Linking sporadic hospital clusters during a community surge of the severe acute respiratory coronavirus virus 2 (SARS-CoV-2) B.1.617.2 delta variant: The utility of whole-genome sequencing

Abstract

Sporadic clusters of healthcare-associated coronavirus disease 2019 (COVID-19) occurred despite intense rostered routine surveillance and a highly vaccinated healthcare worker (HCW) population, during a community surge of the severe acute respiratory coronavirus virus 2 (SARS-CoV-2) B.1.617.2 δ (delta) variant. Genomic analysis facilitated timely cluster detection and uncovered additional linkages via HCWs moving between clinical areas and among HCWs sharing a common lunch area, enabling early intervention.

Nosocomial SARS-CoV-2 transmission in multi-bedded hospital cubicles over successive pandemic waves: Lower mortality but wider spread with Omicron despite enhanced infection-prevention measures

“…Up to December 2021, whole-genome-sequencing (WGS) revealed that all hospital-onset-cases were attributable to the Delta-variant (N=47). 9 The first Omicron case was identified in a returned traveler on 24 th December 2021. By January 2022, all hospital-onset cases demonstrated S-gene dropout on PCR-testing, indicative of the Omicron-variant.…”

Genomic Investigation to Identify Sources of Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Healthcare Personnel in an Acute Care Hospital

“…Notably, our study included periods of time with varying institutional respiratory PPE recommendations (including half of the study period when medical facemasks rather than N95 respirators were required for routine COVID-19 patient care, in part to ensure adequate N95 respiratory supply). Our study suggests that community exposures are the most common source of COVID-19 among HCP [ 21 , 22 ]. SARS-CoV-2 seropositivity has been associated with community exposures, but not with healthcare occupational exposures (ie, caring for patients with COVID-19, exposure to aerosol-generating procedures) [ 18 , 23–25 ].…”

The limits of genomic sequencing for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) exposure investigations: For nosocomial outbreak reconstruction, community exposures matter, too

“…Genomic clusters were detected based on wholegenome similarity analysis (ie, when sequences are ≤3 singlenucleotide polymorphisms different and fall in the same branch of the genome similarity tree). 10 As revealed by genomic sequencing, most nosocomial-onset and HCW cases clustered on a separate phylogenetic branch from community-onset COVID-19 cases managed in isolation from the onset (Fig. 1a), suggesting disparate introductions.…”

“…9 We utilized contact tracing and genomic sequencing to investigate nosocomial-onset COVID-19 cases. 10 All inpatient COVID-19 cases and HCW cases over 1 month (August 20-September 17, 2021) with a cycle threshold value (Ct) <31 were sent for sequencing using the ARTIC protocol on Oxford Nanopore minION sequencers (Oxford Nanopore Technologies, Oxford, UK). Contact tracing was performed for all nosocomial-onset COVID-19 cases, all community-onset COVID-19 cases initially managed outside isolation areas, as well as all HCWs at work during their infective periods.…”