Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Novel variants continue to emerge in the SARS-CoV-2 pandemic. University testing programs may provide timely epidemiologic and genomic surveillance data to inform public health responses. We conducted testing from September 2021 to February 2022 in a university population under vaccination and indoor mask mandates. A total of 3,048 of 24,393 individuals tested positive for SARS-CoV-2 by RT-PCR; whole genome sequencing identified 209 Delta and 1,730 Omicron genomes of the 1,939 total sequenced. Compared to Delta, Omicron had a shorter median serial interval between genetically identical, symptomatic infections within households (2 versus 6 days, P = 0.021). Omicron also demonstrated a greater peak reproductive number (2.4 versus 1.8), and a 1.07 (95% confidence interval: 0.58, 1.57; P < 0.0001) higher mean cycle threshold value. Despite near universal vaccination and stringent mitigation measures, Omicron rapidly displaced the Delta variant to become the predominant viral strain and led to a surge in cases in a university population.
Article activity feed
-
-
SciScore for 10.1101/2022.04.27.22274375: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: COVID-19 vaccination status was collected at enrollment, updated monthly, and updated at or after collection of the SARS-CoV-2 positive samples. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study limitations include the lack of routine surveillance testing of the entire campus population. …
SciScore for 10.1101/2022.04.27.22274375: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: COVID-19 vaccination status was collected at enrollment, updated monthly, and updated at or after collection of the SARS-CoV-2 positive samples. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study limitations include the lack of routine surveillance testing of the entire campus population. Follow-up symptom data was missing for some individuals and therefore we do not know if some asymptomatic cases were pre-symptomatic. We rely on self-report of vaccine status and could not reference state registries. However, state registry data may be incomplete or delayed, especially for students from other states. A limitation of our Ct analysis is the change in swab type during the study which may impact viral load, and we therefore restricted our viral load analysis to only one swab type. We also did not account for repeat infections. Finally, this study included only people on a single university campus who participated in the research study, and who are on average, younger, healthier, and more educated than the general population. In conclusion, we found rapid replacement of the SARS-CoV-2 Delta variant with the Omicron variant within a highly vaccinated university population. As we move into the next phases of the pandemic, real-time data around viral kinetics and genomic epidemiology of emerging variants will be important to guide our national strategies on mitigating respiratory virus spread.
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.
-
