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.