key: cord-0819541-yq469tka
authors: Currie, D. W.; Moreno, G. K.; Delahoy, M. J.; Pray, I. W.; Jovaag, A.; Braun, K. M.; Cole, D.; Shechter, T.; Fajardo, G. C.; Griggs, C. A.; Yandell, B. S.; Goldstein, S.; Bushman, D.; Segaloff, H. E.; Kelly, G. P.; Pitts, C. J.; Lee, C.; Grande, K. M.; Kita-Yarbro, A.; Grogran, B.; Mader, S.; Baggott, J.; Bateman, A. C.; Westergaard, R. P.; Tate, J. E.; Friedrich, T.; Kirking, H. L.; O'Connor, D.; Killerby, M. E.
title: Description of a University COVID-19 Outbreak and Interventions to Disrupt Transmission, Wisconsin, August - October 2020.
date: 2021-05-10
journal: nan
DOI: 10.1101/2021.05.07.21256834
sha: 1d6b1e17fc75c5eacfc8b2ce3f941d0f5c115efb
doc_id: 819541
cord_uid: yq469tka

University settings have demonstrated potential for COVID-19 outbreaks, as they can combine congregate living, substantial social activity, and a young population predisposed to mild illness. Using genomic and epidemiologic data, we describe a COVID-19 outbreak at the University of Wisconsin (UW)-Madison. During August - October 2020, 3,485 students tested positive, including 856/6,162 students living in residence halls. Case counts began rising during move-in week for on-campus students (August 25-31, 2020), then rose rapidly during September 1-11, 2020. UW-Madison initiated multiple prevention efforts, including quarantining two residence halls; a subsequent decline in cases was observed. Genomic surveillance of cases from Dane County, where UW-Madison is located, did not find evidence of transmission from a large cluster of cases in the two residence halls quarantined during the outbreak. Coordinated implementation of prevention measures can effectively reduce SARS-CoV-2 spread in university settings and may limit spillover to the community surrounding the university.

contacts (defined as being within 6 feet of an in infected person for at least 15 minutes within a 24-hour after the full-hall quarantine. Students could quarantine at their (permanent) home rather than in the analysis. To calculate attack rates among roommates of positive cases, index cases were defined as the 1 6 1 resident with the first positive SARS-CoV-2 test result within a room in a residence hall. Susceptible 1 6 2 students were defined as residents sharing a room with an index case that had not previously tested 1 6 3 positive for SARS-CoV-2. Roommate attack rates were defined as the proportion of susceptible students 1 6 4 who had a positive SARS-CoV-2 specimen collected within 2-14 days after the index case specimen 1 6 5 collection, consistent with the virus incubation period. 24 1 6 6 Epidemiologic data analyses were performed using SAS software, version 9.4 (SAS Institute, 1 6 7 Cary, NC), and RStudio, version 1.2.1335 (RStudio Team, Boston, MA). 1 6 8 Whole Genome Sequencing 1 6 9 Sample selection criteria 1 7 0 Sequences for this study were derived from 262 anterior nasal swab samples from UW-Madison 1 7 1 students living in the two residence halls experiencing the largest outbreaks, Residence Halls A and B, 1 7 2 with collection dates between September 8-22, 2020. Viral RNA (vRNA) isolation 1 7 4 Anterior nasal swabs received in viral transport medium (VTM) were centrifuged at 21,130 x g 1 7 5 for 30 seconds at room temperature. Viral RNA (vRNA) was extracted from 100 μ l of VTM using the 1 7 6 Viral Total Nucleic Acid Purification kit (Promega, Madison, WI, USA) on a Maxwell RSC 48 1 7 7 (Promega, Madison, WI, USA) instrument and was eluted in 50 μ L of nuclease free H 2 O. All genomic 1 7 8 samples were processed using a modified ARTIC tiled amplicon approach. 25 ,26 1 7 9 Complementary DNA (cDNA) generation 1 8 0 cDNA was synthesized using a modified ARTIC Network approach. 25, 27 Briefly, vRNA was USA) using random hexamers and deoxynucleotide triphosphates (dNTPs). Reaction conditions were as 1 8 3 follows: 1 μ L of random hexamers and 1 µL of dNTPs were added to 11 μ L of sample RNA, heated to 1 8 4 . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted May 10, 2021. ; 65˚C for 5 minutes, then cooled to 4˚C for 1 minute. Final concentrations were 2.5µM for random 1 8 5 hexamers and 0.5µM for dNTPs. Then 7 μ L of a master mix (4 μ L 5x RT buffer, 1 μ L 0.1M 1 8 6 dithiothreitol (DTT), 1 µL RNaseOUT RNase Inhibitor, and 1 μ L SSIV RT) were added and incubated 1 8 7 at 42˚C for 10 minutes, 70˚C for 10 minutes, and then 4˚C for 1 minute. 1 8 8 Multiplex PCR to generate SARS-CoV-2 genomes 1 8 9 A SARS-CoV-2-specific multiplex PCR for Nanopore sequencing was performed, similar to 1 9 0 amplicon-based approaches as previously described. 25, 27 In short, primers for 96 overlapping amplicons spanning the entire genome with amplicon lengths of 500 bp and overlapping by 75 to 100 bp between 1 9 2 the different amplicons were used to generate cDNA. Primers used in this manuscript were designed by Ipswich, MA, USA) using the following cycling conditions: 98ºC for 30 seconds, followed by 25 cycles of 98ºC for 15 seconds and 65ºC for 5 minutes, followed by an indefinite hold at 4ºC. Following amplification, samples were pooled before Oxford Nanopore Technologies (ONT) library prep. Amplified PCR product was purified using a 1:1 ratio of AMPure XP beads (Beckman Coulter, with Oxford Nanopore kit SQK-LSK109 and its Native Barcodes (EXP-NBD104 and EXP-NBD114). Specifically, samples were end-repaired using the NEBNext Ultra II End Repair/dA-Tailing Module . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted May 10, 2021. ;

Samples were then tagged with ONT sequencing adaptors according to the modified one-pot ligation 1 1 (SNV). To test the hypothesis that roommates are more likely to have similar viral sequences than non- 2 3 4 roommate pairs, we linked data from 33 roommate pairs in which both roommates had sequencing data 2 3 5 and performed a permutation test comparing the percent overlap in single nucleotide polymorphism 2 3 6 (SNP) identities between roommate pairs and random pairs of sequences derived from Residence Halls 2 3 7 A and B. We performed a Mann-Whitney U test to compare the amount of diversity shared in roommate 2 3 8 pairs and random pairs. . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 10, 2021. ; https://doi.org/10.1101/2021.05.07.21256834 doi: medRxiv preprint Hospitalization was rare for both students and staff (<1.0%). Specimen collection occurred before symptom onset for 4.6% of student cases, while a positive result was reported before symptom onset for 2 5 7 0.7% of student cases. Among student cases, 902 (25.9%) were associated with an on-campus residence 2 5 8 hall, 1,019 (29.2%) were associated with off-campus housing clusters, and 460 (13.2%) were associated 2 5 9 with FSL ( Table 1) ; the remainder were not linked to housing-specific clusters. Multiple mitigation measures were put into place to reduce transmission during the week of Residence Halls A and B during September 9-23, 2020, as these residence halls were experiencing the highest percent positivity, and transitioning from biweekly to weekly COVID-19 screening tests for all 2 6 5 students residing in any residence hall (Figure 1) . The local health department, which maintains 2 6 6 jurisdiction for off-campus housing, also required testing and quarantine for 26 FSL house chapters. . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 10, 2021. ; https://doi.org/10.1101/2021.05.07.21256834 doi: medRxiv preprint halls were asked to quarantine in place for 14 days starting September 9, 2020. In addition, we used a divergence phylogeny, colored by residence hall, to compare the number illustrates that substantial mixing of viral genetic lineages between the two residence halls 2 8 5 occurred, indicating that outbreaks of COVID-19 within these residence halls were not distinct and 2 8 6 resulted from intermingling between residents. Whole genome sequencing among students from two residence halls 2 8 8 We sequenced complete viral genomes from 262 (44.7%) of the 586 specimens taken from 2 8 9 students living in Residence Halls A and B (Figure 3) . Using a Dane County-centric phylogeny, we Almost two-thirds of sequences from the residence halls (172/262; 65.6%) form a cluster in the 20A 2 9 2 . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 10, 2021. Across all residence halls, 81.6% of residents had a roommate. Percent positivity was higher 3 0 7 overall among students with roommates (15.4%) than those without roommates (7.3%) (p<0.0001). Of (19.6%) tested positive within 2-14 days. ( Table 2) . 3 

Genetic distance comparisons between roommate pairs and non-roommate pairs within Residence Halls A and B revealed significantly higher levels of overlap in SNV identities between roommate pairs compared to random pairs. Specifically, 32/33 (97.0%) roommate pairs had viruses that . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 10, 2021. ; https://doi.org/10.1101/2021.05.07.21256834 doi: medRxiv preprint those with symptomatic and asymptomatic SARS-CoV-2 infections, quarantine of roommates, and strategy for the Spring 2021 semester, increasing the frequency of testing to twice per week for students 3 5 0 living on-campus and living off-campus in nearby zip codes and has reduced turnaround time for results 3 5 1 to less than 24 hours. 36, 37 Further evaluation of serial testing strategies, including UW-Madison's modified strategy for the spring 2021 semester, is needed to determine optimal testing frequency in IHE 3 5 3 settings and to prioritize populations for testing when capacity is limited. The high proportion of 3 5 4 infected students who were symptomatic (>80.0%) suggests that even in young adults, SARS-CoV-2 3 5 5 infection is frequently associated with at least mild symptoms, reinforcing the importance of educating students on COVID-19 symptoms, symptom monitoring, testing, and self-isolation when symptoms 3 5 7 develop (even if only mild). 38 3 5 8 Roommates live in close contact with each other, providing substantial opportunities for 3 5 9 transmission. 39 At UW-Madison, roommates were not required to wear masks within their rooms; within residence halls had an estimated attack rate of 19.6%, and a larger proportion of students with genomes collected from 33 roommate pairs found a high proportion of identical sequences, suggesting 3 6 4 . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 10, 2021. ; https://doi.org/10.1101/2021.05.07.21256834 doi: medRxiv preprint transmission occurred either within the roommate pair or based on a shared exposure. Given the elevated between UW-Madison students and the broader community. 11, [13] [14] [15] [16] [17] [18] [19] Our sequencing data covering 44.7% associated with these residence halls gave rise to few descendent infections, with little evidence that Residence Halls A and B and the suspension of most non-essential on-campus activity for two weeks, CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Finally, roommate attack rate calculations were limited in that campus testing data did not include CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 10, 2021. ;  public health authorities are critical in halting transmission, both within the campus community and to 4 1 2 the broader local community. Our findings suggest important strategies for IHEs and universities in 4 1 3 preventing outbreaks include move-in testing with quarantine while awaiting results and frequent 4 1 4 subsequent serial screening testing with rapid turnaround times, in addition to physical distancing, Given the elevated risk of transmission among roommate pairs, strategies to reduce the density of This investigation also demonstrates the use of genomic surveillance to provide a more comprehensive these tools can be used by universities and health departments to monitor spillover into the community . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 10, 2021. ; https://doi.org/10.1101/2021.05.07.21256834 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 10, 2021 *student affiliation was prioritized over staff, such that those identified as both students and staff 4 2 7 are categorized as students * † anyone with at least one symptom is considered symptomatic; asymptomatic does not 4 3 0 distinguish between those that were truly asymptomatic and those that were missing least two of the following symptoms: fever, chills, myalgia, headache, sore throat, loss of smell, 4 3 6 or loss of taste. 4 3 7 . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 10, 2021. ; *includes aggregated data from 10 residence halls not listed here that had fewer than 10 total cases each; attack rates in these halls ranged from 1.9%-5.6%

* † one room included in the roommate attack rate analysis housed three residents, while all others housed two residents; in the room with two susceptible residents, neither tested positive within 2-14 days of the index case.

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It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

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Wisconsin, August 1 -October 31, 2020* *10 student case-patients affiliated with both a residence hall and a fraternity or sorority are categorized as Residence Hall Students. Student was considered the primary affiliation, such that any student who was also a staff member was categorized as a student.

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It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 10, 2021.

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It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 10, 2021. . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted May 10, 2021. ; https://doi.org/10.1101/2021.05.07.21256834 doi: medRxiv preprint . CC-BY 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

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