Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center study.

We determined the prevalence and epidemiological characteristics of COVID-19 in Jakarta and neighboring areas, Indonesia from March 2020 to February 2021, based on nasopharyngeal/oropharyngeal (NP/OP) swab specimens that were tested at the Eijkman Institute for Molecular Biology, Jakarta. NP/OP swab specimens were collected from COVID-19 suspects or individuals in contact tracing programs from primary healthcare centers (PHC) and hospitals. The specimens were screened for the SARS-CoV-2 by qRT-PCR. Demography data and clinical symptoms were collected using national standardized laboratory form. Of 64,364 specimens, 10,130 (15.7%) were confirmed positive for SARS-CoV-2, with the peak prevalence of infection in March 2020 (26.3%) follow by in January 2021 (23.9%) and February 2021 (21.8%). We found that the positivity rate of the specimens from Jakarta, West Java, and Banten was 16.3%, 13.3%, and 16.8%, respectively. Positivity rate was higher in specimens from hospitals (16.9%) than PHC (9.4%). Of the positive specimens, 29.6% were from individuals aged >60 years old, followed by individuals aged 41-60 years old (24.2%). Among symptomatic cases of SARS-CoV-2, the most common symptoms were cough, fever, and a combination of both cough & fever. In conclusion, this study illustrates the prevalence and epidemiological characteristics from one COVID-19 diagnostic center in Jakarta and neighbouring areas in Indonesia.

Immunogenicity and Reactogenicity of CoronaVac: A Cohort Study

The ongoing COVID-19 pandemic remained a major public health concern despite a large-scale deployment of vaccines. One of the vaccines is CoronaVac, an inactivated vaccine. The efficacy of the vaccine was estimated at 50.7–83.5% in clinical trials. However, the real-world efficacy often differed. This study described CoronaVac post-vaccination reactogenicity and immunogenicity. Serum was collected on days 0, 28, 56 and 84 from participants who received CoronaVac in March–May 2021. Anti-SARS-CoV-2 Spike receptor binding domain was measured using an Elecsys®quantitative assay. Participants were interviewed for adverse events (AEs) one week after vaccination. Reported AEs were fatigue, fever, runny nose, headache, muscle pain, pain at injection site, and paresthesia. Females reported more incidents than males. However, the frequency was similar between immunologically naïve and pre-immune participants. In the naïve group, the antibody titer was 61.7 ±84.2 U/mL (mean ±SD) on day 28 and increased to 99.3 ±91.9 U/mL on day 56. The titer peaked on day 56 across all age groups, but a reduction of 18.0–26.3% was observed on day 84. A titer-boosting effect was observed in pre-immune participants with a baseline titer of 139.0 ±101.0 U/mL, which increased to 206.7 ±77.4 U/mL on day 28, and remained steady until day 84. Hence, CoronaVac elicited an antibody response in naïve and pre-immune participants, with mild AEs.

Whole-Genome Sequencing of SARS-CoV-2 Infection in a Cluster of Immunocompromised Children in Indonesia.

Background: Thus far, Indonesia has recorded over 4,000,000 confirmed COVID-19 cases and 144,000 fatalities; 12.8% of cases have been in children under 18 years. Whole-genome viral sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been demonstrated to help differentiate hospital-acquired infection from community-acquired coronavirus disease 2019 (COVID-19) infection. Our study highlighted the use of WGS to investigate the origin of infection among pediatric oncology patients in Jakarta. The aim of our study was to evaluate clinical and laboratory characteristics and also the efficacy of using WGS to confirm hospital-acquired COVID-19 infection in a cluster of immunocompromised children within a single ward of a tertiary hospital in metropolitan Jakarta based on quasispecies, viral load, and admission dates. Method: Real-time reverse-transcription polymerase chain reaction (RT-PCR) from nasopharyngeal (NP) swabs was used to diagnose the patients and also guardians and healthcare workers (HCWs) in the ward, followed by WGS of RT-PCR positive cases to establish their phylogenetic relationships. Result: Using WGS, we showed that SARS-CoV-2 transmission in a cluster of children with underlying malignancy was characterized by high similarity of whole virus genome, which suggests nosocomial transmission.