Investigating Transmission Patterns and Genome Sequencing of SARS-CoV-2 in University College Dublin

Abstract Background This study describes the investigation and management of multiple outbreaks of SARS-Cov2 during the second and third wave of the pandemic at University College Dublin, Ireland from September 2020 to September 2021. Methods Relevant data were gathered as part of the public health outbreak investigations led by the UCD Internal Covid Control Team (ICCT) in collaboration with the public health teams of the Health Service Executive (HSE). Results are presented for PCR (polymerase chain reaction) confirmed cases and their close contacts, reported to the UCD ICCT between September 2020 to September 2021. Results There were 214 cases notified to ICCT. Among these, 153 cases were in residence on-campus cases. 73 epidemiologically linked clusters identified, where the number of cases linked with each cluster varied between 1 to 27. Additional cases during this period had no obvious epidemiological link to the identified clusters. Of 902 close contacts with PCR test results, 31.5% (n = 284) tested positive. 77% (n = 219) self-reported with mild to moderately symptoms while 23% (n = 65) self-reported as asymptomatic. Retrospective Whole Genome Sequence (WGS) analysis was undertaken after the outbreaks had subsided. The test positive cases were grouped into 6 clusters, and it was shown that many of the apparent sporadic cases were included in these clusters. Conclusions The proportion of close contacts testing positive varied significantly throughout the pandemic, with testing policy and type of exposure having the greatest impact. Whole genome sequencing can give a better understanding of webs of transmission to complement epidemiological investigations. It is now possible to undertake sequencing in real time where it can make a contribution to outbreak control and resolution. Public Health professionals should become familiar with WGS and bioinformatics as useful tools in their armory for the control of all communicable diseases not only SARS-CoV-2. Key messages • Combined epidemiological investigations and Whole Genome Sequencing (WGS) provide crucial insights into campus COVID-19 outbreaks, guiding effective control measures. • WGS integration enhances understanding of transmission patterns, identifies clusters, and equips public health professionals with data-driven approaches for outbreak management beyond SARS-CoV-2.