Apoptosis and Phagocytosis as Antiviral Mechanisms.

Viruses are infectious entities that make use of the replication machinery of their hosts to produce more progenies, causing disease and sometimes death. To counter viral infection, metazoan hosts are equipped with various defense mechanisms, from the rapid-evoking innate immune responses to the most advanced adaptive immune responses. Previous research demonstrated that cells in fruit flies and mice infected with Drosophila C virus and influenza, respectively, undergo apoptosis, which triggers the engulfment of apoptotic virus-infected cells by phagocytes. This process involves the recognition of eat-me signals on the surface of virus-infected cells by receptors of specialized phagocytes, such as macrophages and neutrophils in mice and hemocytes in fruit flies, to facilitate the phagocytic elimination of virus-infected cells. Inhibition of phagocytosis led to severe pathologies and death in both species, indicating that apoptosis-dependent phagocytosis of virus-infected cells is a conserved antiviral mechanism in multicellular organisms. Indeed, our understanding of the mechanisms underlying apoptosis-dependent phagocytosis of virus-infected cells has shed a new perspective on how hosts defend themselves against viral infection. This chapter explores the mechanisms of this process and its potential for developing new treatments for viral diseases.

Efficacy, Immunogenicity, and Safety of COVID-19 Vaccines in Patients with Autoimmune Diseases: A Systematic Review and Meta-Analysis.

Patients with autoimmune diseases are among the susceptible groups to COVID-19 infection because of the complexity of their conditions and the side effects of the immunosuppressive drugs used to treat them. They might show impaired immunogenicity to COVID-19 vaccines and have a higher risk of developing COVID-19. Using a systematic review and meta-analysis, this research sought to summarize the evidence on COVID-19 vaccine efficacy, immunogenicity, and safety in patients with autoimmune diseases following predefined eligibility criteria. Research articles were obtained from an initial search up to 26 September 2022 from PubMed, Embase, EBSCOhost, ProQuest, MedRxiv, bioRxiv, SSRN, EuroPMC, and the Cochrane Center of Randomized Controlled Trials (CCRCT). Of 76 eligible studies obtained, 29, 54, and 38 studies were included in systematic reviews of efficacy, immunogenicity, and safety, respectively, and 6, 18, and 4 studies were included in meta-analyses for efficacy, immunogenicity, and safety, respectively. From the meta-analyses, patients with autoimmune diseases showed more frequent breakthrough COVID-19 infections and lower total antibody (TAb) titers, IgG seroconversion, and neutralizing antibodies after inactivated COVID-19 vaccination compared with healthy controls. They also had more local and systemic adverse events after the first dose of inactivated vaccination compared with healthy controls. After COVID-19 mRNA vaccination, patients with autoimmune diseases had lower TAb titers and IgG seroconversion compared with healthy controls.

Monkeypox: A Comprehensive Review.

The 2022 multi-country monkeypox outbreak in humans has brought new public health adversity on top of the ongoing coronavirus disease 2019 (COVID-19) pandemic. The disease has spread to 104 countries throughout six continents of the world, with the highest burden in North America and Europe. The etiologic agent, monkeypox virus (MPXV), has been known since 1959 after isolation from infected monkeys, and virulence among humans has been reported since the 1970s, mainly in endemic countries in West and Central Africa. However, the disease has re-emerged in 2022 at an unprecedented pace, with particular concern on its human-to-human transmissibility and community spread in non-endemic regions. As a mitigation effort, healthcare workers, public health policymakers, and the general public worldwide need to be well-informed on this relatively neglected viral disease. Here, we provide a comprehensive and up-to-date overview of monkeypox, including the following aspects: epidemiology, etiology, pathogenesis, clinical features, diagnosis, and management. In addition, the current review discusses the preventive and control measures, the latest vaccine developments, and the future research areas in this re-emerging viral disease that was declared as a public health emergency of international concern.

Perceived risk of infection and death from COVID-19 among community members of low- and middle-income countries: A cross-sectional study.

Background: Risk perceptions of coronavirus disease 2019 (COVID-19) are considered important as they impact community health behaviors. The aim of this study was to determine the perceived risk of infection and death due to COVID-19 and to assess the factors associated with such risk perceptions among community members in low- and middle-income countries (LMICs) in Africa, Asia, and South America. Methods: An online cross-sectional study was conducted in 10 LMICs in Africa, Asia, and South America from February to May 2021. A questionnaire was utilized to assess the perceived risk of infection and death from COVID-19 and its plausible determinants. A logistic regression model was used to identify the factors associated with such risk perceptions. Results: A total of 1,646 responses were included in the analysis of the perceived risk of becoming infected and dying from COVID-19. Our data suggested that 36.4% of participants had a high perceived risk of COVID-19 infection, while only 22.4% had a perceived risk of dying from COVID-19. Being a woman, working in healthcare-related sectors, contracting pulmonary disease, knowing people in the immediate social environment who are or have been infected with COVID-19, as well as seeing or reading about individuals infected with COVID-19 on social media or TV were all associated with a higher perceived risk of becoming infected with COVID-19. In addition, being a woman, elderly, having heart disease and pulmonary disease, knowing people in the immediate social environment who are or have been infected with COVID-19, and seeing or reading about individuals infected with COVID-19 on social media or TV had a higher perceived risk of dying from COVID-19. Conclusions: The perceived risk of infection and death due to COVID-19 are relatively low among respondents; this suggests the need to conduct health campaigns to disseminate knowledge and information on the ongoing pandemic.

Molnupiravir: A lethal mutagenic drug against rapidly mutating severe acute respiratory syndrome coronavirus 2-A narrative review.

Broad-spectrum antiviral agents targeting viral RNA-dependent RNA polymerase (RdRp) are expected to be a key therapeutic strategy in the ongoing coronavirus disease 2019 (COVID-19) pandemic and its future variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19. Molnupiravir is a nucleoside analog that in vivo experiments have been reported to inhibit the replication of SARS-CoV-2, the virus that causes COVID-19. Clinical trials of molnupiravir as a therapy for patients with mild-to-moderate COVID-19 also suggest its significant therapeutic efficacy in comparison to placebo. Molnupiravir is lethally mutagenic against viral RNA, but its effect on host cell DNA is being questioned. Herein, the safety concerns of molnupiravir are discussed with recent findings from published reports and clinical trials. The unchanged efficacy of molnupiravir against mutated SARS-CoV-2 variants is also highlighted. With its administration via the oral route, molnupiravir is expected to turn the tide of the COVID-19 pandemic.

Monkeypox: Immune response, vaccination and preventive efforts.

Infectious threats to humans are continuously emerging. The 2022 worldwide monkeypox outbreak is the latest of these threats with the virus rapidly spreading to 106 countries by the end of September 2022. The burden of the ongoing monkeypox outbreak is manifested by 68,000 cumulative confirmed cases and 26 deaths. Although monkeypox is usually a self-limited disease, patients can suffer from extremely painful skin lesions and complications can occur with reported mortalities. The antigenic similarity between the smallpox virus (variola virus) and monkeypox virus can be utilized to prevent monkeypox using smallpox vaccines; treatment is also based on antivirals initially designed to treat smallpox. However, further studies are needed to fully decipher the immune response to monkeypox virus and the immune evasion mechanisms. In this review we provide an up-to-date discussion of the current state of knowledge regarding monkeypox virus with a special focus on innate immune response, immune evasion mechanisms and vaccination against the virus.

Relapse prevention group therapy via video-conferencing for substance use disorder: protocol for a multicentre randomised controlled trial in Indonesia.

BACKGROUND: Substance use disorder (SUD) is a leading contributor to the global burden of disease. In Indonesia, the availability of formal treatment for SUD falls short of the targeted coverage. A standardised therapeutic option for SUD with potential for widespread implementation is required, yet evidence-based data in the country are scarce. In this study, we developed a cognitive behavioural therapy (CBT)-based group telemedicine model and will investigate effectiveness and implementability in a multicentre randomised controlled trial. METHODS: A total of 220 participants will be recruited from the social networks of eight sites in Indonesia: three hospitals, two primary healthcare centres and three rehabilitation centres. The intervention arm will participate in a relapse prevention programme called the Indonesia Drug Addiction Relapse Prevention Programme (Indo-DARPP), a newly developed 12-week module based on CBT and motivational interviewing constructed in the Indonesian context. The programme will be delivered by a healthcare provider and a peer counsellor in a group therapy setting via video-conferencing, as a supplement to participants' usual treatments. The control arm will continue treatment as usual. The primary outcome will be the percentage increase in days of abstinence from the primarily used substance in the past 28 days. Secondary outcomes will include addiction severity, quality of life, motivation to change, psychiatric symptoms, cognitive function, coping, and internalised stigma. Assessments will be performed at baseline (week 0), post-treatment (week 13), and 3 and 12 months post-treatment completion (weeks 24 and 60). Retention, participant satisfaction, and cost-effectiveness will be assessed as the implementation outcomes. ETHICS AND DISSEMINATION: The study protocol was reviewed and approved by the Ethics Committees of Universitas Indonesia and Kyoto University. The results will be disseminated via academic journals and international conferences. Depending on trial outcomes, the treatment programme will be advocated for adoption as a formal healthcare-based approach for SUD. TRIAL REGISTRATION NUMBER: UMIN000042186.

Designing an epitope vaccine against Dermatophagoides pteronyssinus: An in silico study.

The house dust mite, Dermatophagoides pteronyssinus, is a major source of the inhaled allergen Der p 1, which causes immunoglobulin E (IgE)-mediated hypersensitivity reactions manifesting in allergic diseases. To date, no drugs or vaccines effectively treat or prevent Der p 1 sensitization. We applied in silico immunoinformatics to design T-cell and B-cell epitopes that were specified and developed from the allergen Der p 1 of D. pteronyssinus. We identified the conserved epitope areas by predicting the accessibility and flexibility of B-cell epitopes, and the percentage of human leukocyte antigen representing T cells. Molecular docking using HADDOCK software indicated three optimal clusters: cluster 6 (z-score: -2.1), cluster 1 (z-score: -1.2), and cluster 3 (z-score: -0.6). The most negative Z-score was found in cluster 6, which represented three epitopes. The interaction between A chain proteins (IgE protein residues) and B chains (Der p 1 protein residues) exhibited a knowledge-based FADE and contact value >1, suggesting the best protein interactions occurred in the conserved area. Molecular dynamic simulation further predicted the stable nature of Der p 1 protein. The IQRDNGYQP region is the best candidate to be utilized as a D. pteronyssinus epitope vaccine, which could be used in the development of allergen-specific immunotherapy.

Global prevalence of prolonged gastrointestinal symptoms in COVID-19 survivors and potential pathogenesis: A systematic review and meta-analysis.

Background: This study aimed to determine the cumulative prevalence of prolonged gastrointestinal (GI) symptoms, including nausea, vomiting, diarrhea, lack of appetite, abdominal pain, and dysgeusia, in survivors of both mild and severe COVID-19 worldwide and to discuss the potential pathogenesis.   Methods: Three databases (PubMed, Scopus, and Web of Science) were searched for relevant articles up to January 30, 2021. Data on study characteristics, clinical characteristics during follow-up, the number of patients with prolonged GI symptoms, and total number of COVID-19 survivors were retrieved according to PRISMA guidelines. The quality of eligible studies was assessed using the Newcastle-Ottawa scale. The pooled prevalence of specific prolonged GI symptoms was calculated and the association between COVID-19 severity and the occurrence of prolonged GI symptoms was assessed if appropriate.   Results: The global prevalence of prolonged nausea was 3.23% (95% CI: 0.54%-16.53%) among 527 COVID-19 survivors. Vomiting persisted in 93 of 2,238 COVID-19 survivors (3.19%, 95% CI: 1.62%-6.17%) and prolonged diarrhea was found in 34 of 1,073 survivors (4.12%, 95% CI: 1.07%-14.64%). A total of 156 patients among 2,238 COVID-19 survivors (4.41%, 95% CI: 1.91%-9.94%) complained of persistent decreased or loss of appetite. The cumulative prevalence of prolonged abdominal pain was 1.68% (95% CI: 0.84%-3.32%), whereas persistent dysgeusia was identified in 130 cases among 1,887 COVID-19 survivors (7.04%, 95% CI: 5.96%-8.30%). Data was insufficient to assess the relationship between COVID-19 severity and the occurrence of all prolonged GI symptoms.   Conclusion: Persistent GI symptoms among COVID-19 survivors after discharge or recovery raises a concern regarding the long-term impact of the COVID-19 infection on the quality of life of the survivors. Despite several potential explanations proposed, studies that aim to follow patients after recovery from COVID-19 and determine the pathogenesis of the prolonged symptoms of COVID-19 survivors are warranted.   PROSPERO registration: CRD42021239187.

Anosmia and dysgeusia in SARS-CoV-2 infection: incidence and effects on COVID-19 severity and mortality, and the possible pathobiology mechanisms - a systematic review and meta-analysis.

Background: The present study aimed to determine the global prevalence of anosmia and dysgeusia in coronavirus disease 2019 (COVID-19) patients and to assess their association with severity and mortality of COVID-19. Moreover, this study aimed to discuss the possible pathobiological mechanisms of anosmia and dysgeusia in COVID-19. Methods: Available articles from PubMed, Scopus, Web of Science, and preprint databases (MedRxiv, BioRxiv, and Researchsquare) were searched on November 10th, 2020. Data on the characteristics of the study (anosmia, dysgeusia, and COVID-19) were extracted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. Newcastle-Ottawa scale was used to assess research quality. Moreover, the pooled prevalence of anosmia and dysgeusia were calculated, and the association between anosmia and dysgeusia in presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was assessed using the Z test. Results: Out of 32,142 COVID-19 patients from 107 studies, anosmia was reported in 12,038 patients with a prevalence of 38.2% (95% CI: 36.5%, 47.2%); whereas, dysgeusia was reported in 11,337 patients out of 30,901 COVID-19 patients from 101 studies, with prevalence of 36.6% (95% CI: 35.2%, 45.2%), worldwide. Furthermore, the prevalence of anosmia was 10.2-fold higher (OR: 10.21; 95% CI: 6.53, 15.96, p < 0.001) and that of dysgeusia was 8.6-fold higher (OR: 8.61; 95% CI: 5.26, 14.11, p < 0.001) in COVID-19 patients compared to those with other respiratory infections or COVID-19 like illness. To date, no study has assessed the association of anosmia and dysgeusia with severity and mortality of COVID-19. Conclusion: Anosmia and dysgeusia are prevalent in COVID-19 patients compared to those with the other non-COVID-19 respiratory infections. Several possible mechanisms have been hypothesized; however, future studies are warranted to elucidate the definitive mechanisms of anosmia and dysgeusia in COVID-19. Protocol registration: PROSPERO CRD42020223204.

Persistence of long COVID symptoms in COVID-19 survivors worldwide and its potential pathogenesis - A systematic review and meta-analysis.

The study sought to determine the prevalence of persistent long COVID symptoms such as anxiety, depression, dizziness, chest pain, sleep difficulty, palpitations, weight loss, and hair loss among coronavirus disease 2019 (COVID-19) survivors worldwide and to discuss the potential pathogeneses. Potential studies were searched in three databases (PubMed, Scopus, and Web of Science) as of January 30, 2021. Data on study characteristics, patient characteristics during the follow-up, the number of patients with persistent long COVID symptoms and total COVID-19 survivors were collected according to PRISMA guidelines. To assess the quality of studies, the Newcastle-Ottawa scale was used. The estimated prevalence of each long COVID symptom and the association between COVID-19 severity and the occurrence of prolonged symptoms was assessed, if appropriate. The global prevalence of prolonged anxiety was 15.76% (95%CI: 6.36%, 25.15%). Chest pain persisted in 10.36% (239/3,224) of COVID-19 patients (95%CI: 4.92%, 15.80%). Prolonged depression was found in 24 of 548 COVID-19 survivors with an estimated prevalence of 4.32% (95%CI: 2.62%, 6.03%) and dizziness was presented in 4.83% (118/2,219, 95%CI: 1.50%, 8.16%) after recovery. Hair loss was complained by 527 of 2,251 recovered patients (cumulative prevalence of 24.76%, 95%CI: 19.60%, 29.91%), while weight loss was identified in 37 cases among 452 COVID-19 survivors (8.19%, 95%CI: 5.66%, 10.71%). Prolonged palpitation was experienced by 19.38% (211/1,926) survivors with 95%CI: 2.40%, 41.16%. Sleep difficulty was found in 541 of 2,622 COVID-19 survivors (17.87%, 95%CI: 7.55%, 28.20%). The association between COVID-19 severity and the occurrence of persistent long COVID symptoms was not analyzed due to the lack of data. In conclusion, persistent psychological symptoms are frequently reported among COVID-19 survivors. Follow-up studies with a longer duration and larger population are warranted to assess the extent of prolonged symptoms and the quality of life of COVID-19 survivors. Despite various potential pathogeneses that have been hypothesized, a definitive mechanism is yet to be addressed. PROSPERO registration: CRD42021247172.

Global prevalence of persistent neuromuscular symptoms and the possible pathomechanisms in COVID-19 recovered individuals: A systematic review and meta-analysis.

This study was conducted to determine the prevalence of prolonged neuromuscular symptoms, including fatigue, anosmia, headache, myalgia, and joint pain in COVID-19 survivors hospitalized with mild, moderate, or severe infections worldwide. The search was conducted up to January 30th, 2021 using three databases (PubMed, Scopus, and Web of Science) to identify potentially eligible studies. Data on study characteristics, follow-up characteristics, and severity of COVID-19 during hospitalization were collected in accordance with PRISMA guidelines. The Newcastle-Ottawa scale was used to assess the quality of relevant articles. The estimated prevalence of specific prolonged neuromuscular symptoms and the association between COVID-19 severity and occurrence of prolonged neuromuscular symptoms was analyzed wherever appropriate. Database search yielded 4,050 articles and 22 articles were included for meta-analysis. The estimated prevalence of prolonged fatigue was recorded in 21.2% (95%CI: 11.9%- 34.8%) of 3,730 COVID-19 survivors. Persistent anosmia was recorded in 239 of 2,600 COVID-19 survivors (9.7%, 95%CI: 6.1%-15.2%). In 84 out of 2,412 COVID-19 survivors (8.9%, 95%CI: 3.2%-22.6%), prolonged headache was observed. A total of 53 out of 1,125 COVID-19 patients (5.6%, 95%CI: 2.1%-14.2%) complained of persistent myalgia even after being discharged from the hospital. The prevalence of prolonged joint pain was in 15.4% (95%CI: 8.2%-27.2%) of subjects. Due to data scarcity on COVID-19 severity and prolonged neuromuscular symptoms, association analysis could not be conducted. Widespread concern regarding long-term impacts of COVID-19 was raised after several studies reported prolonged symptoms in COVID-19 survivors. Numerous theories have been proposed to address this concern; however, as the research on this pandemic is still ongoing, no explanation is definitive yet. Therefore, follow-up studies in COVID-19 survivors after recovery from COVID-19 are warranted to determine the pathogenesis of prolonged symptoms. PROSPERO registration: CRD42021242332.

COVID-19 Vaccines: Current Status and Implication for Use in Indonesia.

The coronavirus disease 2019 (COVID-19) has inflicted catastrophic damages in public health, economic and social stability-putting life globally on hold in 2020 and presumably a year more. Indonesia bears a heavy burden of the pandemic, counting the highest case prevalence and fatality rate in all of Southeast Asia. One hope remains in the groundbreaking universal effort in search of a vaccine against the causative virus SARS-CoV-2, which has shown success unparalleled in human vaccine development thus far. An array of modalities including novel techniques are being utilized as vaccine platforms, with the closest to phase III clinical trial completion being mRNA (manufactured by Moderna and BioNTech/Pfizer), inactivated virus (Sinovac, Sinopharm), viral vector (Oxford/AstraZeneca, Gamaleya, Janssen/Johnson&Johnson, CanSino), and protein subunit (Novavax). The vaccine produced by BioNTech/Pfizer has been deployed to the public as the first ever licensed COVID-19 vaccine. In this review, we will review all of these modalities on their safety and immunogenicity, phase II/III trial results of the nine vaccine candidates and current situation as of 29 December 2020, as well as the implication for use and distribution in Indonesia. COVID-19 vaccine progress, however, is moving exceedingly fast and new advances are unfolding on a daily basis, to which we hope an update to this review can be published in early 2021.

Multiplexed tat-Targeting CRISPR-Cas9 Protects T Cells from Acute HIV-1 Infection with Inhibition of Viral Escape.

HIV-1 cure strategy by means of proviral knock-out using CRISPR-Cas9 has been hampered by the emergence of viral resistance against the targeting guide RNA (gRNA). Here, we proposed multiple, concentrated gRNA attacks against HIV-1 regulatory genes to block viral escape. The T cell line were transduced with single and multiple gRNAs targeting HIV-1 tat and rev using lentiviral-based CRISPR-Cas9, followed by replicative HIV-1NL4-3 challenge in vitro. Viral p24 rebound was observed for almost all gRNAs, but multiplexing three tat-targeting gRNAs maintained p24 suppression and cell viability, indicating the inhibition of viral escape. Multiplexed tat gRNAs inhibited acute viral replication in the 2nd round of infection, abolished cell-associated transmission to unprotected T cells, and maintained protection through 45 days, post-infection (dpi) after a higher dose of HIV-1 infection. Finally, we describe here for the first time the assembly of all-in-one lentiviral vectors containing three and six gRNAs targeting tat and rev. A single-vector tat-targeting construct shows non-inferiority to the tat-targeting multi-vector in low-dose HIV-1 infection. We conclude that Cas9-induced, DNA repair-mediated mutations in tat are sufficiently deleterious and deplete HIV-1 fitness, and multiplexed disruption of tat further limits the possibility of an escape mutant arising, thus elevating the potential of CRISPR-Cas9 to achieve a long-term HIV-1 cure.

Correction to: Suicidal ideation, psychopathology and associated factors among HIV-infected adults in Indonesia.

An amendment to this paper has been published and can be accessed via the original article.

Suicidal ideation, psychopathology and associated factors among HIV-infected adults in Indonesia.

BACKGROUND: Suicidal behavior is a prevalent psychiatric emergency in HIV-infected adults. Detection of suicidal ideation is important in planning early psychiatric intervention and optimizing HIV/AIDS management. Characterization of suicidal ideation among HIV-infected adults is crucial; however, practically there is no data in Indonesia, the country with the second largest burden of HIV/AIDS epidemic in Asia. This study aims to identify suicidal ideation and analyze the associated psychopathology and determining factors among HIV-infected adults in Indonesia. METHODS: An observational cross-sectional study was conducted among HIV-infected adults aged 18-65 years old receiving antiretroviral therapy (ART). Measurement using Symptom Checklist-90 (SCL-90) was performed to assess the existing psychopathology. Firth's penalized logistic regression analysis was performed to identify factors associated with suicidal ideation. RESULTS: A total of 86 subjects were recruited. Most subjects were male (65.1%), median age was 35 years, and median latest CD4 count was 463 cells/µl. Lifetime suicidal ideation was identified in 20 subjects (23.3%). Mean SCL-90 T-score for depressive and anxiety symptoms were both significantly higher among subjects with suicidal ideation (M = 60.75, SD = 12.0, p = 0.000 and M = 57.9, SD = 2.8, p = 0.001, respectively) compared to those without. Bivariate analyses showed that lifetime suicidal ideation was associated with depressive and anxiety symptoms, non-marital status, CD4 count < 500 cells/µl, and efavirenz use. Multivariate analysis identified that a single-point increase in SCL-90 depression symptoms score (AOR 1.16, 95% CI 4.5-123.6, p = 0.000) and efavirenz use (AOR 5.00, 95% CI 1.02-24.6, p = 0.048) were significant independent factors related to suicidal ideation. CONCLUSION: Suicidal ideation is commonly found among Indonesian HIV-infected adults on ART. Depressive symptoms and efavirenz use are independent factors related to the presence of suicidal ideation. Thus, early screening of psychopathology as well as substitution of efavirenz with other ART regiment are recommended to prevent suicide and improve HIV/AIDS management outcome.

Characterization of HIV-1 CRF01_AE env Genes Derived from Recently Infected Indonesian Individuals.

To eradicate human immunodeficiency virus type 1 (HIV-1) infection, a comprehensive strategy including preventive vaccine development is needed. Envelope glycoproteins (Env) play a central role in viral infection and are the major targets of humoral immune responses. Therefore, Env is a candidate vaccine antigen, and its characterization is necessary for vaccine development. The characterization of the transmitted/founder (T/F; i.e., recently infected) virus that is responsible for the establishment of infection and induction of primary anti-HIV-1 immune responses is important. We herein established HIV-1 env clones derived from recently infected Indonesian individuals. All env genes were classified into CRF01_AE. The immunological characterization of env clones was performed by neutralization tests using a series of broadly neutralizing antibodies. The present study is the first to immunologically characterize the CRF01_AE T/F virus circulating in Indonesia.

piRNA-Guided CRISPR-like Immunity in Eukaryotes.

Eukaryotic genomes contain virus-derived sequences called endogenous virus elements (EVEs). The majority of EVEs are related to retroviruses, which integrate into the host genome in order to replicate. Some retroviral EVEs encode a function; for example, some produce proteins that block infection by related viruses. EVEs derived from nonretroviral viruses - also recently found in many eukaryotic genomes - are more enigmatic. Here, we summarize the evidence that EVEs can act as templates to generate Piwi-interacting RNAs (piRNAs), whose canonical function is sequence-specific silencing of transposable elements (TEs) to maintain genomic integrity. We argue that EVEs may thus enable heritable, sequence-specific antiviral immune memory in eukaryotes - analogous to CRISPR-Cas immunity in prokaryotes.

Frailty among HIV-1 Infected Adults under Antiretroviral Therapy in Indonesia.

BACKGROUND: Increasing age of HIV-1 infected population brought about the risk of frailty as comorbidity, whose prevalence is higher in low and middle-income countries (LMICs). Indonesia as an LMIC also bears a major burden of HIV-1 epidemic with a similarly aging population, but the prevalence of frailty and its predictors are unknown. OBJECTIVES: To identify the prevalence of frailty and analyze its associated factors, among HIV-1 infected adults under antiretroviral therapy in Indonesia. METHODS: A cross-sectional study was conducted among HIV-infected individuals with inclusion criteria of age ≥30 years old and underwent ART for at least 6 months. The main assessment was done using Fried's frailty phenotype score, which categorizes subjects into non-frail, pre-frail, or frail. Factors associated with frailty were characterized and multiple logistic regression analysis was performed. RESULTS: A total of 164 subjects were recruited; male subjects were 118 (72%), the median age was 40.5 years old, and the median CD4 nadir was 53 cells/µl. Frailty was identified among 90 (54.9%) subjects with 84 (51.2%) identified as pre-frail and 6 (3.7%) as frail, with dominant frailty phenotype was weakness in grip strength. The multivariate model showed that depression was the only factor significantly correlated with pre-frailty and frailty (OR 2.14; 95% CI 1.04-4.43, p=0.036). CONCLUSION: Frailty is a common occurrence among HIV-infected patients under ART, with depression as an independent predictive factor.

CRISPR/Cas9 system targeting regulatory genes of HIV-1 inhibits viral replication in infected T-cell cultures.

The CRISPR/Cas9 system provides a novel and promising tool for editing the HIV-1 proviral genome. We designed RNA-guided CRISPR/Cas9 targeting the HIV-1 regulatory genes tat and rev with guide RNAs (gRNA) selected from each gene based on CRISPR specificity and sequence conservation across six major HIV-1 subtypes. Each gRNA was cloned into lentiCRISPRv2 before co-transfection to create a lentiviral vector and transduction into target cells. CRISPR/Cas9 transduction into 293 T and HeLa cells stably expressing Tat and Rev proteins successfully abolished the expression of each protein relative to that in non-transduced and gRNA-absent vector-transduced cells. Tat functional assays showed significantly reduced HIV-1 promoter-driven luciferase expression after tat-CRISPR transduction, while Rev functional assays revealed abolished gp120 expression after rev-CRISPR transduction. The target gene was mutated at the Cas9 cleavage site with high frequency and various indel mutations. Conversely, no mutations were detected at off-target sites and Cas9 expression had no effect on cell viability. CRISPR/Cas9 was further tested in persistently and latently HIV-1-infected T-cell lines, in which p24 levels were significantly suppressed even after cytokine reactivation, and multiplexing all six gRNAs further increased efficiency. Thus, the CRISPR/Cas9 system targeting HIV-1 regulatory genes may serve as a favorable means to achieve functional cures.