The Ugandan Severe Acute Respiratory Syndrome -Coronavirus 2 (SARS-CoV-2) Model: A Data Driven Approach to Estimate Risk

  1. Betty Nannyonga
  2. Henry Kyobe Bosa
  3. Yonas Tegegn Woldermariam
  4. Pontiano Kaleebu
  5. John M Ssenkusu
  6. Tom Lutalo
  7. Willford Kirungi
  8. Fredrick Edward Makumbi
  9. Vincent A Ssembatya
  10. Henry G Mwebesa
  11. Diana Atwine
  12. Jane Ruth Aceng
  13. Rhoda K Wanyenze

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Abstract

Objectives

The first case of Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) was identified on March 21, 2020, in Uganda. The number of cases increased to 8,287 by September 30, 2020. By May throughout June, most of the cases were predominantly imported cases of truck drivers from neighbouring countries. Uganda responded with various restrictions and interventions including lockdown, physical distancing, hand hygiene, and use of face masks in public, to control the growth rate of the outbreak. By end of September 2020, Uganda had transitioned into community transmissions and most of the reported cases were locals contacts and alerts. This study assessed risks associated with SARS-CoV-2 in Uganda, and presents estimates of the reproduction ratio in real time. An optimal control analysis was performed to determine how long the current mitigation measures such as controlling the exposure in communities, rapid detection, confirmation and contact tracing, partial lockdown of the vulnerable groups and control at the porous boarders, could be implemented and at what cost.

Methods

The daily confirmed cases of SARS-CoV-2 in Uganda were extracted from publicly available sources. Using the data, relative risks for age, gender, and geographical location were determined. Four approaches were used to forecast SARS-CoV-2 in Uganda namely linear exponential, nonlinear exponential, logistic and a deterministic model. The discrete logistic model and the next generation matrix method were used to estimate the effective reproduction number.

Results

Results showed that women were at a higher risk of acquiring SARS-CoV-2 than the men, and the population attributable risk of SARS-CoV-2 to women was 42.22%. Most of the women affected by SARS-CoV-2 were likely contacts of cargo truck drivers at the boarders, where high infection rates were reported. Although most deaths in Uganda were in the age group of 60-69, the highest case fatality rate per 1000 was attributable the age group of 80-89, followed by 70-79. Geographically, Amuru had the highest relative risk compared to the national risk to SARS-CoV-2. For the case of mitigation scenarios, washing hands with 70% com pliance and regular hand washing of 6 times a day, was the most effective and sustainable to reduce SARS- CoV-2 exposure. This was followed by public wearing of face masks if at least 60% of the population complied, and physical distancing by 60% of the population. If schools, bars and churches were opened without compliance, i.e., no distancing, no handwashing and no public wearing of face masks, to mitigation measures, the highest incidence was observed, leading to a big replacement number. If mitigation measures are not followed by the population, then there will be high incidences and prevalence of the virus in the population.

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  1. ScreenIT

    SciScore for 10.1101/2020.12.28.20248922: (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

    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: 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.

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  2. Version published to 10.1101/2020.12.28.20248922v1 on medRxiv