Main menu

Investigation of intra-hospital SARS-CoV-2 transmission using nanopore whole genome sequencing


Background

During the SARS-CoV-2 pandemic, healthcare workers (HCWs) are exposed to infection both at work and in their communities. Determining where HCWs might have been infected is challenging based on epidemiological data alone. At Akershus University Hospital, Norway, several clusters of possible intra-hospital SARS-CoV-2 transmission were identified based on routine contact tracing. To investigate these clusters further, we added whole genome sequencing (WGS) of SARS-CoV-2 virus to routine contact tracing among HCWs and between HCWs and patients. This study illustrates both the potential power and challenges with high-resolution genotyping in outbreak settings.

Aim

The aim was to determine whether clusters of suspected intra-hospital SARS-CoV-2 transmission could be resolved by combining WGS of SARS-CoV-2 with contact tracing data.

Methods

Epidemiological data were collected during routine contact tracing of PCR-confirmed SARS-CoV-2 positive HCWs. Possible outbreaks were identified as wards with two or more infected HCWs defined as close contacts who tested positive for SARS-CoV-2 less than three weeks apart. Viral RNA from naso-/oropharyngeal samples underwent nanopore sequencing according to the manufacturer’s instructions (Oxford Nanopore Technologies) in direct compliance to the Artic Network protocol (https://artic.network/ncov-2019).

Results

Five outbreaks were suspected from contact tracing. Viral consensus sequences from 24 HCWs, two patients and seven anonymous samples were analysed. Two outbreaks were confirmed, one refuted, two remained undetermined. One new potential outbreak was discovered.

Conclusion

Combined with epidemiological data, nanopore WGS was a useful tool for investigating intra-hospital SARS-CoV-2 transmission. WGS helped resolve questions about possible outbreaks and guide local infection prevention and control measures.

Authors: Alexander Hesselberg Løvestad, Silje Bakken Jørgensen, Nina Handal, Ole Herman Ambur, Hege Vangstein Aamot

入門

MinION Starter Packを購入 ナノポア製品の販売 シークエンスサービスプロバイダー グローバルディストリビューター

ナノポア技術

ナノポアの最新ニュースを購読 リソースと発表文献 Nanopore Communityとは

Oxford Nanoporeについて

ニュース 会社沿革 持続可能性 経営陣 メディアリソース & お問い合わせ先 投資家向け パートナー向け Oxford Nanopore社で働く 現在の募集状況 営業上の情報 BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
Japanese flag