New severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases in the UK reached a peak during the first wave of the COVID-19 pandemic. Aggressive non-pharmaceutical interventions such as social distancing and lockdowns were implemented in the UK to slow down the virus's spread by late March. Since SARS-CoV-2 is a novel virus and people did not have prior immunity to the virus, healthcare organizations tried to adapt to the pandemic with new infection control policies and non-pharmaceutical measures during the first few weeks of the pandemic.
The major preventative interventions introduced included community social distancing policies that led to mandatory nation-wide lockdown, restriction of hospital visitors, and universal surgical mask use by healthcare workers. With respect to the incidence of SARS-CoV-2, nosocomial cases, community cases, and infection in a healthcare cohort all followed the same course and decreased shortly after the introduction of community social distancing measures. The high prevalence of infection complicates transmission analysis and hence the contribution of various vectors to nosocomial infection or the effectiveness of these non-pharmaceutical interventions are not clear.
Currently, the second wave of the pandemic is ongoing in many countries, including the UK and health care systems are overwhelmed with hospitals preparing for a further influx of COVID-19 patients. Therefore, it is essential to gather the data from the first few weeks of the pandemic to help healthcare organizations plan for future increases in cases.
Epidemiological description of cases diagnosed during the first wave. On the left hand y-axis , the grey bar chart displays new cases over time between March 10th and April 31st. Over the same period the right hand y axis shows incidence of nosocomial cases (orange line) and, the proportion (%) of screened HCW with confirmed infection reporting symptom onset (black line) with peak period of infectivity ± 2 days (dashed black line), with IgG seroprevalence of HCW (green). Overlaid is 5 key dates in public policy and infection control (A) March 13th; testing recommended for all inpatients with cough and fever. (B) March 16th; strong government advice for social distancing; (C) March 23rd; implementation of national lockdown (D) March 25th; exclusion of hospital visitors (E) March 28th; mandatory use of surgical masks for all patient interactions under 2 metres.
Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 cases
Recently, a team of researchers from the King's College London, Guy's and St Thomas' NHS Foundation Trust, and St Thomas' Hospital, London analyzed comprehensive epidemiological and viral nanopore sequence data from 574 patients with SARS-CoV-2 infection confirmed by a PCR test in March 2020. This combined genomic and epidemiological analysis spans 19 days of massive community transmission in London during the first few months of the pandemic, which was the main duration of nosocomial transmission, with 90 definite or probable nosocomial cases across the healthcare institution.
This study is published on the preprint server medRxiv*.
The team analyzed clusters of nosocomial cases based on overlapping ward-stays during the 14-day incubation period and the similarity in the SARS-CoV-2 genome sequence. This method grouped 63 (79%) out of 80 sequenced probable and confirmed nosocomial cases into 14 clusters with a median of 4 patients.
They could not find any genetic support for most of the epidemiological clusters and genomics revealed the presence of several contemporaneous outbreaks in single epidemiological clusters. The researchers measured and compared hospital enrichment to community cases in order to increase confidence in the clusters, which were 1-14 fold enriched.
Infected health care workers were the major contributors to nosocomial transmission during the first wave
By applying genomics, they were able to estimate the incubation period for nosocomial transmission, with a lower bound median of 6 days and an upper bound of 9 days. Six (43%) clusters spanned multiple wards, and there was evidence of cryptic transmission. Community-onset cases were not found in over half of the clusters, especially on the elective hospital site, which shows that health care workers are the transmission vectors. Based on these findings, the authors concluded that community social distancing had a dominant impact on bringing down nosocomial transmission by reducing infection in health care workers.
In summary, this study endorses routine use of genome sequencing for investigating SARS-CoV-2 outbreaks and offers a framework for the interpretation of data that questions over-reliance on using epidemiology alone in these investigations. The data gathered from this study shows that infected health care workers in the community were the major contributors to nosocomial transmission during the first wave of the COVID-19 pandemic, and this transmission was interrupted by the implementation of community social distancing measures.
During the second wave, the return of community transmission offers an opportunity to examine if nosocomial transmission returns with the same intensity while universal mask use and social distancing policies are in place. This will help decide if additional interventions such as regular testing or rapid genome sequencing are required to stop nosocomial transmission. Currently, a multi-site clinical trial is investigating if real-time sequencing for analyzing outbreaks can aid infection control teams in interrupting viral transmission.
"In summary, this study supports the routine use of genome sequencing for SARS-CoV-2 outbreak investigation and provides a framework for data interpretation that calls into question continued reliance on using epidemiology alone."
medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.
- Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 transmission identifies community social distancing as the dominant intervention reducing outbreaks Luke B Snell, Chloe L Fisher, Usman Taj, Blair Merrick, Adela Alcolea-Medina, Themoula Charalampous, Adrian W Signell, Harry D Wilson, Gilberto Betancor, Mark Tan Kia Ik, Emma Cunningham, Penelope R Cliff, Suzanne Pickering, Rui Pedro Galao, Rahul Batra, Stuart J D Neil, Michael H Malim, Katie J Doores, Sam T Douthwaite, Gaia Nebbia, Jonathan D Edgeworth, Ali R Awan, The COVID-19 Genomics UK (COG-UK) consortium medRxiv 2020.11.17.20232827; doi: https://doi.org/10.1101/2020.11.17.20232827, https://www.medrxiv.org/content/10.1101/2020.11.17.20232827v1