Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

Use of integrated genomic surveillance by local public health authorities: Recommendations based on a mixed-methods study of current adoption, applications and success factors, Germany, 2023

BackgroundIntegrated genomic surveillance (IGS), i.e. the integrated analysis of pathogen whole genome sequencing and classical epidemiological data, can contribute substantially to the disease surveillance and infection prevention activities of local public health authorities (LPHAs).AimOur aim was to characterise how LPHAs use IGS, and factors required or important for their implementation, in the context of the German public health system.MethodsWe employed a mixed-methods design combining a quantitative survey of 60 LPHAs in three German states with five qualitative case studies based on LPHAs in four German localities and one state-level public health authority.ResultsApproximately half of LPHAs reported adoption of IGS; applications included outbreak analysis (n = 25), targeting and evaluation of infection control measures (n = 25 and n = 18, respectively) and characterisation of pathogen transmission chains (n = 25). Factors identified as required or important for the implementation of IGS in LPHAs included fast sample-to-result turnaround times, organisational data interpretation capabilities and clearly defined surveillance sampling strategies. Based on the case studies in which the adoption of IGS was successful, we formulate recommendations for implementing IGS at the level of LPHAs, including establishment of dedicated IGS analysis teams within LPHAs, use of user-friendly digital solutions (e.g. browser-based dashboards) for data exchange and analysis, and implementation of IGS in collaboration with local academic institutions.ConclusionOur analysis paves the way for increasing the implementation of IGS by LPHAs in Germany and other countries with similarly structured public health systems.

SARS-CoV-2 Diversity and Transmission on a University Campus across Two Academic Years during the Pandemic

BACKGROUND

Institutions of higher education (IHE) have been a focus of SARS-CoV-2 transmission studies but there is limited information on how viral diversity and transmission at IHE changed as the pandemic progressed.

METHODS

Here we analyze 3606 viral genomes from unique COVID-19 episodes collected at a public university in Seattle, Washington from September 2020 to September 2022.

RESULTS

Across the study period, we found evidence of frequent viral transmission among university affiliates with 60% (n = 2153) of viral genomes from campus specimens genetically identical to at least one other campus specimen. Moreover, viruses from students were observed in transmission clusters at a higher frequency than in the overall dataset while viruses from symptomatic infections were observed in transmission clusters at a lower frequency. Although only a small percentage of community viruses were identified as possible descendants of viruses isolated in university study specimens, phylodynamic modeling suggested a high rate of transmission events from campus into the local community, particularly during the 2021-2022 academic year.

CONCLUSIONS

We conclude that viral transmission was common within the university population throughout the study period but that not all university affiliates were equally likely to be involved. In addition, the transmission rate from campus into the surrounding community may have increased during the second year of the study, possibly due to return to in-person instruction.

Navigating Novel Viral Challenges: Understanding, Tracking, and Mitigating Emerging Threats

The emergence of new viral threats continues to pose significant challenges to global health security [...].

Possibility of intrauterine transmission from mother to fetus/newborn: Systematic review and meta-analysis of diagnostic methods to detect SARS-CoV-2 infection

Several studies have reported vertical transmission of SARS-CoV-2; however, information regarding intrauterine transmission based on diagnostic methods to detect SARS-CoV-2 infection is scarce. A systematic review and meta-analysis was conducted to identify and explore the studies that attempt to ascertain the possibility of intrauterine transmission of SARS-CoV-2 infection according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA 2020) statement. The results demonstrate that SARS-CoV-2 can be transmitted intrauterine, as detected by clinical manifestations (1.00, 95 % CI: 1.00 - 1.00, 0.51, 95 % CI: 0.22 - 0.80), imaging (0.50, 95 % CI: 0.24 - 0.76, 0.03, 95 % CI: 0.00 - 0.17), molecular (1. 00, 95 % CI: 1.00 - 1.00, 0.92, 95 % CI: 0.77 - 1.00), immunological (0.32, 95 % CI: 0.10 - 0.57, 0.34, 95 % CI: 0.11 - 0.61), and histological approaches (0.79, 95 % CI: 0.52 - 0.98) in maternal and fetal/neonatal specimens, respectively. The possibility of intrauterine transmission of SARS-CoV-2 from mother to fetus/newborn was 41 % (95 % CI 0.37 - 0.45). We might confirm/verify the intrauterine transmission of SARS-CoCV-2 from mother to fetus/newborn.

Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population

Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the coronavirus disease 2019 (COVID-19) pandemic extends into its fourth year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in higher education settings and will inform public health policy during pandemics. In this study, we generated 793 whole-genome sequences collected over an entire academic year in a university population in Indiana, USA. We clearly captured the rapidity with which Delta variant was wholly replaced by Omicron variant across the West Lafayette campus over the length of two academic semesters in a community with high vaccination rates. This mirrored the emergence of Omicron throughout the state of Indiana and the USA. Further, phylogenetic analyses demonstrated that there was a more diverse set of potential geographic origins for Omicron viruses introduction into campus when compared to Delta. Lastly, statistics indicated that there was a more significant role for international and out-of-state migration in the establishment of Omicron variants at Purdue. This surveillance workflow, coupled with viral genomic sequencing and phylogeographic analyses, provided critical insights into SARS-CoV-2 transmission dynamics and variant arrival.

COVID-19 associated with universities in England, October 2020-February 2022

OBJECTIVES

The aim of this study was to describe the epidemiology of COVID-19 cases at universities in England (October 2020-February 2022) and investigate factors associated with rates of COVID-19 among students during autumn/winter of 2021/22.

STUDY DESIGN

The study was an observational retrospective study using routine contact tracing data.

METHODS

Estimates of COVID-19 cases among students and staff at universities were described. Student cases aged 18-24 years were calculated as a percentage of all cases within that age group. Count regression was used to explore university characteristics associated with case numbers.

RESULTS

We identified 102,382 cases among students and 28,639 among staff. Student cases reflected trends in the wider population of the same age group, but the observed fraction aged 18-24 years who were students was consistently below the expected level (32%). Phased reopening of universities in March-May 2021 was associated with small peaks but low absolute numbers. Russell group membership, campus universities, and higher student proportions in halls of residence were all associated with increased case numbers.

CONCLUSIONS

COVID-19 case numbers among students in England varied considerably. At no time were the observed case numbers as high as expected from community prevalence. Characteristics of universities associated with higher case rates can inform future guidance for higher education settings.