Management and containment of a SARS-CoV-2 Beta variant outbreak at the Malawi University of Science and Technology
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Abstract
Outbreaks of COVID at university campuses can spread rapidly and threaten the broader community. We describe the management of an outbreak at a Malawian university in April-May 2021 during Malawi’s second wave. Classes were suspended following detection of infections by routine testing and campus-wide PCR mass testing was conducted. Fifty seven cases were recorded, 55 among students, two among staff. Classes resumed 28 days after suspension following two weeks without cases. Just 6.3% of full-time staff and 87.4% of outsourced staff tested while 65% of students at the main campus and 74% at the extension campus were tested. Final year students had significantly higher positivity and lower testing coverage compared to freshmen. All viruses sequenced were beta variant and at least four separate virus introductions onto campus were observed. These findings are useful for development of campus outbreak responses and indicate the need to emphasize staff, males and senior students in testing.
Article Summary Line
Successful management of a campus outbreak using test trace and isolate approach with resumption within a month following suspension of all in-person classes. Trends in voluntary testing by gender, age and year of study that can help in formation of future management approaches.
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SciScore for 10.1101/2021.11.25.21266298: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Nasopharyngeal swab specimens were collected by trained personnel and placed in a 3-mL tube of viral transport medium (Mantacc MBT-010, Miraclean Technology, Shenzhen, China) to be used for both antigen testing and RT-PCR testing. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: Specimens were determined to be positive for SARS-CoV-2 when the E gene and RdRP genes were detected with an exponential growth curve and a cycle threshold (Ct) value <31, and negative when these genes could not be detected. Table 2: Resources
Software and Algorithms Sentences Resources The … SciScore for 10.1101/2021.11.25.21266298: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Nasopharyngeal swab specimens were collected by trained personnel and placed in a 3-mL tube of viral transport medium (Mantacc MBT-010, Miraclean Technology, Shenzhen, China) to be used for both antigen testing and RT-PCR testing. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: Specimens were determined to be positive for SARS-CoV-2 when the E gene and RdRP genes were detected with an exponential growth curve and a cycle threshold (Ct) value <31, and negative when these genes could not be detected. Table 2: Resources
Software and Algorithms Sentences Resources The resulting assemblies where cleaned in Geneious. Geneioussuggested: (Geneious, RRID:SCR_010519)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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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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