Early Introduction and Rise of the Omicron Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variant in Highly Vaccinated University Populations
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Abstract
Background
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible in vaccinated and unvaccinated populations. The dynamics that govern its establishment and propensity toward fixation (reaching 100% frequency in the SARS-CoV-2 population) in communities remain unknown. Here, we describe the dynamics of Omicron at 3 institutions of higher education (IHEs) in the greater Boston area.
Methods
We use diagnostic and variant-specifying molecular assays and epidemiological analytical approaches to describe the rapid dominance of Omicron following its introduction into 3 IHEs with asymptomatic surveillance programs.
Results
We show that the establishment of Omicron at IHEs precedes that of the state and region and that the time to fixation is shorter at IHEs (9.5–12.5 days) than in the state (14.8 days) or region. We show that the trajectory of Omicron fixation among university employees resembles that of students, with a 2- to 3-day delay. Finally, we compare cycle threshold values in Omicron vs Delta variant cases on college campuses and identify lower viral loads among college affiliates who harbor Omicron infections.
Conclusions
We document the rapid takeover of the Omicron variant at IHEs, reaching near-fixation within the span of 9.5–12.5 days despite lower viral loads, on average, than the previously dominant Delta variant. These findings highlight the transmissibility of Omicron, its propensity to rapidly dominate small populations, and the ability of robust asymptomatic surveillance programs to offer early insights into the dynamics of pathogen arrival and spread.
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SciScore for 10.1101/2022.01.27.22269787: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources At Northeastern University, affiliates self-collected anterior nares specimens, and RNA was extracted from the clinical specimens using the Thermo Fisher Scientific Applied Biosystems™ MagMAX™ Viral/Pathogen II (MVP II) Nucleic Acid Isolation Kit. Thermo Fisher Scientific Applied Biosystems™suggested: NoneResults from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:There are several limitations to the generalizability of this study. While universities contain individuals from …
SciScore for 10.1101/2022.01.27.22269787: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources At Northeastern University, affiliates self-collected anterior nares specimens, and RNA was extracted from the clinical specimens using the Thermo Fisher Scientific Applied Biosystems™ MagMAX™ Viral/Pathogen II (MVP II) Nucleic Acid Isolation Kit. Thermo Fisher Scientific Applied Biosystems™suggested: NoneResults from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:There are several limitations to the generalizability of this study. While universities contain individuals from different communities, features of a university such as the age distribution, the availability of residential life, and extracurricular activities could influence Omicron dynamics. Furthermore, the degree to which potential superspreader events could be important – not just for the initial seeding of Omicron, but for its continued spread – is not captured here. For example, it is possible that the spread of Omicron in other types of communities may be slower if the structure of the social network differs40, resulting in fewer opportunities for clustered transmission. Additionally, our work is limited by a few differences between MA and IHEs. For example, reduced vaccination rates in MA, relative to IHEs, may contribute to the relative fitness of Delta vs. Omicron. Moreover, MA testing may be biased towards Delta samples if symptomatic testing occurs more frequently with Delta than with Omicron. What can we learn from the spread of Omicron through universities that could help us to mitigate future waves of SARS-CoV-2 or other pathogens? First, for SARS-CoV-2, sites that have characteristics like IHEs can be informative early detection sites. We note two of many reasons: (1) IHEs contain individuals from a variety of backgrounds who travel and intermix at the university and in the larger community, and (2) IHEs have implemented university-wide asymptomatic screening ...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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