Background Indonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can potentially affect their transmissibility, as well as the performance of diagnostics, vaccines, and therapeutics. Objectives We aimed to investigate the dynamics of circulating SARS-CoV-2 variants over a 15-month period in Bogor and its surrounding areas in correlation with the first and second wave of COVID-19 in Indonesia. Methods Nasopharyngeal and oropharyngeal swab samples collected from suspected patients from Bogor, Jakarta and Tangerang were confirmed for SARS-CoV-2 infection with RT-PCR. RNA samples of those confirmed patients were subjected to whole genome sequencing using the ARTIC Network protocol and sequencer platform from Oxford Nanopore Technologies (ONT). Results We successfully identified 16 lineages and six clades out of 202 samples (male n = 116, female n = 86). Genome analysis revealed that Indonesian lineage B.1.466.2 dominated during the first wave (n = 48, 23.8%) while Delta variants (AY.23, AY.24, AY.39, AY.42, AY.43 dan AY.79) were dominant during the second wave (n = 53, 26.2%) following the highest number of confirmed cases in Indonesia. In the spike protein gene, S_D614G and S_P681R changes were dominant in both B.1.466.2 and Delta variants, while N439K was only observed in B.1.466.2 (n = 44) and B.1.470 (n = 1). Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta variants, consistent with those changes being characteristic of Delta variants in general. Conclusions We demonstrated a shift in SARS-CoV-2 variants from the first wave of COVID-19 to Delta variants in the second wave, during which the number of confirmed cases surpassed those in the first wave of COVID-19 pandemic. Higher proportion of unique mutations detected in Delta variants compared to the first wave variants indicated potential mutational effects on viral transmissibility that correlated with a higher incidence of confirmed cases. Genomic surveillance of circulating variants, especially those with higher transmissibility, should be continuously conducted to rapidly inform decision making and support outbreak preparedness, prevention, and public health response.

Background: The opioid receptor μ-1 (OPRM1) has become one of the most studied genes in pharmacogenetics, as this gene encodes the μ-opioid receptor (MOR), which plays a role in opioid drugs response, as well as in various disorders. One of its variants, A118G, which is found at a high frequency in the Asian population, has been associated with loss of sensitivity to and an increased requirement for analgesics in the treatment of pain, increased pain sensitivity, various types of substance dependencies, and the development of breast cancer. However, there are still limited reports about this gene polymorphism in the Indonesian population. Objective: The study aimed to determine the allele frequencies of the OPRM1 A118G polymorphism among the Indonesian population. Method: A cross-sectional study of 158 subjects, comprising 79 males and 79 females, was conducted among Indonesians, and genotype analysis was carried out by a modified allele-specific Polymerase Chain Reaction (PCR) method. Results: A frequency of 60.4% was found for the G allele among Indonesian samples, with a higher frequency being present in males (66.5%). The A allele was found at frequencies of 33.5% and 45.6% in males and females, respectively. A significant difference in allele frequency was found between males and females (p = 0.029, OR = 1.659, 95% CI [1.052–2.614]), while there was no significant difference in genotype frequencies between groups. Conclusion: A high prevalence of the OPRM1 A118G polymorphism was found in the Indonesian population, with the G allele frequency tending to be higher in males.

Opioid receptor mu-1 (OPRM1) A118G gene polymorphism has been widely studied as a strong candidate gene for increasing risk of drug addiction. However, the association is still controversial concerning the effect of A118G polymorphisms on drug addiction seems to be different inter-ethnic. The prevalence of OPRM1 A118G polymorphism is found to be low in the European American population but high in the Asian population. To date, there are very limited reports on this polymorphism in the Indonesian population and its association with drug addiction. Here, we carry out the genotyping of OPRM1 A118G polymorphism in Indonesian population using amplification refractory mutation system polymerase chain reaction (ARMS-PCR) method. The result shows that the OPRM1 A118G polymorphism is relatively higher compared with other Asian countries. When comparing the frequency of the genotype and allele between the normal (n = 83) and the drug-addicted (n = 83) subjects, no significant difference in prevalence was found in neither genotype (p = 0.066, 95% CI [confidence interval]) nor allele (p = 0.432; 95% CI) between the groups. Our results suggest that there is no direct effect of OPRM1 A118G gene polymorphism on the risk of drug addiction (including stimulants, marijuana, and benzodiazepine) among Indonesian; instead, social factors might play a key role.

Recombinant human interferon alpha-2a (hIFNα-2a) is therapeutic protein that widely used in hepatitis B/C and several cancer treatments. We developed higher molecular weight of hIFNα-2a to improve protein pharmacokinetic profile. The protein was designed as a fusion protein with human serum albumin as protein tag. The protein was produced in Pichia pastoris with 85 kDa in size. This research was aimed to purify, characterize and determine the stability expression of open reading frame (ORF) encoding Fusion and Non fusion forms of hIFNα-2a. The proteins were purified using affinity chromatography and characterized using SDS PAGE and Western Blotting methods. Protein recovery yield was determined by ELISA. Stability expression was applied in generation time until 90th generation. The results showed that the Fusion and Non fusion proteins were successfully purified with 74-79% of protein recovery. The proteins can be recognized by specific monoclonal antibody and verified as hIFNα-2a Fusion and Non fusion with 85 kDa and 19 kDa in size respectively. The expression stability showed that the proteins were still produced in Pichia pastoris until 90th generation time with no significant difference of expression level. To conclude, the expression level of ORFs encoding Fusion and Non fusion hIFNα-2a was stable until 90th generations.