lineage classification, BA.2.24 was detected in all 12 NC specimens, but the CM specimens included a mixture of multiple strains of the Omicron variant. The haplotype network analysis suggested that the NC infection spread from a single route of entry from the community. NC and CM tended to be more strongly associated with Tokyo than with Osaka. It was also suggested that the disease spread from Tokyo in approximately 2 to 3 weeks. Conclusion: Whole-genome analysis and haplotype network analysis can be used to analyze the transmission routes of viral infections and provide useful information for future infection control.</p>

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