key: cord-0715275-ovetojwg authors: Weil, A. A.; Sohlberg, S. L.; O'Hanlon, J. A.; Casto, A. M.; Emanuels, A. W.; Lo, N. K.; Greismer, E. P.; Magedson, A. M.; Wilcox, N. C.; Kim, A. E.; Back, L.; Frazar, C. D.; Pelle, B.; Sibley, T. R.; Ilcisin, M.; Lee, J.; Ryke, E. L.; Craft, J. C.; Schwabe-Fry, K. M.; Fay, K. A.; Cho, S.; Han, P. D.; Heidl, S. J.; Pfau, B. A.; Truong, M.; Zhong, W.; Srivatsan, S. R.; Harb, K. F.; Gottlieb, G. S.; Hughes, J. P.; Nickerson, D. A.; Lockwood, C. M.; Starita, L. M.; Bedford, T.; Shendure, J. A.; Chu, H. Y. title: SARS-CoV-2 Epidemiology on a Public University Campus in Washington State date: 2021-03-17 journal: nan DOI: 10.1101/2021.03.15.21253227 sha: 11b8a5546114bf2eb20e55bdd20fe9ae2ea7cc43 doc_id: 715275 cord_uid: ovetojwg Background: Testing programs have been utilized as part of SARS-CoV-2 mitigation strategies on university campuses, and it is not known which strategies successfully identify cases and contain outbreaks. Objective: Evaluation of a testing program to control SARS-CoV-2 transmission at a large university. Design: Prospective longitudinal study using remote contactless enrollment, daily mobile symptom and exposure tracking, and self-swab sample collection. Individuals were tested if the participant was (1) exposed to a known case, developed new symptoms, or reported high-risk behavior, (2) a member of a group experiencing an outbreak, or (3) at baseline upon enrollment. Setting: An urban, public university during Autumn quarter of 2020. Participants: Students, staff, and faculty. Measurements: SARS-CoV-2 PCR testing was conducted, and viral genome sequencing was performed. Results: We enrolled 16,476 individuals, performed 29,783 SARS-CoV-2 tests, and detected 236 infections. Greek community affiliation was the strongest risk factor for testing positive. 75.0% of positive cases reported at least one of the following: symptoms (60.8%), exposure (34.7%), or high-risk behaviors (21.5%). 88.1% of viral genomes (52/59) sequenced from Greek-affiliated students were genetically identical to at least one other genome detected, indicative of rapid SARS-CoV-2 spread within this group, compared to 37.9% (11/29) of genomes from non-Greek students and employees. Limitations: Observational study. Conclusion: In a setting of limited resources during a pandemic, we prioritized testing of individuals with symptoms and high-risk exposure during outbreaks. Rapid spread of SARS-CoV-2 occurred within outbreaks without evidence of further spread to the surrounding community. A testing program focused on high-risk populations may be effective as part of a comprehensive university-wide mitigation strategy to control the SARS-CoV-2 pandemic. (see Supplemental Text), [16] ). A sample was considered positive if three or four replicates for possible asymptomatic. A case who tested positive/inconclusive was defined as "symptomatic" if 157 they reported symptoms on their daily attestation survey within the seven days prior to testing or 158 if they reported symptoms on the day of testing. "Presymptomatic" was defined as those who 159 only reported symptoms in the week following testing, either on their daily attestation or follow-160 up survey. If no symptoms were reported before or after testing on the daily attestation or follow-161 up survey, they were considered "asymptomatic." Participants who did not complete their daily 162 attestations or the follow-up survey, and who reported no symptoms at the time of testing were 163 labeled as "possible asymptomatic" cases. A total of 11,633 (70.6%) participants were tested at least once (Supplemental Table 2 ). Tests CC-BY-NC-ND 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) Table 6 ). Reported frequency of hand washing, mask-wearing, and 219 social distancing were not associated with positivity. Greek Community Outbreak 222 Thirty cases were identified in the Greek community during the first 10 days of the study, which 223 prompted outbreak testing. Test positivity trends in the Greek community demonstrated a 224 unique epidemiologic curve compared to the non-Greek students, employees, and the county 225 ( Figure 3A, [25] ). Outbreaks within Greek houses were concurrent, but with unique individual 226 timelines, and involved both fraternities and sororities ( Figure 3B ). 68.3% of Greek members 227 reported sharing a living space with 6 or more people, compared to only 14.0% of non-Greek 228 students. During 37 days of outbreak testing, serial testing frequently identified individuals who 229 tested negative several times prior to testing positive ( Figure 3C ). . CC-BY-NC-ND 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) High coverage genomes were generated for 88 SARS-CoV-2 samples collected from unique 233 individuals between September 27th and November 28th. 59 were collected from Greek-234 affiliated students, 24 from non-Greek-affiliated students, and 5 from faculty or staff. In Figure 235 4A, a phylogenetic tree of 1700 SARS-CoV-2 genomes collected statewide, including the 88 236 samples from this study, is shown. Multiple study samples appear in each of the four major 237 clades (20A, 20B, 20C, 20G) circulating in the county and state during this timeframe. Most viral genomes from this study (56/88, 63.6%) grouped into one large cluster that included ancestor of the larger cluster at September 22nd (95% CI: September 1 st -29th) and the smaller 249 cluster at September 27th (95% CI: September 20th -October 4th). These two dates occur just 250 prior to the sharp increase in cases observed in our study among Greek students, which peaked 251 on approximately October 7th-8th ( Figure 3A ). The last sample mapping to either of these sub-252 clusters was collected November 12th. This date roughly coincides with the end of the Greek 253 outbreak as measured by the percent positivity rate ( Figure 3A) . Among the over 500 viral 254 genomes collected state-wide after November 12th, including 9 collected by this study, none 255 have descended from the viruses responsible for the Greek community olutbreak. Two smaller clusters of viral genomes from this study are shown in Figure 4A . CC-BY-NC-ND 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 March 17, 2021. ; https://doi.org/10.1101/2021.03.15.21253227 doi: medRxiv preprint affiliated students and one from a non-Greek student. This cluster has a most recent common 259 ancestor dating to October 31st (95% CI: October 17 th -November 1st). The second contains 260 three genomes from non-Greek-affiliated students and one faculty/staff member with a most 261 recent common ancestor dating to November 3rd (95% CI: October 11th-November 16th). Viral 262 genomes from Greek-affiliated students were most likely to cluster with other study samples; CC-BY-NC-ND 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) [28] . In our study, SARS-CoV-2 test positivity rates in the 280 university community were substantially lower than in the surrounding areas. This is likely due in 281 part to increased testing availability, particularly for those without symptoms. However, it is also 282 possible that focused testing of high-risk groups prevented and mitigated campus-wide 283 outbreaks. Outbreak testing was an essential part of our testing strategy. In our study, Greek affiliation was 285 the most important risk factor for testing positive, and more than two-thirds of the cases 286 detected in this study were in Greek-affiliated students. A study conducted at an Arkansas 287 university, in which 91% of identified SARS-CoV-2 cases occurred in Greek-affiliated students, 288 previously implicated this group as high-risk for contracting COVID-19 [29] . We observed cases 289 in more than half of our university's Greek chapters, and the genomic analysis and outbreak 290 dynamics indicate that transmission occurred at a rapid pace both within and among fraternities 291 and sororities. However, later in the quarter, the decreased test positivity rate among this group 292 became comparable to the rates observed among the non-Greek participants. We believe this 293 . CC-BY-NC-ND 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 March 17, 2021. ; https://doi.org/10.1101/2021.03.15.21253227 doi: medRxiv preprint decline was driven in part by our aggressive testing strategy in Greek-affiliated students, which 294 identified pre-and asymptomatic cases, and was followed by effective contact tracing. Genomic analysis of a subset of the SARS-CoV-2 samples collected in this study revealed 296 major differences between those from Greek community members and those from non-Greek 297 community members. In particular, sequenced samples from Greek students were much more 298 likely than samples from non-Greek students or from faculty/staff to form clusters. Our hypothesis that social behaviors, rather than housing arrangements, drove the Greek outbreak 307 is supported by our analyses that rapid spread occurred not only within, but also among Greek 308 houses. We did not observe evidence of Greek-related virus spread into the wider community. Given 310 that a limited number of SARS-CoV-2 genomes were sequenced, this does not rule out 311 "spillover" of virus from the Greek outbreak into the outside community, but to date, none of the 312 sequenced SARS-CoV-2 samples collected state-wide appear to descend from the Greek 313 outbreak virus. In addition to members of the Greek community, participants who identified as Latinx or 315 Hispanic experienced increased rates of test positivity. This is consistent with COVID-19 316 incidence rates in Washington State, where Hispanic individuals represented 13% of state 317 residents, but 33% of COVID-19 cases [26] . This highlights the need for more targeted and 318 equitable distribution of testing and contact tracing resources in this high-risk population. . CC-BY-NC-ND 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 March 17, 2021. ; https://doi.org/10.1101/2021.03.15.21253227 doi: medRxiv preprint Testing and behavioral interventions are cost-effective interventions to control outbreaks on college campuses; however, prioritization of testing is critical, and scarcity of laboratory supplies with testing people experiencing symptoms, may be sufficient to stop on-campus transmission 346 and prevent community spread in a setting of limited resources during a pandemic. . CC-BY-NC-ND 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. . CC-BY-NC-ND 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) . CC-BY-NC-ND 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. . CC-BY-NC-ND 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) CC-BY-NC-ND 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. . CC-BY-NC-ND 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. CC-BY-NC-ND 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 March 17, 2021. . CC-BY-NC-ND 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) . CC-BY-NC-ND 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. Other Asian 0 (0%) 0 (0%) 11 (100%) 11 . CC-BY-NC-ND 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 March 17, 2021. . CC-BY-NC-ND 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 March 17, 2021. In the past 7 days, how often did you try to stay 6 feet away from people who don't live with you? ΒΆ . CC-BY-NC-ND 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 March 17, 2021. CC-BY-NC-ND 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 March 17, 2021. . CC-BY-NC-ND 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) . CC-BY-NC-ND 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) . CC-BY-NC-ND 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. . CC-BY-NC-ND 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. . CC-BY-NC-ND 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) To minimize the possibility of contact with high-risk people during the testing process, 534 individuals were tested in two physically separate groups. The first was for participants reporting 535 symptoms or a high-risk exposure, and the second was for lower-risk study participants without 536 these risk factors. . CC-BY-NC-ND 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. CC-BY-NC-ND 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 March 17, 2021. ; https://doi.org/10.1101/2021.03.15.21253227 doi: medRxiv preprint In the enrollment survey, participants reported frequency of COVID-19 prevention behaviors cleaning or disinfecting items and surfaces in their living or workspace, and 73.4% reported 565 always social distancing ("In the past 7 days, how often did you try to stay 6 feet away from . CC-BY-NC-ND 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 March 17, 2021. ; https://doi.org/10.1101/2021.03.15.21253227 doi: medRxiv preprint to-students-from-the-united-states/ 624 . CC-BY-NC-ND 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) . CC-BY-NC-ND 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 March 17, 2021. ; https://doi.org/10.1101/2021.03.15.21253227 doi: medRxiv preprint Changing Age Distribution of the COVID-19 Pandemic -United States How Colleges Became the New Covid Hot Spots Implementation of a Pooled Surveillance Testing 597 Program for Asymptomatic SARS-CoV-2 Infections on a College Campus SARS-CoV-2 Control on a Large Urban College 601 Tracking and Treating COVID-19 in Human Waste Markedly heterogeneous COVID-19 testing plans 609 among US colleges and universities. medRxiv Centers for Disease Control 613 and Prevention About the UW How the pandemic will affect autumn quarter learning (Message to students from the United 621 Novel coronavirus information Research electronic data capture (REDCap)--a 625 metadata-driven methodology and workflow process for providing translational research 28 The Seattle Flu Study: a multiarm community-based 635 prospective study protocol for assessing influenza prevalence, transmission and 636 genomic epidemiology Preliminary support for a "dry swab, extraction 639 free" protocol for SARS-CoV-2 testing via RT-qPCR. bioRxiv Cross-Sectional Prevalence of SARS-CoV-2 Among 641 Skilled Nursing Facility Employees and Residents Across Facilities in Seattle Cryptic transmission of SARS-CoV-2 in 645 seattleflu/assembly Seattle Flu Study Nextstrain: real-time tracking of pathogen evolution GISAID: Global initiative on sharing all influenza data-from 652 vision to reality University of Washington University of Washington SARS-CoV-2 sequencing reveals rapid 673 transmission from college student clusters resulting in morbidity and deaths in vulnerable 674 populations. medRxiv College Campuses and COVID-19 Mitigation: Clinical 680 and Economic Value SCAN Data Results Greater Seattle Coronavirus 682 We would like to thank the study participants. We also thank UW Environmental Health & Safety