Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK

Abstract

IntroductionThroughout the global COVID-19 pandemic, nosocomial transmission has represented a major concern for healthcare settings and has accounted for many infections diagnosed within hospitals. As restrictions ease and novel variants continue to spread, it is important to uncover the specific pathways by which nosocomial outbreaks occur to understand the most suitable transmission control strategies for the future.MethodsIn this investigation, SARS-CoV-2 genome sequences obtained from 694 healthcare workers and 1,181 patients were analyzed at a large acute NHS hospital in the UK between September 2020 and May 2021. These viral genomic data were combined with epidemiological data to uncover transmission routes within the hospital. We also investigated the effects of the introduction of the highly transmissible variant of concern (VOC), Alpha, over this period, as well as the effects of the national vaccination program on SARS-CoV-2 infection in the hospital.ResultsOur results show that infections of all variants within the hospital increased as community prevalence of Alpha increased, resulting in several outbreaks and super-spreader events. Nosocomial infections were enriched amongst older and more vulnerable patients more likely to be in hospital for longer periods but had no impact on disease severity. Infections appeared to be transmitted most regularly from patient to patient and from patients to HCWs. In contrast, infections from HCWs to patients appeared rare, highlighting the benefits of PPE in infection control. The introduction of the vaccine at this time also reduced infections amongst HCWs by over four-times.DiscussionThese analyses have highlighted the importance of control measures such as regular testing, rapid lateral flow testing alongside polymerase chain reaction (PCR) testing, isolation of positive patients in the emergency department (where possible), and physical distancing of patient beds on hospital wards to minimize nosocomial transmission of infectious diseases such as COVID-19.

Combining viral genomics and clinical data to assess risk factors for severe COVID-19 (mortality, ICU admission, or intubation) amongst hospital patients in a large acute UK NHS hospital Trust

“…Indeed, nationally over 15% of all cases have been estimated as having been hospital acquired in the first wave in the UK [ 54 ], with up to 20% of infections in inpatients and 73% in HCW due to nosocomial transmission [ 55 ]. It has been suggested that up to 80% of nosocomial infections were caused by only 20% of patients due to “super-spreader” events [ 14 ], with such rapid outbreak dynamics having been previously characterised in at least one outbreak at PHU [ 56 ].…”

“…Whilst the data described here do not span the emergence of variants such as Delta and Omicron, they do represent the emergence and subsequent rapid expansion of the first VOC, Alpha (B.1.1.7). Increased prevalence of Alpha in the local region led to increased transmission of a range of currently circulating variants within the hospital [ 56 ]. Interestingly, Table 1 shows that the rate of severe cases amongst Alpha cases (36.9%) was actually slightly lower than amongst non-Alpha cases (40.2%), suggesting that Alpha cases may present a lower risk of severe outcomes in our dataset compared to other variants ( Table 1 ).…”

Evaluating pooled testing for asymptomatic screening of healthcare workers in hospitals

“…Nosocomial SARS-CoV-2 infections in both patients and healthcare workers (HCWs) have been documented throughout the SARS-CoV-2 pandemic [1][2][3][4]. Several interventions have been put in place to prevent the spread of SARS-CoV-2 in hospitals in England including the use of enhanced personal-protective equipment (PPE), cohorting of suspected patients and symptomatic and regular asymptomatic testing of HCWs [5].…”