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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.
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Olfactory and taste dysfunctions have emerged as symptoms of COVID-19. Among individuals with COVID-19 enrolled in a household study, loss of taste and/or smell was the fourth most commonly reported symptom (26/42; 62%), and among household contacts, it had the highest positive predictive value (83%; 95% CI: 55-95%) for COVID-19. These findings support consideration of loss of taste and/or smell in possible case identification and testing prioritization for COVID-19.
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BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), presents with a broad range of symptoms. Existing COVID-19 case definitions were developed from early reports of severely ill, primarily hospitalized, patients. Symptom-based case definitions that guide public health surveillance and individual patient management in the community must be optimized for COVID-19 pandemic control. MethodsWe collected daily symptom diaries and performed RT-PCR on respiratory specimens over a 14-day period in 185 community members exposed to a household contact with COVID-19 in the Milwaukee, Wisconsin and Salt Lake City, Utah metropolitan areas. We interpreted the discriminatory performance (sensitivity, specificity, predictive values, F1 score, Youdens index, and prevalence estimation) of individual symptoms and common case definitions according to two principal surveillance applications (i.e., individual screening and case counting). We also constructed novel case definitions using an exhaustive search with over 73 million symptom combinations and calculated bias-corrected and accelerated bootstrap confidence intervals stratified by children versus adults. FindingsCommon COVID-19 case definitions generally showed high sensitivity (8696%) but low positive predictive value (PPV) (3649%; F1 score 5263) in this community cohort. The top performing novel symptom combinations included taste or smell dysfunction. They also improved the balance of sensitivity and PPV (F1 score 7880) and reduced the number of false positive symptom screens. Performance indicators were generally lower for children (<18 years of age). InterpretationExisting COVID-19 case definitions appropriately screened in community members with COVID-19. However, they led to many false positive symptom screens and poorly estimated community prevalence. Absent unlimited, timely testing capacity, more accurate case definitions may help focus public health resources. Novel symptom combinations incorporating taste or smell dysfunction as a primary component better balanced sensitivity and specificity. Case definitions tailored specifically for children versus adults should be further explored. FundingThis research was wholly supported by the U.S. Centers for Disease Control and Prevention. DisclaimerThe findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the U.S. Centers for Disease Control and Prevention/the Agency for Toxic Substances and Disease Registry. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSCoronavirus disease 2019 (COVID-19) incidence has accelerated globally over the last several months. As the full spectrum of clinical presentations has come into clearer focus, symptom-based clinical screening and case surveillance has also evolved. Preliminary understanding of the clinical manifestation of COVID-19 was driven primarily by descriptions of hospitalized patients, as early testing algorithms prioritized more severely ill persons with classic lower respiratory symptoms and fever. Since then, more data from ambulatory settings have emerged. We searched PubMed from 1 December 2019 to 21 August 2020 for studies that assessed the diagnostic performance of case surveillance definitions for COVID-19. We found no studies examining the discriminatory performance of case surveillance definitions among contacts with mild to moderate symptoms with documented exposure to persons with COVID-19. Nonetheless, we found nine highly relevant studies: seven original reports and two review articles. Five original studies evaluated individual, self-reported symptoms (two among healthcare workers in the United States, one among healthcare workers in the Netherlands, and one online survey for the general public in Somalia) and concluded that using dysfunction of taste or smell for routine COVID-19 screening likely had utility. The fifth study had a similar conclusion based on self-reported symptoms and laboratory results collected via smartphone from the general public in the United States and the United Kingdom. Another original study modeled the substantial effect that multiple revisions to the COVID-19 case definition had on the reported disease burden in the Chinese population. Lastly, an original study illustrated the shift in discriminatory performance of established influenza surveillance case definitions for influenza between adults and children. Age-specific differences in case definition performance may also apply to COVID-19. Two articles reviewed predictive algorithms to define outpatient COVID-19 illness and risk of hospitalization. The reviewed studies were limited in that they were either restricted to individual signs or symptoms, or they incorporated blood tests or imaging that required in-person access to medical care. Added value of this studyThe discriminatory performance of case surveillance definitions for COVID-19 is important for implementing effective epidemic mitigation strategies. Our study illustrates the performance of case definitions in community members with household exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based solely on symptom profiles. Prior work overrepresented healthcare workers or otherwise studied non-representative populations, and they did not examine across the age spectrum. Our study also provides a novel framework for refining definitions. Using 15 symptoms associated with COVID-19 for all contacts regardless of disease status, we systematically evaluated the discriminatory performance of individual symptoms and previously defined case surveillance definitions across ages and according to two core surveillance applications: 1) screening non-hospitalized individuals to prioritize public health interventions, and 2) estimating the number of non-hospitalized persons with COVID-19 (i.e., community-based syndromic surveillance). We also constructed novel symptom combinations that effectively performed both functions and improved upon widely used case surveillance definitions that may help to target interventions in the absence of unlimited laboratory diagnostic capacity. Our analyses highlight the importance of ongoing re-evaluation of symptom-based surveillance definitions to suit the intended purpose and population under surveillance. Based on our results, which were derived from household members of all ages, case surveillance definition performance may improve if developed separately for adults and children. Implications of all the available evidenceCase definitions for COVID-19 should be tailored to maximize the discriminatory performance dependent upon its intended use. Existing COVID-19 case definitions screened in most community members with COVID-19, but also yielded a high number of false positive results. When unlimited, timely diagnostic testing is not available symptom combinations with improved accuracy (i.e., more balanced sensitivity and specificity) may help focus resources, such as recommending self-isolation among community contacts.
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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.
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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.
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BackgroundApproximately 67% of U.S. households have pets. Limited data are available on SARS-CoV-2 in pets. We assessed SARS-CoV-2 infection in pet cohabitants as a sub-study of an ongoing COVID-19 household transmission investigation. MethodsMammalian pets from households with [≥]1 person with laboratory-confirmed COVID-19 were eligible for inclusion from April-May 2020. Demographic/exposure information, oropharyngeal, nasal, rectal, and fur swabs, feces, and blood were collected from enrolled pets and tested by rRT-PCR and virus neutralization assays. FindingsWe enrolled 37 dogs and 19 cats from 34 of 41 eligible households. All oropharyngeal, nasal, and rectal swabs tested negative by rRT-PCR; one dogs fur swabs (2%) tested positive by rRT-PCR at the first animal sampling. Among 47 pets with serological results from 30 households, eight (17%) pets (4 dogs, 4 cats) from 6 (20%) households had detectable SARS-CoV-2 neutralizing antibodies. In households with a seropositive pet, the proportion of people with laboratory-confirmed COVID-19 was greater (median 79%; range: 40-100%) compared to households with no seropositive pet (median 37%; range: 13-100%) (p=0.01). Thirty-three pets with serologic results had frequent daily contact ([≥]1 hour) with the human index patient before the persons COVID-19 diagnosis. Of these 33 pets, 14 (42%) had decreased contact with the human index patient after diagnosis and none (0%) were seropositive; of the 19 (58%) pets with continued contact, 4 (21%) were seropositive. InterpretationsSeropositive pets likely acquired infection from humans, which may occur more frequently than previously recognized. People with COVID-19 should restrict contact with animals. FundingCenters for Disease Control and Prevention, U.S. Department of Agriculture