The COVID-19 pandemic has resulted in massive global disruptions with considerable impact on the delivery of health services and national health programmes. Since the detection of the first COVID-19 case on 5th March 2020, the Royal Government of Bhutan implemented a number of containment measures including border closure and national lockdowns. Against the backdrop of this global COVID-19 pandemic response, there was a sudden surge of locally-transmitted malaria cases between June to August 2020. There were 20 indigenous cases (zero Plasmodium falciparum and 20 Plasmodium vivax) from a total of 49 cases (seven P. falciparum and 42 P. vivax) in 2020 compared to just two from a total of 42 in 2019. Over 80% of the cases were clustered in malaria endemic district of Sarpang. This spike of malaria cases was attributed to the delay in the delivery of routine malaria preventive interventions due to the COVID-19 pandemic. As a result, Bhutan is unlikely to achieve the national goal of malaria elimination by 2020.

Malaria in Bhutan has fallen significantly over the last decade. As Bhutan attempts to eliminate malaria in 2022, this study aimed to characterize the space–time clustering of malaria from 2010 to 2019. Malaria data were obtained from the Bhutan Vector-Borne Disease Control Program data repository. Spatial and space–time cluster analyses of Plasmodium falciparum and Plasmodium vivax cases were conducted at the sub-district level from 2010 to 2019 using Kulldorff’s space–time scan statistic. A total of 768 confirmed malaria cases, including 454 (59%) P. vivax cases, were reported in Bhutan during the study period. Significant temporal clusters of cases caused by both species were identified between April and September. The most likely spatial clusters were detected in the central part of Bhutan throughout the study period. The most likely space–time cluster was in Sarpang District and neighboring districts between January 2010 to June 2012 for cases of infection with both species. The most likely cluster for P. falciparum infection had a radius of 50.4 km and included 26 sub-districts with a relative risk (RR) of 32.7. The most likely cluster for P. vivax infection had a radius of 33.6 km with 11 sub-districts and RR of 27.7. Three secondary space–time clusters were detected in other parts of Bhutan. Spatial and space–time cluster analysis identified high-risk areas and periods for both P. vivax and P. falciparum malaria. Both malaria types showed significant spatial and spatiotemporal variations. Operational research to understand the drivers of residual transmission in hotspot sub-districts will help to overcome the final challenges of malaria elimination in Bhutan.