Quality of National Disease Surveillance Reporting before and during COVID-19: A Mixed-Method Study in Indonesia.

BACKGROUND: Global COVID-19 outbreaks in early 2020 have burdened health workers, among them surveillance workers who have the responsibility to undertake routine disease surveillance activities. The aim of this study was to describe the quality of the implementation of Indonesia's Early Warning and Response Alert System (EWARS) for disease surveillance and to measure the burden of disease surveillance reporting quality before and during the COVID-19 epidemic in Indonesia. METHODS: A mixed-method approach was used. A total of 38 informants from regional health offices participated in Focus Group Discussion (FGD) and In-Depth Interview (IDI) for informants from Ministry of Health. The FGD and IDI were conducted using online video communication. Yearly completeness and timeliness of reporting of 34 provinces were collected from the application. Qualitative data were analyzed thematically, and quantitative data were analyzed descriptively. RESULTS: Major implementation gaps were found in poorly distributed human resources and regional infrastructure inequity. National reporting from 2017-2019 showed an increasing trend of completeness (55%, 64%, and 75%, respectively) and timeliness (55%, 64%, and 75%, respectively). However, the quality of the reporting dropped to 53% and 34% in 2020 concomitant with the SARS-CoV2 epidemic. CONCLUSIONS: Report completeness and timeliness are likely related to regional infrastructure inequity and the COVID-19 epidemic. It is recommended to increase report capacities with an automatic EWARS application linked systems in hospitals and laboratories.

Seroprevalence of SARS-CoV-2 antibodies in Bali Province: Indonesia shows underdetection of COVID-19 cases by routine surveillance.

The international tourist destination of Bali reported its first case of Coronavirus Disease 2019 or COVID-19 in March 2020. To better understand the extent of exposure of Bali's 4.3 million inhabitants to the COVID-19 virus, we performed two repeated cross-sectional serosurveys stratified by urban and rural areas. We used a highly specific multiplex assay that detects antibodies to three different viral antigens. We also assessed demographic and social risk factors and history of symptoms. Our results show that the virus was widespread in Bali by late 2020, with 16.73% (95% CI 12.22-21.12) of the population having been infected by that time. We saw no differences in seroprevalence between urban and rural areas, possibly due to extensive population mixing, and similar levels of seroprevalence by gender and among age groups, except for lower seroprevalence in the very young. We observed no difference in seroprevalence between our two closely spaced surveys. Individuals reporting symptoms in the past six months were about twice as likely to be seropositive as those not reporting symptoms. Based upon official statistics for laboratory diagnosed cases for the six months prior to the survey, we estimate that for every reported case an additional 52 cases, at least, were undetected. Our results support the hypothesis that by late 2020 the virus was widespread in Bali, but largely undetected by surveillance.

Recombinant viruses initiated the early HIV-1 epidemic in Burkina Faso.

We analyzed genetic diversity and phylogenetic relationships among 124 HIV-1 and 19 HIV-2 strains in sera collected in 1986 from patients of the state hospital in Ouagadougou, Burkina Faso. Phylogenetic analysis of the HIV-1 env gp41 region of 65 sequences characterized 37 (56.9%) as CRF06_cpx strains, 25 (38.5%) as CRF02_AG, 2 (3.1%) as CRF09_cpx, and 1 (1.5%) as subtype A. Similarly, phylogenetic analysis of the protease (PR) gene region of 73 sequences identified 52 (71.2%) as CRF06_cpx, 15 (20.5%) as CRF02_AG, 5 (6.8%) as subtype A, and 1 (1.4%) was a unique strain that clustered along the B/D lineage but basal to the node connecting the two lineages. HIV-2 PR or integrase (INT) groups A (n = 17 [89.5%]) and B (n = 2 [10.5%]) were found in both monotypic (n = 11) and heterotypic HIV-1/HIV-2 (n = 8) infections, with few HIV-2 group B infections. Based on limited available sampling, evidence suggests two recombinant viruses, CRF06_cpx and CRF02_AG, appear to have driven the beginning of the mid-1980s HIV-1 epidemic in Burkina Faso.