Study uses whole genome sequencing to trace SARS-CoV-2 transmission within Welsh hospital

By Dr. Chinta SidharthanReviewed by Aimee MolineuxOct 17 2022

In a recent study published in the Journal of Hospital Infection, researchers used whole genome sequencing to examine the patients-to-staff, staff-to-patients, and staff-to-staff transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in hospitals in Wales.

Background

Since the detection of the first case of coronavirus disease 2019 (COVID-19) in Wales in February 2020, the country experienced two waves of SARS-CoV-2 outbreaks over the spring and fall-winter months that year. While national lockdowns were enforced to disrupt the community transmission of the virus, healthcare-associated infections within hospitals proved to be harder to control.

Understanding the efficacy of the infection control measures used to detect and contain the spread of SARS-CoV-2 within hospitals is essential to prevent the overall transmission of COVID-19.

About the study

The present study focused on a regional healthcare unit in Wales that received emergency admissions of suspected COVID-19 cases from rural and urban areas of the country. Real-time polymerase chain reaction (PCR) testing was carried out on oral and nasopharyngeal swabs. All samples with a cycle threshold below 30 were used for whole genome sequencing.

An automated phylogenetics pipeline was used to analyze the sequences and assign them to one of the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages or putatively assign them to one of the United Kingdom (U.K.) transmission groups based on ancestral state reconstruction.  The lineage and transmission group data were correlated to epidemiological information for further analysis.

A team of hospital staff, an epidemiologist, infection prevention and control (IP&C) authorities, and public health doctors investigated the outbreak according to the Health Board’s outbreak management guidelines. Hospital staff and patients were screened. The information from the COVID-19 test results was combined with real-time epidemiology and whole genome sequence data and information on staff shifts, patient movement, and staff sickness to determine the outbreak.

Confirmed cases were defined based on positive PCR test results, epidemiological link to another confirmed case, and sample assignment to a U.K transmission group within the B.1.1.311 PANGO lineage. Samples without the whole genome sequence information were considered probable cases if the patient or staff was residing or working, respectively, during the outbreak in any of the affected wards.

Community-acquired cases and samples associated with lineages other than B.1.1.311 were excluded from the analysis.

Results

The results demonstrated the rapid transmission of SARS-CoV-2 among patients and staff within a ward despite infection control measures such as personal protective equipment (PPE). The outbreak, which comprised 85 cases within the hospital and at least 10 cases in another hospital, spanned three secondary clusters and began with one primary case (P0), despite P0’s PCR test showing a high cycle threshold value.

The authors believe this outbreak was a typical super-spreader event, characterized by an explosive increase in the initial stages, followed by sustained transmission. Given the largely isolated cubicle that P0 was admitted in, as well as the lack of contact or shared areas with other patients or staff infected during the same period, the study stated that the spread of SARS-CoV-2 through droplets or fomites was highly unlikely, and the transmission could have potentially occurred in the corridor and desk area.

The findings indicate that person-to-person spread was the more likely mode of the sequential spread of SARS-CoV-2, rather than the entire ward being infected through one airborne event. Pre- or minimally symptomatic hospital intermediaries may have carried the infection to other wards.

Although SARS-CoV-2 transmission occurred despite adherence to PPE use, there were no documented transmission cases after P0 was transferred to an intensive therapy unit where staff used PPEs and filtering facepiece 3 (FFP3) masks suitable for aerosol-generating procedures.

According to the authors, the factors that contributed to the outbreak include sharing of staff between multiple wards, patient movement, improper ventilation, shared facilities, and incomplete adherence to control measures such as using PPE.

Conclusions

To summarize, the study explored the single-patient origin widespread transmission of SARS-CoV-2 in two hospitals in Wales and investigated the factors that contributed to the outbreak.

The results suggested that early identification and isolation of patients would help limit the spread of the virus. Furthermore, other measures such as additional staffing to avoid sharing of staff between wards, improved PPE design for better fit and comfort, the use of specific masks such as FFP3 to cut down on aerosol spread, and improved hospital design to increase ventilation and reduce shared spaces could significantly decrease the transmission of SARS-CoV-2 in hospitals.