Is Nigeria really on top of COVID-19? Message from effective reproduction number
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Abstract
Following the importation of Covid-19 into Nigeria on the 27 February 2020 and then the outbreak, the question is: how do we anticipate the progression of the ongoing epidemics following all the intervention measures put in place? This kind of question is appropriate for public health responses and it will depend on the early estimates of the key epidemiological parameters of the virus in a defined population. In this study, we combined a likelihood-based method using a Bayesian framework and compartmental model of the epidemic of Covid-19 in Nigeria to estimate the effective reproduction number (R(t)) and basic reproduction number (R_0). This also enables us to estimate the daily transmission rate (β) that determines the effect of social distancing. We further estimate the reported fraction of symptomatic cases. The models are applied to the NCDC data on Covid-19 symptomatic and death cases from 27 February 2020 and 7 May 2020. In this period, the effective reproduction number is estimated with a minimum value of 0.18 and a maximum value of 1.78. Most importantly, the R(t) is strictly greater than one from April 13 till 7 May 2020. The R_0 is estimated to be 2.42 with credible interval: (2.37, 2.47). Comparing this with the R(t) shows that control measures are working but not effective enough to keep R(t) below one. Also, the estimated fractional reported symptomatic cases are between 10 to 50%. Our analysis has shown evidence that the existing control measures are not enough to end the epidemic and more stringent measures are needed.
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SciScore for 10.1101/2020.05.16.20104471: (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: We detected the following sentences addressing limitations in the study:The results presented in this study should be interpreted as a guild line with the following caveats in mind. First, imported cases are not reported daily. Considering the porosity of Nigeria borders, we expect more imported cases to be coming from other neighbouring African countries by land (8, 19, 20). Inadequate reporting may affect …
SciScore for 10.1101/2020.05.16.20104471: (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: We detected the following sentences addressing limitations in the study:The results presented in this study should be interpreted as a guild line with the following caveats in mind. First, imported cases are not reported daily. Considering the porosity of Nigeria borders, we expect more imported cases to be coming from other neighbouring African countries by land (8, 19, 20). Inadequate reporting may affect our estimates as we might have overestimated the burden of the pandemic because more imported cases that have not been counted probably contributed to the transmission. Under-reporting of local cases also occurs (proportion symptomatic showed that the reporting rate is between 10% and 50%.), however, this is less likely to affect our estimate, because underreporting of local cases will have a multiplier effect on both force of infection and new cases, which cancels out for the estimation of the effective reproduction number. The difference between imported and local cases explains why our estimate of effective reproduction in Figure 1A is far different from the one in Figure 3. Second, the role of asymptomatic patients in the dynamic of Covid-19 has not been fully understood (21, 22). There is evidence that these group of people contributes to the transmission process (12, 21, 22). Though we included them in our compartmental model, the likelihood model does not adjust for asymptomatic patients. This may impair the estimates as what we thought as under-reporting may be many asymptomatic patients who are fueling transmission and cannot be accou...
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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