ABSTRACT
Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the current coronavirus disease 2019 (COVID-19) pandemic extends into its third year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in a higher education setting that will inform pubic health policy during pandemics. In this study, we performed whole-genome sequencing of 537 of 1,717 SARS-CoV-2 positive nasopharyngeal/nasal swab samples collected for nearly 20 months from the two university populations in Wisconsin, United States. We observed that the viral sequences were distributed into 57 lineages/sub-lineages belonging to 15 clades of which the majority were from 21K (Omicron, 36.13%) and 21J (Delta, 30.91%). Nearly 40% (213) of the sequences were Omicron of which BA.1 and its eight descendent lineages account for 91%, while the remaining belong to BA.2 and its six descendent lineages. The independent analysis of these two universities sequences revealed significant differences in circulating the SARS-CoV-2 variants. The genome-based analysis of closely-related strains along with phylogenetic clusters had identified that potential virus transmission occurred within as well as between universities, and between the university and local community. Although this study improves our understanding of distinct transmission patterns of circulating variants in local universities, expanding the genomic surveillance capacity will aid local jurisdictions in identifying emerging SARS-CoV-2 variants like BA.4 and BA.5, and improve data-driven public health mitigation and policy efforts.
ABSTRACT
Two years after the emergence of SARS-CoV-2, there is still a need for better ways to assess the risk of transmission in congregate spaces. We deployed active air samplers to monitor the presence of SARS-CoV-2 in real-world settings across communities in the Upper Midwestern states of Wisconsin and Minnesota. Over 29 weeks, we collected 527 air samples from 15 congregate settings and detected 106 SARS-CoV-2 positive samples, demonstrating SARS-CoV-2 can be detected in air collected from daily and weekly sampling intervals. We expanded the utility of air surveillance to test for 40 other respiratory pathogens. Surveillance data revealed differences in timing and location of SARS-CoV-2 and influenza A virus detection in the community. In addition, we obtained SARS-CoV-2 genome sequences from air samples to identify variant lineages. Collectively, this shows air surveillance is a scalable, cost-effective, and high throughput alternative to individual testing for detecting respiratory pathogens in congregate settings.
ABSTRACT
Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties, and limited viral transmission between counties, following the statewide "Safer at Home" public health order, which went into effect 25 March 2020. Our results suggest that early containment efforts suppressed the spread of SARS-CoV-2 within Wisconsin.
