Analysis of SARS-CoV-2 Genomes from West Java, Indonesia

West Java Health Laboratory (WJHL) is one of the many institutions in Indonesia that have sequenced SARS-CoV-2 genome. Although having submitted a large number of sequences since September 2020, however, these submitted data lack advanced analyses. Therefore, in this study, we analyze the variant distribution, hotspot mutation, and its impact on protein structure and function of SARS-CoV-2 from the collected samples from WJHL. As many as one hundred sixty-three SARS-CoV-2 genome sequences submitted by West Java Health Laboratory (WJHL), with collection dates between September 2020 and June 2021, were retrieved from GISAID. Subsequently, the frequency and distribution of non-synonymous mutations across different cities and regencies from these samples were analyzed. The effect of the most prevalent mutations from dominant variants on the stability of their corresponding proteins was examined. The samples mostly consisted of people of working-age, and were distributed between female and male equally. All of the sample sequences showed varying levels of diversity, especially samples from West Bandung which carried the highest diversity. Dominant variants are the VOC B.1.617.2 (Delta) variant, B.1.466.2 variant, and B.1.470 variant. The genomic regions with the highest number of mutations are the spike, NSP3, nucleocapsid, NSP12, and ORF3a protein. Mutation analysis showed that mutations in structural protein might increase the stability of the protein. Oppositely, mutations in non-structural protein might lead to a decrease in protein stability. However, further research to study the impact of mutations on the function of SARS-CoV-2 proteins are required.

RNA sequence analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic patients with COVID-19

OBJECTIVES

The characterization of asymptomatic and mildly symptomatic patients with COVID-19 by observing changes in gene expression profile and possible bacterial coinfection is relevant to be investigated. We aimed to identify transcriptomic and coinfection profiles in both groups of patients.

METHODS

A ribonucleic acid (RNA) sequence analysis on nasopharyngeal swabs were performed using a shotgun sequencing pipeline. Differential gene analysis, viral genome assembly, and metagenomics analysis were further performed using the retrieved data.

RESULTS

Both groups of patients underwent a cilia modification and mRNA splicing. Modulations in macroautophagy, epigenetics, and cell cycle processes were observed specifically in the asymptomatic group. Modulation in the RNA transport was found specifically in the mildly symptomatic group. The mildly symptomatic group showed modulation in the RNA transport and upregulation of autophagy regulator genes and genes in the complement system. No link between viral variants and disease severity was found. Microbiome analysis revealed the elevation of Streptococcus pneumoniae and Veillonella parvula proportion in symptomatic patients.

CONCLUSION

A reduction in the autophagy influx and modification in the epigenetic profile might be involved in halting the disease progression. A global dysregulation of RNA processing and translation might cause more severe outcomes in symptomatic individuals. Coinfection by opportunistic microflora should be taken into account when assessing the possible outcome of SARS-CoV-2 infection.

Malaria elimination in West Java, Indonesia: A descriptive-and-qualitative study

BACKGROUND OBJECTIVES

Following World Health Organization (WHO) plans for thirty-five malaria-endemic countries, Indonesia will eliminate malaria by 2030. As one of the Indonesian provinces, West Java targeted subnational malaria elimination in 2022. This article aims to describe malaria surveillance data and elimination programs, including weaknesses in sustaining the program.

METHODS

This study used secondary data from malaria surveillance information system regencies/cities' case reports for 2019-2022 and achievement data of sub-national malaria elimination certification from each regency/city from 2014-2022. The data was confirmed from the evaluation study document, analysis of reported cases, and interviews.

RESULTS

Most cases were confirmed by microscopic examination (84.1% in 2021 and 94.4% in 2022) and rapid diagnostic tests (57% in 2019 and 58.1% in 2020). Malaria is more prevalent among men (93% in 2019, 95% in 2020, 96% in 2021, and 95.9% in 2022) and productive ages of 15-64 years (98.8% in 2019, 100% in 2020, 99.2% in 2021, and 98.8% in 2022), frequently occurs in the military (56.3% in 2019, 75.7% in 2020, 45.2% in 2021) and police (40.5% in 2022), often uses passive case detection for identifying cases (97.9% in 2019 and 2020, 95.2% in 2021, and 97.6% in 2022), and the majority undergo inpatient treatment (86.4% in 2019, 81.7% in 2021, and 82.6% in 2022). Most positive cases originated from imported cases, and last indigenous cases were still found in 2019. Plasmodium vivax dominated malaria cases and and relapses were high (55.0% in 2020, and 47.3% in 2022).

INTERPRETATION CONCLUSION

All regencies/cities have obtained sub-national malaria elimination certification in 2022. West Java has the potential to be verified for Java-Bali sub-national malaria elimination targeted in 2023, albeit cases of imported malaria still occur. It is imperative to address the issue of imported cases transitioning into locally transmitted cases (introduced) by effective coordination across all regencies/cities and inter-provincial efforts.

Evaluation of a real-time PCR assay performance to detect Mycobacterium tuberculosis, rifampicin, and isoniazid resistance in sputum specimens: a multicenter study in two major cities of Indonesia

Background

Tuberculosis (TB) is one of the major global health issues due to its high mortality rate, especially in low- and middle-income countries. One of the key success points of the TB eradication program is early TB diagnosis, which requires rapid and accurate diagnostic testing. This study aimed to evaluate the performance of a newly developed RT-PCR kit (Indigen MTB/DR-TB RT-PCR) in a routine TB clinical setting.

Method

A multi-fluorescence RT-PCR assay was designed and developed to detect regions within IS6110, rpoB, katG, and inhA of the Mycobacterium tuberculosis (MTB) genes. Sputum specimens were obtained from suspected TB patients who visited TB healthcare facilities in two major cities of Indonesia from September 2022 to May 2023. Specimens were assessed using Indigen MTB/DR-TB RT-PCR, acid-fast bacillus (AFB) smear microscopy, MTB culture, and drug susceptibility testing (DST) methods. Fisher's exact test (χ2) was used to analyze the Indigen performance relative to culture methods.

Result

The performance of Indigen MTB/DR-TB RT-PCR to detect MTB was assessed using 610 sputum specimens obtained from suspected patients. The overall sensitivity and specificity were 94.12% (95% CI: 90.86-96.48%) and 98.32% (95% CI: 96.20-99.46%), respectively. When the analysis was performed on AFB smear-negative TB subjects (386 subjects), a lower sensitivity level was found at 78.57% (95% CI: 68.26-86.78%), while the specificity level remained similar at 98.34% (95% CI: 96.18-99.46%). The overall performance of Indigen MTB/DR-TB RT-PCR to detect MTB showed substantial agreement with the MTB culture method (kappa value 0.93). In comparison to DST, the sensitivity and specificity levels of Indigen to detect RIF resistance or INH resistance were 78.2% (95% CI: 61.8-90.2%) and 82.8% (95% CI: 64.2-94.2%), respectively, while the specificity level for both groups was at 100% (95% CI, 87.7-100%).

Conclusion

Indigen MTB/DR-TB RT-PCR demonstrated reliable performance for TB molecular diagnostic testing and can be implemented in routine TB diagnostic settings.