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SARS-CoV-2 sequencing reveals rapid transmission from college student clusters resulting in morbidity and deaths in vulnerable populations

Our take —

Using genomic sequencing of SARS-CoV-2 positive individuals from communities surrounding three academic institutions in La Cross County, Wisconsin, preceding and during college re-opening, this study, available as a preprint and thus not yet peer reviewed, demonstrated how endemic SARS-CoV-2 strains can rapidly spread within a large intermixing susceptible group of newly introduced individuals and spill-over into neighboring vulnerable populations. Supporting previous findings that outbreaks among younger individuals precede outbreaks among older populations, these data suggest that alternate strategies such as frequent and widespread testing of all university students regardless of on-campus housing status, rather than pre-/re-entry screening alone, may be important for outbreak prevention.

Study design

Retrospective Cohort

Study population and setting

Using surveillance and sequencing data from Gundersen Healthcare System’s diagnostic laboratories serving Wisconsin, Iowa and Minnesota, this study assessed the role of college reopening on community transmission in La Cross County, Wisconsin. The database included sequencing of all SARS-CoV-2 positive cases diagnosed between March 18 and September 9, 2020, noting a rapid rise in September 2020 in La Cross County coinciding with three local college campus re-openings. A total of 514 genome-length sequences of the SARS-CoV-2 virus were obtained from the March to September period via next generation sequencing. Through phylogenetic analyses and the use of college/university curated online “COVID19 Dashboards”, the genetic similarities between each viral sequence were used to infer college-associated viral clusters and identify likely transmission events within La Crosse County, Wisconsin.

Summary of Main Findings

Rapid increase in cases among younger people occurred in early September, which largely concentrated around two viral clusters circulating at that time, designated College A and College B, and occurring around increases in cases as ascertained through local college Dashboards. Through the genomic sequencing and assessments of time lags, college-associated viral clusters of endemic SARS-CoV-2 strains within younger individuals were identified to be the source of multiple transmission events into the broader community, including skilled nursing facilities (resulting in two fatalities).

Study Strengths

This study utilized a well described viral whole-genome isolation, amplification, sequencing, and analysis workflow and made effective use of varying data types from multiple sources to support their conclusions.


Only those samples processed by Gundersen Healthcare System’s diagnostic labs were available for sequencing. As such, students in dormitories who were tested by university labs were not represented though it is expected their viral genomes would be similar. The community experienced an increased prevalence of the college-associated viral clusters around the time of college re-openings, which cannot be ruled out as responsible for the observed outbreak in the skilled nursing facility. It is also unclear what quality control steps were conducted for each sample prior to the generation of a sample-specific consensus sequence, as no details are provided.

Value added

Through genomic sequencing, this study linked an outbreak among college-aged individuals to transmission events within vulnerable/older individuals living in the surrounding community, supporting previous research noting increased SARS-CoV-2 infections among younger individuals often precedes an increase of cases among older individuals. Based on their observations, the authors suggest pre-/re-entry testing of students would fail to prevent such outbreaks within areas of active community transmission and instead recommend the use of frequent widespread testing of the entire student population, regardless of housing status, to prevent such outbreaks.

This review was posted on: 19 December 2020