Genotypic Analysis of Transmitted and Acquired HIV Drug Resistance in People Living with HIV/AIDS in Surabaya, Indonesia, from 2018 to 2019.

BACKGROUND: Despite the availability of various effective antiretroviral (ARV) drugs, human immunodeficiency virus (HIV) infection has come with HIV drug resistance (HIVDR), which compromises its effectiveness in reducing HIV-related morbidity, mortality, and transmission. The emergence of transmitted (TDR) and acquired HIVDR (ADR) among antiretroviral therapy (ART)-naïve and experienced individuals have been reported in several Indonesian regions. Therefore, continuous HIVDR surveillance is needed in Indonesia, especially in Surabaya, which is identified as having the highest prevalence of HIV infection in East Java; thus, this study aimed to identify the emergence of TDR and ADR among people living with HIV/acquired immune deficiency syndrome (AIDS) (PLWHA). METHODS: Fifty-eight PLWHA infected with HIV type 1 (HIV-1), comprising 21 and 37 ART-naïve and experienced individuals were enrolled in this study, respectively. Blood samples collected from study participants were subjected to genotypic analysis, mainly towards the pol gene encoding protease (PR gene) and reverse transcriptase (RT gene) of HIV-1. RESULTS: Seventeen PR and 21 RT genes were successfully amplified and sequenced from 29 samples. HIV-1 subtyping revealed CRF01_AE as the most dominant subtype (24/29; 82.76%), followed by subtype B (3/29; 10.34%). Uncommon subtypes, including subtype D and a recombinant containing subtypes B and G genomic fragments, were also identified. TDR for PR inhibitors was not detected; however, TDR and ADR for RT inhibitors were identified in 11.11% and 41.67% of samples, respectively. Two amino acid insertions at position 69 of the RT gene (69ins), a previously never-reported mutation in Indonesia, were identified in this study. CONCLUSION: Both TDR and ADR have emerged among PLWHA residing in Surabaya, East Java, Indonesia. Uncommon drug-resistance mutations and subtypes were identified in this study. These situations might hamper ART efficacy and treatment success. Continuous surveillance of HIVDR is necessary to monitor both TDR and ADR in Indonesia.

Spatial-temporal transmission dynamics of HIV-1 CRF01_AE in Indonesia.

Human immunodeficiency virus type 1 (HIV-1) remains a serious health threat in Indonesia. In particular, the CRF01_AE viruses were the predominant HIV-1 strains in various cities in Indonesia. However, information on the dynamic transmission characteristics and spatial-temporal transmission of HIV-1 CRF01_AE in Indonesia is limited. Therefore, the present study examined the spatial-temporal transmission networks and evolutionary characteristics of HIV-1 CRF01_AE in Indonesia. To clarify the epidemiological connection between CRF01_AE outbreaks in Indonesia and the rest of the world, we performed phylogenetic studies on nearly full genomes of CRF01_AE viruses isolated in Indonesia. Our results showed that five epidemic clades, namely, IDN clades 1-5, of CRF01_AE were found in Indonesia. To determine the potential source and mode of transmission of CRF01_AE, we performed Bayesian analysis and built maximum clade credibility trees for each clade. Our study revealed that CRF01_AE viruses were commonly introduced into Indonesia from Southeast Asia, particularly Thailand. The CRF01_AE viruses might have spread through major pandemics in Asian countries, such as China, Vietnam, and Laos, rather than being introduced directly from Africa in the early 1980s. This study has major implications for public health practice and policy development in Indonesia. The contributions of this study include understanding the dynamics of HIV-1 transmission that is important for the implementation of HIV disease control and prevention strategies in Indonesia.

Cytokine profiles of mild-to-moderate SARS-CoV-2 infected and recovered pre-vaccinated individuals residing in Indonesia.

Background: Accumulating evidence suggests the involvement of cytokine-mediated inflammation, in clinical severity and death related to SARS-CoV-2 infection, especially among pre-vaccinated individuals. An increased risk of death was also described among SARS-CoV-2 recovered individuals, which might be correlated with prolonged inflammatory responses. Despite being among the countries with the highest cumulative deaths due to COVID-19, evidence regarding cytokine profiles among SARS-CoV-2 infected and recovered pre-vaccinated individuals in Indonesia is scarce. Thus, this study aimed to describe the cytokines profiles of pre-vaccinated individuals residing in Indonesia, with mild-to-moderate SARS-CoV-2 infection and those who recovered. Methods: Sixty-one sera from 24 hospitalized patients with mild-to-moderate SARS-CoV-2 infection, 24 individuals recovered from asymptomatic-to-moderate SARS-CoV-2 infection, and 13 healthy controls unexposed to SARS-CoV-2 were used in this study. Quantification of serum cytokine levels, including IL-6, IL-8, IP-10, TNF-α, CCL-2, CCL-3, CCL-4, and CXCL-13, was performed using a Luminex multi-analyte-profiling (xMAP)-based assay. Results: The levels of IL-8 along with CCL-2 and CCL-4, were significantly higher (p ≤ 0.01) in hospitalized patients with mild-to-moderate SARS-CoV-2 infection and recovered individuals compared to healthy controls. However, no significant difference was observed in these cytokine levels between infected and recovered individuals. On the other hand, there were no significant differences in several other cytokine levels, including IL-6, IL-10, TNF-α, CCL-3, and CXCL-13, among all groups. Conclusion: IL-8, CCL-2, and CCL-4 were significantly elevated in pre-vaccinated Indonesian individuals with mild-to-moderate SARS-CoV-2 infection and those who recovered. The cytokine profiles described in this study might indicate inflammatory responses not only among SARS-CoV-2 infected, but also recovered individuals.

Seroprevalence of SARS-CoV-2 anti-spike IgG antibody among COVID-19 vaccinated individuals residing in Surabaya, East Java, Indonesia.

Background: To limit the SARS-CoV-2 transmission, the Indonesian government launched a COVID-19 vaccination program in January 2021. Studies on the clinical treatment and implementation of COVID-19 vaccination have shown promising results; however, it is necessary to estimate the effectiveness of the vaccines. With the ongoing COVID-19 pandemic, studies have highlighted the impact of COVID-19 vaccines, especially CoronaVac, on Indonesian healthcare workers. To get a better picture of how the vaccines work in Indonesia, it is necessary to estimate the prevalence of SARS-CoV-2 anti-S IgG antibody induced by the COVID-19 vaccine in individuals who have already received two-to-three doses of vaccines. Materials and Methods: Four-hundred and ninety-six whole-blood samples were collected from participants residing in Surabaya, East Java, Indonesia, who received a minimum of a two-dose COVID-19 vaccine. Serums were then isolated from the blood and subjected to detect SARS-CoV-2 anti-S IgG antibodies using a lateral flow immunochromatographic assay. Results: The prevalence of positive anti-S-IgG antibodies was 91.7% (455/496) in all participants receiving a minimum of a two-dose COVID-19 vaccine. As many as 209 (85.3%) and 141 (96.6%) participants were seropositive for receiving CoronaVac and AstraZeneca, respectively. Meanwhile, all participants receiving two-dose CoronaVac with one booster dose of Moderna (105/100%) were seropositive (p < 0.05). Age, comorbidity, and time after the last vaccine were significantly correlated with seropositivity (p < 0.05). Conclusion: Different vaccines might produce different antibody responses. Adopting a stronger policy regarding the administration of booster doses might be beneficial to elicit positive anti-S-IgG antibodies, especially among older individuals, those with comorbid diseases, and those with a longer time after the second vaccination dose.

Subtype Distribution and Drug Resistance Patterns Among HIV-1 Strains Prevalent in Makassar, Indonesia.

Human immunodeficiency virus type 1 (HIV-1) is characterized by a large degree of genetic variability because of high rates of recombination and mutation, sizable population sizes, and rapid replication. Therefore, this study investigated HIV-1 subtype distribution and the appearance of drug resistance mutations (DRMs) in viruses that are prevalent in Makassar, South Sulawesi, Indonesia. The HIV-1 pol, env, and gag genes were amplified from 63 infected individuals and sequenced for a subtyping analysis. CRF01_AE was identified as the predominant HIV-1 circulating recombinant form (CRF) in Makassar, South Sulawesi, Indonesia. Subtype B and recombinant viruses containing CRF01_AE, CRF02_AG, and/or subtype B gene fragments were also detected. Several major DRMs against non-nucleoside reverse transcriptase inhibitors were found among antiretroviral therapy (ART)-experienced subjects, whereas ART-naive subjects did not possess any transmitted drug resistance. The prevalence of DRMs was very high among ART-experienced subjects; therefore, further surveillance is required in this region.

SARS-CoV-2 IgG antibody status in unvaccinated and 2-dose vaccinated Indonesians by AstraZeneca.

Indonesia began deploying a COVID-19 vaccine in January 2021, prioritising vaccination for high-risk groups such as healthcare workers, the elderly and those with comorbidities, and ending with the general public due to limited vaccine availability. Our study aimed to evaluate antibody response in Indonesians who had received two doses of the vaccine vs. those who had not. The study design was a cohort study involving 46 unvaccinated people and 23 people who had received the second dose of the AstraZeneca vaccine in three months. Methods used for the qualitative and quantitative detection of IgG antibodies included rapid RI-GHA and ELISA tests. Findings showed that positive IgG antibodies qualitatively detected by the rapid RI-GHA test were significantly higher in those vaccinated (60.9%) than in unvaccinated people (26.1%). Using the ELISA assay, all vaccinated individuals qualitatively showed positive antibodies (cut-off ≥4.33 BAU/ml), and the average quantitative titer of anti-SARS-CoV-2 s-RBD IgG was significantly higher in vaccinated (157.06±238.68 BAU/ml) than in unvaccinated (51.90±87.60 BAU/ml) individuals. Some unvaccinated individuals with no history of infection were found to have anti-SARS-CoV-2 antibodies that may have been previously asymptomatic, although their mean antibody titers were certainly lower than those in the 2-dose group. Approximately 56% of vaccinated individuals had antibody titers above 60 BAU/ml as a cut-off for protective threshold, a significantly higher proportion than unvaccinated individuals. In conclusion, vaccination with two doses AstraZeneca increased anti-SARS-CoV-2 antibodies which resulted in enhanced immunity against symptomatic COVID-19.

Viral shedding and the durability of immunoglobulin G antibodies to severe acute respiratory syndrome coronavirus 2.

We followed 45 participants in Surabaya, Indonesia, for 10 months and compared their PCR and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G (IgG) results. As much as 13 out of 45 participants were IgG seropositive at least once while the remaining 32 stayed IgG seronegative throughout the study. Among 13 seropositive participants, 9 were consecutively seropositive at least twice and were eligible for IgG longevity evaluation. The duration of IgG detection varied from 47 to ≥233 days. We observed intermittent re-positive PCR results suggestive of viral shedding in participants with a longer duration of IgG detection.

Seroepidemiological study of SARS-CoV-2 infection in East Java, Indonesia.

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a global pandemic, including Indonesia. However, there are only limited data regarding the precise prevalence of the COVID-19 pandemic in Indonesia. Here, to estimate the magnitude of SARS-CoV-2 infection in East Java, Indonesia, we investigated the prevalence of immunoglobulin G (IgG) antibodies. We enrolled 1,819 individuals from June to December 2020 and observed that the subjects' overall prevalence of IgG antibody to SARS-CoV-2 was 11.4% (207/1,819). The prevalence of anti-SARS-CoV-2 antibodies differed significantly between the job/occupation groups (P = 0.0001). A greater prevalence of IgG was detected in laboratory technicians (who take samples from suspected cases and deal with polymerase chain reaction [PCR] procedures, 22.2%) compared to medical personnel who see and take direct care of patients with COVID-19 (e.g., physicians and nurses, 6.0%), other staff in medical facilities (2.9%), general population (12.1%) and non-COVID-19 patients (14.6%). The highest prevalence among age groups was in the 40-49-year-olds (14.8%), and the lowest prevalence was in the 20-29-year-olds (7.4%). However, the younger population still showed a higher prevalence than generally reported, suggesting greater exposure to the virus but less susceptibility to the disease. A geographical difference was also observed: a higher prevalence in Surabaya (13.1%) than in Jombang (9.9%). In conclusion, the COVID-19 outbreak among asymptomatic populations was characterized by a high prevalence of infection in East Java, Indonesia.

Identification of HIV-1 subtypes and drug resistance mutations among HIV-1-infected individuals residing in Pontianak, Indonesia.

INTRODUCTION: The present study investigated the HIV-1 subtype classification in addition to prevalence of drug resistance mutations (DRMs) in antiretroviral therapy (ART)-experienced and ART-naïve residents of Pontianak, West Kalimantan, Indonesia. METHODS: Whole blood samples collected from 30 HIV-1-infected individuals, comprising 19 ART-experienced and 11 ART-naïve individuals, were subjected to RNA and DNA extraction, followed by HIV-1 genes amplification and sequencing analysis. HIV-1 subtyping was classified on viral pol genes encoding reverse transcriptase (RT gene) and protease (PR gene) accompanied by the env and gag genes. DRMs in the RT and PR genes were also analyzed. RESULTS: CRF01_AE was identified as the predominant circulating recombinant form (CRF) of HIV-1 in both ART-experienced and ART-naïve individuals. In addition, CRF02_AG, subtype B, recombinant virus expressing CRF01_AE and subtype B viral genomic fragments, also recombinant virus containing CRF01_AE and CRF02_AG genomic fragments were also identified. Acquired drug resistance (ADR) was identified in 28.5% of ART-experienced individuals, while no transmitted drug resistance was identified in ART-naïve individuals. CONCLUSIONS: This study identified CRF01_AE as the most predominant HIV-1 CRF distributing in Pontianak, Indonesia. The prevalence of ADR is considered to be high; thus, further surveillance is needed in this region.

Detection of human immunodeficiency virus type 1 transmitted drug resistance among treatment-naive individuals residing in Jakarta, Indonesia.

The presence of transmitted drug resistance (TDR) in human immunodeficiency virus type 1 (HIV-1) infected individuals naive to antiretroviral therapy, may affect the effectiveness of treatment. Jakarta, the capital city of Indonesia, recorded the highest number of cumulative HIV infection cases in the country. This study aimed to identify on the appearance of TDR, as well as to identify HIV-1 subtypes circulating among treatment-naive individuals in Jakarta. Whole blood samples collected from 43 HIV-1 infected, treatment-naive individuals. Viral subtyping and drug resistance testing were performed on HIV-1 pol genes amplified using nested polymerase chain reaction. CRF01_AE was detected most frequently in Jakarta (73.08%). Drug resistance-related major mutation was not detected in protease fragments of pol gene, but two major mutations, K103N (6.67%) and Y181C (6.67%), were detected in reverse transcriptase fragments of pol gene. Our results suggest that TDR was emerged in Jakarta at a certain extent, thus further surveillance study to monitor the TDR prevalence and circulating HIV-1 subtypes in this region is considered to be necessary.

2018-2019 Update on the Molecular Epidemiology of HIV-1 in Indonesia.

The HIV type 1 (HIV-1) epidemic has continued to grow in Indonesia; however, continuous updates on the epidemiology of HIV-1 in Indonesia remain challenging because it is the biggest archipelago in the world. Furthermore, the emergence of HIV drug resistance (HIVDR) has had a negative impact on the treatment of infected individuals. In this study, we performed HIV-1 subtyping and the detection of HIVDR in 105 HIV-1-infected individuals residing in various cities in Indonesia during 2018-2019. The results obtained identified CRF01_AE as the major epidemic HIV-1 strain, responsible for 81.9% of infection cases, followed by subtype B (12.4%), CRF02_AG (3.8%), CRF52_01B (1%), and a recombinant between CRF01_AE and CRF02_AG (1.0%). Major drug resistance-associated mutations against reverse transcriptase inhibitors were detected in 20% of samples. These results suggest that CRF01_AE is a major HIV-1 strain in Indonesia, while CRF02_AG is emerging. The prevalence of HIVDR in Indonesia needs to be monitored.

First Report on HHV-6 Infection Among HIV-Infected Individuals Residing in Surabaya, Indonesia.

BACKGROUND: Morbidity and mortality from acquired immunodeficiency syndrome (AIDS) are often associated with the reactivation of a herpes virus infection. Human herpesvirus-6 (HHV-6) is usually common in childhood infections that remain latent and can act as opportunists during immunosuppression to reactivate and cause disease. In human immunodeficiency virus (HIV)-infected patients, the impact of HHV-6 infection can be an up-regulator of HIV replication and accelerate progress towards AIDS. However, studies on HHV-6 infection have never been done in Surabaya, Indonesia. PURPOSE: To determine the presence of HHV-6 infection among HIV-infected individuals residing in Surabaya, Indonesia. PATIENTS AND METHODS: Plasma and peripheral blood mononuclear cells (PBMCs) were collected from 85 HIV-infected individuals in Universitas Airlangga Hospital, Surabaya, as well as 85 healthy controls. DNA extracted from PBMCs was subjected to PCR to determine HHV-6 infection, while plasma of HIV-infected individuals was used for viral RNA quantification using real-time PCR. RESULTS: HHV-6 infection was detected in 17.6% (15/85) of HIV-infected individuals, and in 3.53% (3/85) of healthy controls. Thus, HHV-6 infection was more likely to be found in HIV-infected individuals than in healthy controls (odds ratio 5.85; 95% confidence interval, 1.6-21). The HHV-6B was the most common subtype identified in both HIV-infected individuals (12/15) and healthy controls (3/3). The HHV-6A and co-infection between HHV-6A and HHV-6B were only found in HIV-infected individuals (2/15 and 1/15, respectively). Viral RNA load of HIV-infected individuals was not correlated to HHV-6 infection. CONCLUSION: Our results indicate the emergence of HHV-6 infection among HIV-infected individuals residing in Surabaya, Indonesia, and the risk of HHV-6 infection was higher in HIV-infected individuals than in healthy controls.

The Emergence of HIV-1 Transmitted Drug Resistance Mutations Among Antiretroviral Therapy-naive Individuals in Buleleng, Bali, Indonesia.

BACKGROUND: the global scale-up of antiretroviral therapy (ART) is the primary factor contributing to the decline in deaths from acquired immune deficiency syndrome (AIDS)-related illnesses. However, the emergence of transmitted drug resistance (TDR) compromises the effects of ART in treatment-naïve individuals, which may hinder treatment success. The present study aimed to identify the presence of TDR among treatment-naive individuals in Buleleng, Bali, which is currently ranked sixth among Indonesian provinces with the highest cumulative human immunodeficiency virus type 1 (HIV-1) infection cases. METHODS: thirty-nine ART-naive individuals in Buleleng Regency General Hospital were enrolled in the present study. Blood samples from participants were subjected to a genotypic analysis. RESULTS: 28 protease (PR) and 30 reverse transcriptase (RT) genes were successfully amplified and sequenced from 37 samples. HIV-1 subtyping revealed CRF01_AE as the dominant circulating recombinant form in the region. No TDR for PR inhibitors was detected; however, TDR for RT inhibitors was identified in five out of 30 samples (16.7%). CONCLUSION: these results indicate the emergence of TDR among ART-naive individuals in Buleleng, Bali. This issue warrants serious consideration because TDR may hamper treatment success and reduce ART efficacy among newly diagnosed individuals. Continuous surveillance with a larger sample size is necessary to monitor TDR among ART-naive individuals.

Genotypic Characterization of Human Immunodeficiency Virus Type 1 Isolated from Antiretroviral Treatment-Experienced Individuals in Buleleng Regency, Bali, Indonesia.

Bali, the first province to report a case of HIV in 1987, was placed sixth among Indonesian provinces with the highest cumulative number of HIV cases in 2017. As a popular tourist destination, the spread of genetic variants of HIV through international travel may become a cause for concern in Bali. Tourism is mostly concentrated in south Bali; thus, HIV in less popular regions in north Bali, such as Buleleng Regency, may have viral characteristics different from that in south Bali. Forty-three protease (PR), 40 reverse transcriptase (RT), 27 gag, and 23 env genes were sequenced from 48 samples derived from antiretroviral treatment-experienced individuals. Subtyping revealed CRF01_AE as the dominant circulating recombinant form of HIV-1 in north Bali. Although no major mutation was detected in PR genes, several major mutations were identified in 4 out of the 40 RT genes (10%), indicating the emergence of HIV-1 drug resistance in this region.

DETECTION OF HUMAN HERPESVIRUS-8 ANTIGEN IN HIV-INFECTED PATIENTS IN EAST JAVA, INDONESIA.

BACKGROUND: Co-infection of human herpesvirus-8 (HHV-8) in HIV-positive people might cause Kaposi's sarcoma. Early detection of HHV-8 may prevent the onset of clinical manifestations. In Indonesia, detection of HHV-8 antigen in HIV-positive patients has yet to be reported. The intention of this research was to examine the presence of HHV-8 antigen in HIV-positive patients in East Java, Indonesia. MATERIAL AND METHODS: 103 serum samples were collected from HIV-positive patients in Surabaya and Tulungagung, East Java, Indonesia. Serums were then tested for the presence of HHV-8 antigen by using sandwich ELISA. RESULTS: Human Herpesvirus-8 antigen was detected in 15 samples (14.5%). The presence of HHV-8 infection in HIV-positive patients did not present differently in males and females and among different age groups. Human immunodeficiency virus-positive serum samples were collected from 23 homosexual men, 25 intravenous drug users (IVDUs) and 52 heterosexuals. In the male homosexual group, HHV-8 antigen was detected in 21.7% (5/23) of the samples, while in the intravenous drug user group (IVDUs), 16% (4/25) of the samples were found to have HHV-8 antigen. CONCLUSION: This research found the presence of HHV-8 antigen in 14.5% of patients in East Java, Indonesia. It is recommended that patients with a positive result should receive further examination to detect any clinical manifestations related to HHV-8 infection, especially in the form of Kaposi's sarcoma lesions, so that the illness can be appropriately managed.