Methods: Three SEIR models were developed using the R programming software ODIN interface based on COVID-19 case data from 1 September 2020 to 29 March 2021. The models were validated and subsequently used to provide forecasts of daily cases from 14 October 2020 to 29 March 2021 based on three movement control phases.
Results: We found that the R values had reduced by 59.1% from an initial high of 2.2 during the Nationwide Recovery Movement Control Order (RMCO) to 0.9 during the Movement Control Order (MCO) and Conditional MCO (CMCO) phases. In addition, the observed cumulative and daily highest cases were much lower compared to the forecast cumulative and daily highest cases at 64.4% to 98.9% and 68.8% to 99.8%, respectively.
Conclusion: We conclude that the movement control measures were able to progressively reduce the R values during the COVID-19 pandemic. In addition, more stringent movement control measures such as the MCO and CMCO were effective in reducing the R values and case numbers further during the third wave of COVID-19 outbreak in Malaysia due to their higher stringency levels compared to the Nationwide RMCO.
METHODOLOGY/PRINCIPAL FINDINGS: Spatiotemporal analysis of national notified CHIKV case addresses was performed. Between 2009-2022, 12,446 CHIKV cases were reported, with peaks in 2009 and 2020, and a significant shift from predominantly rural cases in 2009-2011 (85.1% rural), to urban areas in 2017-2022 (86.1% urban; p<0.0001). Two Ae. aegypti strains, field-collected MC1 and laboratory Kuala Lumpur (KL) strains, were fed infectious blood containing constructed CHIKV clones, pCMV-p2020A (E1-226A) and pCMV-p2020V (E1-226V) to measure CHIKV replication by real-time PCR and/or virus titration. The pCMV-p2020A clone replicated better in Ae. aegypti cell line Aag2 and showed higher replication, infection and dissemination efficiency in both Ae. aegypti strains, compared to pCMV-p2020V.
CONCLUSIONS/SIGNIFICANCE: This study revealed that a change in circulating CHIKV variants can be associated with changes in vector competence and outbreak epidemiology. Continued genomic surveillance of arboviruses is important.