Dynamics of SARS-CoV-2 transmission at Purdue University

By Tarun Sai LomteMar 4 2022Reviewed by Benedette Cuffari, M.Sc.

In a recent study published on the medRxiv* preprint server, researchers performed genomic surveillance of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its variants in a university setting.

Study: Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant. Image Credit: PLo777 / Shutterstock.com

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

Background

As of March 3, 2022, SARS-CoV-2 has infected over 441 million and caused the deaths of over 5.9 million worldwide. In the United States alone, there have been over 80 million confirmed coronavirus disease 2019 (COVID-19), with over 980,000 reported deaths.

Genomic sequencing is an efficient tool that has helped study SARS-CoV-2 and identify its genomic variants with altered or enhanced transmissibility. The U.S. Centers for Disease Control and Prevention (CDC) and SARS-CoV-2 Interagency Group (SIG) have designated SARS-CoV-2 variants as a variant of interest (VOI), variant of concern (VOC), and high consequence (VOHC). Additionally, a new class termed variants being monitored (VBM) has been included to surveil variants previously classified as VOCs or VOIs that are now less prevalent in circulation in the U.S.

Early into the pandemic, epidemiological studies demonstrated the increased vulnerability of individuals over the age of 65 years and those with comorbidities to COVID-19. However, in the summer of 2020, COVID-19 incidence was highest in the 20-29 age group and coincided with the resumption of physical attendance in universities and colleges. Thus, it was speculated that on-campus academic sessions could lead to community transmission and super-spreading events.

About the study

In the present study, researchers conducted surveillance of SARS-CoV-2 variants in the Purdue University community that included its students, faculty, and other staff personnel from the first week of January 2021 to the first week of May 2021.

The university had initiated a ‘Protect Purdue Plan’ to curb the spread of SARS-CoV-2 and monitor the health of its community. Symptomatic individuals were tested as part of the program, followed by contact tracing.

Moreover, around 10% of students and employees were randomly tested every week by reverse transcription-polymerase chain reaction (RT-PCR) tests. A subset of PCR-positive samples underwent SARS-CoV-2 whole-genome sequencing (WGS).

Sampling for WGS was based on weekly specimens showing PCR results with S-gene target failure (SGTF) and random RT-PCR-positive samples with a cycle threshold (Ct) value less than or equal to 30, as well as a retrospective sampling of positive specimens without SGTF.

Study findings

During the study period, RT-PCR tests were performed on 96,819 students and employees, of which 2,436 (2.5%) were positive. A total of 735 specimens were subject to WGS, which generated 677 high-quality sequences.

Among these 677 samples, WGS was performed in weekly for 431 samples and retrospectively for the remaining samples. WGS data were submitted to Global Initiative on Sharing Avian Influenza Data (GISAID). In the 18 weeks of the study, the team accounted for sequencing around 32% SARS-CoV-2-positive samples weekly in Tippecanoe County, where the university is located.

Symptomatic and asymptomatic cases were 41% and 57% among the sequenced specimens, respectively. WGS identified 36 Pangolin lineages, with the B.1.2 lineage being the most prevalent, accounting for 35.4% of the sequenced samples, followed by the B.1.1.7 lineage (16.1%).

Until week eight into the study, the prevalence of the B.1.2 lineage was above 50%, with a significant reduction in the following weeks. VOC and VBM sequences were prominent from the 12th week of the study, most of which were the Alpha and Iota variants, and the Gamma variant (P.1) sequences emerged in the last weeks.

Phylogenetic analyses of P.1 genomes of the Purdue community were performed in the context of P.1 genomes from a more extensive community throughout the United States and South America. Parsimony score (PS), which helps to identify the number of transitions between geographical regions, was 10.0, thereby implying 10 independent introductions of the Gamma variant to the Purdue community.

Purdue sequences’ PS scores were estimated pairwise with sequences from other states of the U.S. The difference in the PS scores could provide evidence of a particular state contributing to the P.1 sequences in the Purdue community. To this end, Illinois and Indiana states showed a deviation of 4.48 and 2.78 relative to Purdue PS scores, respectively.

Conclusions

Throughout the 18 weeks of the study, the authors generated 677 high-quality SARS-CoV-2 sequences from the samples collected from the Purdue community. PS-based analysis indicated that potential sources for introducing the Gamma variant into the Purdue campus were the states of Indiana, Illinois, New York, and Washington, with the highest migration rates from Indiana and Illinois.

The current research explored the dynamics of SARS-CoV-2 transmission in an academic setting with a vast community. The researchers were able to identify 36 different lineages of SARS-CoV-2 with lineages B.1.2, B.1.1.7, B.1.526, B.1.623, B.1.429, B.1.1.519, P.1, and B.1.234 accounting for about 90% of the entire Purdue sequences.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources