Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus

Weil, Ana A.; Luiten, Kyle G.; Casto, Amanda M.; Bennett, Julia C.; O’Hanlon, Jessica; Han, Peter D.; Gamboa, Luis; McDermot, Evan; Truong, Melissa; Gottlieb, Geoffrey S.; Acker, Zack; Wolf, Caitlin R; Magedson, Ariana; Chow, Eric J; Lo, Natalie; Pothan, Lincoln C.; McDonald, Devon; Wright, Tessa; McCaffrey, Kathryn; Figgins, Marlin D.; Englund, Janet A.; Boeckh, Michael; Lockwood, Christina M.; Nickerson, Deborah A.; Shendure, Jay; Bedford, Trevor

doi:10.1038/s41467-022-32786-z

Cited by 22 publications

(30 citation statements)

References 56 publications

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“…Summarizing, the case illustrates that an Omicron peak took place during a time when classes were not in session, and the return to class in 2022 was marked by rapidly falling disease incidences in the department, despite in-person classes, confirming evidence from the respective studies in U.S. universities [ 14 , 15 , 16 ]. Moreover, the department’s in-class instruction is not an appreciable source of COVID-19 transmission only under the setting of mandatory masking, which is in agreement with the relevant findings in the literature [ 14 ].…”

Section: Discussionsupporting

confidence: 61%

“…In the first category, efforts were made to assess the control plans used for reopening universities (e.g., Boston University in [ 4 ], Harvard/Boston/Duke/Northeastern in [ 5 ], Bristol (UK) in [ 6 ], Southern California in [ 7 ], Purdue in [ 8 ], Tulane in [ 9 ], Clemson in [ 10 ]); or to develop relevant susceptible–exposed–infected–recovered (SEIR) or agent-based (ABM) models in a university environment (e.g., Emory University in [ 11 ], University of Illinois in [ 12 ]). In the second category, research was focused on studying how COVID-19 containment protocols decreased transmission among university students (e.g., Saint Louis University in [ 13 ], Boston University in [ 14 ]) and to assess how the Omicron variant was established in universities (e.g., Harvard/Boston/Northeastern in [ 15 ], University of Washington in [ 16 ]).…”

Section: Background From the Literaturementioning

confidence: 99%

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Evaluating the COVID-19 Containment Protocol in Greek Universities for the Academic Year 2021–2022

Rachaniotis

2022

IJERPH

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The COVID-19 pandemic severely disrupted European universities’ educational process. With the vaccination rollout, in-class instruction broadly resumed beginning in September 2021. In order to mitigate the risks of SARS-CoV-2 transmission, European universities apply COVID-19 containment protocols. The aim of this paper is to evaluate the COVID-19 containment protocol that Greek universities implemented in order to fully reopen in the fall of 2021 and for the entire academic year 2021–2022. A case study was conducted at the Department of Industrial Management and Technology, University of Piraeus (Athens’ port), Greece. Data were collected from November 2021 to July 2022 and a quantitative statistical analysis (descriptive and inferential) was performed. A total of 330 unique (and 43 reinfections) COVID-19 cases were confirmed, including 241 undergraduate students, 73 postgraduate, and 2 doctoral students, 10 faculty, and 4 administrative personnel. Contact tracing reported four confirmed and eight potential cases of in-classroom transmission. The person in charge of implementing the COVID-19 containment protocol in the department ordered more than 6000 rapid tests during this period. The Department of Industrial Management and Technology at the University of Piraeus used a rigorously monitored and coordinated strategy of vaccine promotion, screening/testing, contact tracing, isolation, and quarantine in order to control COVID-19 transmission. The results show, on one hand, that the protocol’s implementation is effective and leads to in-classroom transmission minimization and, on the other hand, verify the hypothesis that the department’s confirmed COVID-19 cases are less (with a mean percentage difference of 50%) than the community’s respective 18–39 age group.

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Section: Discussionsupporting

confidence: 61%

Section: Background From the Literaturementioning

confidence: 99%

Evaluating the COVID-19 Containment Protocol in Greek Universities for the Academic Year 2021–2022

Rachaniotis

2022

IJERPH

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“…This suggests that Omicron is able to evade immunity induced in vaccinated individuals, providing a likely explanation for the rapid surge in Omicron in countries where a large proportion of individuals are fully vaccinated. Previous work has also quantified the reproductive number or relative growth advantage of Omicron in particular countries or settings, showing it to exceed that of previous emerging variants ( Pearson et al., 2021 ; Weil et al., 2022 ) and to be greater among vaccinated individuals ( Paton et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron

Dorp¹,

Goldberg

et al. 2022

Virus Evolution

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New variants of SARS-CoV-2 show remarkable heterogeneity in their relative fitness over both time and space. In this paper we extend the tools available for estimating the selection strength for new SARS-CoV-2 variants to a hierarchical, mixed-effects, renewal equation model. This formulation allows us to estimate selection effects at the global level while incorporating both measured and unmeasured heterogeneity among countries. Applying this model to the spread of Omicron in forty countries, we find evidence for very strong but very heterogeneous selection effects. To test whether this heterogeneity is explained by differences in the immune landscape, we considered several measures of vaccination rates and recent population-level infection as covariates, finding marginally significant effects. We also found a significant positive correlation between the selection advantage of Delta and Omicron at the country level, suggesting that other region-specific explanatory variables of fitness differences do exist. Our method is implemented in the Stan programming language, can be run on standard consumer-grade computing resources, and will be straightforward to apply to future variants.

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“…2). Twenty-two studies were from populations primarily of European ancestry [8,32,[40][41][42][43][44][45][46][47][48][49][50][51][52][53][54][55][56][57][58][59], eight studies on East Asians [60][61][62][63][64][65][66][67], three studies on South Asians [68][69][70], three studies on Latinos [71][72][73], four studies on populations in Africa [74][75][76][77], and one study from West Asia (Turkey [78]). The location of studies, with the prevalence indicated by the color intensity, and the cohort size indicated by the size of the circles, shows that Western countries report the highest prevalence, while studies from East Asia and Africa report the lowest prevalence (Fig.…”

Section: Properties Of Studiesmentioning

confidence: 99%

“…We did not attempt to resolve whether omicron sub-variants have different effects on olfactory dysfunctionthere are too few studies yet that report effects of subvariants on loss of smell [49,51,57]. Some cohorts of the studies were ethnically mixed, but the exact ethnic composition of the cohort was reported in only a few studies (e.g.…”

Section: Limitations Of Our Reviewmentioning

confidence: 99%

Prevalence of Olfactory Dysfunction with the Omicron Variant of SARS-CoV-2: A Systematic Review and Meta-analysis

Bartheld

Wang

2022

Preprint

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The omicron variant is thought to cause less olfactory dysfunction than previous variants of SARS-CoV-2, but the reported prevalence differs greatly between populations and studies. Our systematic review and meta-analysis provide information about regional differences in prevalence as well as an estimate of the global prevalence of olfactory dysfunction based on 41 studies reporting on nearly 600,000 patients infected with the omicron variant. Our estimate of the omicron-induced prevalence of olfactory dysfunction in populations of European ancestry is 11.6%, while it is significantly lower in all other populations, at 2.9-5.4%. When ethnic differences and population sizes are taken into account, the global prevalence of omicron-induced hyposmia in adults is estimated at 5.2%. Omicron's effect on olfaction is 3-4fold lower than that of the alpha or delta variant, according to previous meta-analyses and our analysis of studies that directly compared prevalence of olfactory dysfunction between omicron and previous variants. The profile of prevalence differences between ethnicities mirrors the results of a recent genome-wide association study that implicated a gene locus encoding an odorant-metabolizing enzyme, UDP glycosyltransferase, to be linked to the extent of COVID-related loss of smell. Our analysis is consistent with the hypothesis that this enzyme contributes to the observed population differences.

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Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus

Cited by 22 publications

References 56 publications

Evaluating the COVID-19 Containment Protocol in Greek Universities for the Academic Year 2021–2022

Evaluating the COVID-19 Containment Protocol in Greek Universities for the Academic Year 2021–2022

Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron

Prevalence of Olfactory Dysfunction with the Omicron Variant of SARS-CoV-2: A Systematic Review and Meta-analysis

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