The evolution of chikungunya virus circulating in Indonesia: Sequence analysis of the orf2 gene encoding the viral structural proteins.

Chikungunya virus (CHIKV) is an arthropod-borne virus that has caused several major epidemics globally, including in Indonesia. Although significant progress has been achieved in understanding the epidemiology and genotype circulation of CHIKV in Indonesia, the evolution of Indonesian CHIKV isolates is poorly understood. Thus, our study aimed to perform phylogenetic and mutation analyses of the orf2 gene encoding its viral structural protein to improve our understanding of CHIKV evolution in Indonesia. Complete orf2 gene sequences encoding the viral structural proteins of Indonesian-derived CHIKV were downloaded from GenBank until August 31, 2022. Various bioinformatics tools were employed to perform phylogenetic and mutation analyses of the orf2 gene. We identified 76 complete sequences of orf2 gene of CHIKV isolates originally derived from Indonesia. Maximum likelihood trees demonstrated that the majority (69/76, 90.8%) of Indonesian-derived CHIKV isolates belonged to the Asian genotype, while seven isolates (9.2%) belonged to the East/Central/South African (ECSA) genotype. The Indonesian-derived CHIKV isolates were calculated to be originated in Indonesia around 95 years ago (1927), with 95% highest posterior density (HPD) ranging from 1910 to 1942 and a nucleotide substitution rate of 5.07 × 10-4 (95% HPD: 3.59 × 10-4 to 6.67 × 10-4). Various synonymous and non-synonymous substitutions were identified in the C, E3, E2, 6K, and E1 genes. Most importantly, the E1-A226V mutation, which has been reported to increase viral adaptation in Aedes albopictus mosquitoes, was present in all ECSA isolates. To our knowledge, our study is the first comprehensive research analyzing the mutation and evolution of Indonesian-derived CHIKV based on complete sequences of the orf2 genes encoding its viral structural proteins. Our results clearly showed a dynamic evolution of CHIKV circulating in Indonesia.

The origin and continuing adaptive evolution of chikungunya virus.

Chikungunya virus (CHIKV) is the responsible agent of chikungunya fever, a debilitating arthritic disease in humans. CHIKV is endemic in Africa and Asia, although transmission cycles are considerably different on these continents. Before 2004, CHIKV had received little attention, since it was only known to cause localised outbreaks in a limited region with no fatalities. However, the recent global reemergence of CHIKV has caused serious global health problems and shown its potential to become a significant viral threat in the future. Unexpectedly, the reemergence is more rapid and is geographically more extensive, especially due to increased intensity of global travel systems or failure to contain mosquito populations. Another important factor is the successful adaptation of CHIKV to a new vector, the Aedes albopictus mosquito. Ae. albopictus survives in both temperate and tropical climates, thus facilitating CHIKV expansion to non-endemic regions. The continuous spread and transmission of CHIKV pose challenges for the development of effective vaccines and specific antiviral therapies. In this review, we discuss the biology and origin of CHIKV in Africa as well as its subsequent expansion to other parts of the world. We also review the transmission cycle of CHIKV and its continuing adaptation to its mosquito vectors and vertebrate hosts. More-complete understanding of the continuous evolution of CHIKV may help in predicting the emergence of CHIKV strains with possibly greater transmission efficiency in the future.

SARS-CoV-2, Covid-19, and the debunking of conspiracy theories.

The emergence of a novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has engaged considerable awareness and attention around the world. The associated disease, coronavirus disease 2019 (Covid-19), has now involved virtually all 200 countries. The total number of confirmed cases has been much more than in the two previous outbreaks of human coronaviruses, that is, SARS-CoV and Middle East respiratory syndrome coronavirus. In line with the outbreak escalation, false information about SARS-CoV-2 and its associated disease disseminated globally, particularly through online and social media. Believers in conspiracy theories promote misinformation that the virus is not contagious, is the result of laboratory manipulation or is created to gain profit by distributing new vaccines. The most dangerous effect of this widely disseminated misinformation is it will negatively influence the attitudes and behaviours for preventive measures to contain the outbreak. In this review, I discuss common conspiracy theories associated with SARS-CoV-2 and Covid-19 and consider how we can address and counterbalance these issues based on scientific information and studies.

The mechanisms underlying antigenic variation and maintenance of genomic integrity in Mycoplasma pneumoniae and Mycoplasma genitalium.

Mycoplasma pneumoniae and Mycoplasma genitalium are important causative agents of infections in humans. Like all other mycoplasmas, these species possess genomes that are significantly smaller than that of other prokaryotes. Moreover, both organisms possess an exceptionally compact set of DNA recombination and repair-associated genes. These genes, however, are sufficient to generate antigenic variation by means of homologous recombination between specific repetitive genomic elements. At the same time, these mycoplasmas have likely evolved strategies to maintain the stability and integrity of their 'minimal' genomes. Previous studies have indicated that there are considerable differences between mycoplasmas and other bacteria in the composition of their DNA recombination and repair machinery. However, the complete repertoire of activities executed by the putative recombination and repair enzymes encoded by Mycoplasma species is not yet fully understood. In this paper, we review the current knowledge on the proteins that likely form part of the DNA repair and recombination pathways of two of the most clinically relevant Mycoplasma species, M. pneumoniae and M. genitalium. The characterization of these proteins will help to define the minimal enzymatic requirements for creating bacterial genetic diversity (antigenic variation) on the one hand, while maintaining genomic integrity on the other.

Expressions of inhibitory checkpoint molecules in acute and chronic HBV and HCV infections: Implications for therapeutic monitoring and personalized therapy.

The function of T cells is tightly controlled by positive and negative regulations to ensure both successful pathogen elimination and limitation of immune-mediated pathology. One of the mechanisms to negatively regulate the magnitude and duration of effector T cells is the expression of inhibitory checkpoint molecules (ICs) on the surface membrane of T cells. During acute viral infections, expression of these molecules is upregulated to limit the effector functions following T-cell activation. The expression is subsequently downregulated following viral clearance. In contrast, these molecules are continuously expressed in virus-specific T cells found in persistently infected patients, including cases of chronic hepatitis B virus (HBV) and hepatitis C virus (HCV). The continuously high expression of ICs is responsible for the dysfunctional states of HBV- and HCV-specific T cells in chronic phases, known as T-cell exhaustion. Hence, understanding the regulation of their expression is essential to give insight into pathogenesis as well as the development of effective immune-based antiviral therapies. This review discusses recent updated research on expression of ICs during acute and chronic phases of HBV and HCV infections as well as during the clinical course of antiviral therapy.

Mitochondrial electron transport chain complex III sustains hepatitis E virus replication and represents an antiviral target.

Hepatitis E virus (HEV) infection has emerged as a global health problem. However, no approved medication is available, and the infection biology remains largely elusive. Electron transport chain (ETC), a key component of the mitochondria, is the main site that produces ATP and reactive oxygen species (ROS). By profiling the role of the different complexes of the mitochondrial ETC, we found that pharmacological inhibition of complex III, a well-defined drug target for the treatment of malaria and Pneumocystis pneumonia, potently restricts HEV replication. This effect demonstrated in our HEV models is equivalent to the anti-HEV potency of ribavirin, a widely used off-label treatment for patients with chronic HEV. Mechanistically, we found that this effect is independent of ATP production, ROS level, and pyridine depletion. By using pharmacological inhibitors and genetic approaches, we found that mitochondrial permeability transition pore (MPTP), a newly identified component of ETC, provides basal defense against HEV infection. HEV interferes with the opening of the MPTP. Furthermore, inhibition of the MPTP attenuated the anti-HEV effect of complex III inhibitors, suggesting that the MPTP mediates the antiviral effects of these inhibitors. These findings reveal new insights on HEV-host interactions and provide viable anti-HEV targets for therapeutic development.-Qu, C., Zhang, S., Wang, W., Li, M., Wang, Y., van der Heijde-Mulder, M., Shokrollahi, E., Hakim, M. S., Raat, N. J. H., Peppelenbosch, M. P., Pan, Q. Mitochondrial electron transport chain complex III sustains hepatitis E virus replication and represents an antiviral target.

Interaction of phages, bacteria, and the human immune system: Evolutionary changes in phage therapy.

Phages and bacteria are known to undergo dynamic and co-evolutionary arms race interactions in order to survive. Recent advances from in vitro and in vivo studies have improved our understanding of the complex interactions between phages, bacteria, and the human immune system. This insight is essential for the development of phage therapy to battle the growing problems of antibiotic resistance. It is also pivotal to prevent the development of phage-resistance during the implementation of phage therapy in the clinic. In this review, we discuss recent progress of the interactions between phages, bacteria, and the human immune system and its clinical application for phage therapy. Proper phage therapy design will ideally produce large burst sizes, short latent periods, broad host ranges, and a low tendency to select resistance.

Recombinant identification, molecular classification and proposed reference genomes for hepatitis delta virus.

Hepatitis delta virus (HDV), as a defective sub-virus that co-infects with hepatitis B virus, imposes an emerging global health burden. However, genetic characteristics and molecular classification of HDV remain under investigated. In this study, we have systematically retrieved and analysed a large set of HDV full-length genome sequences and identified novel recombinants. Based on phylogenetic and genetic analyses, we have established an updated classification system for HDV when recombinants were excluded. Furthermore, we have mapped the global distribution of different genotypes and subtypes. Finally, we have compiled a complete set of reference genomes for each subtype and proposed criteria for future identification of novel genotypes and subtypes. Of note, the global distribution map indicates that currently available HDV genetic data remain limited, and thus our proposed classification will likely evolve as future epidemiological data will accumulate. These results will facilitate the future research on the diagnosis, screening, epidemiology, evolution, prevention and clinical management of HDV infection.

The RNA genome of hepatitis E virus robustly triggers an antiviral interferon response.

The outcomes of hepatitis E virus (HEV) infection are diverse, ranging from asymptomatic carrier, self-limiting acute infection, and fulminant hepatitis to persistent infection. This is closely associated with the immunological status of the host. This study aimed to understand the innate cellular immunity as the first-line defense mechanism in response to HEV infection. Phosphorylation of signal transducer and activator of transcription 1, a hallmark of the activation of antiviral interferon (IFN) response, was observed in the liver tissues of the majority of HEV-infected patients but not in the liver of uninfected individuals. In cultured cell lines and primary liver organoids, we found that HEV RNA genome potently induced IFN production and antiviral response. This mechanism is conserved among different HEV strains, including genotypes 1, 3, and 7 as tested. Interestingly, single-stranded HEV RNA is sufficient to trigger the antiviral response, without the requirement of viral RNA synthesis and the generation of an RNA replicative form or replicative intermediate. Surprisingly, the m7 G cap and poly A tail are not required, although both are key features of the HEV genome. Mechanistically, this antiviral response occurs in a retinoic acid-inducible gene-I-independent, melanoma differentiation-associated protein 5-independent, mitochondrial antiviral signaling protein-independent, and ß-catenin-independent but IRF3-dependent and IRF7-dependent manner. Furthermore, the integrity of the Janus kinase-signal transducer and activator of transcription pathway is essentially required. CONCLUSION: HEV infection elicits an active IFN-related antiviral response in vitro and in patients, triggered by the viral RNA and mediated by IFN regulatory factors 3 and 7 and the Janus kinase-signal transducer and activator of transcription cascade; these findings have revealed new insights into HEV-host interactions and provided the basis for understanding the pathogenesis and outcome of HEV infection. (Hepatology 2018;67:2096-2112).

Phylogenetic and immunoinformatic analysis of VP4, VP7, and NSP4 genes of rotavirus strains circulating in children with acute gastroenteritis in Indonesia.

Rotavirus is a major cause of diarrhea in Indonesian children. However, rotavirus vaccines have not been introduced in the national immunization program of Indonesia. Understanding the genetic diversity and conserved antigenic regions of circulating strains are therefore essential to assess the potential efficacy of rotavirus vaccines. We collected fecal samples from hospitalized children less than 5 years of age with acute diarrhea. Rotavirus genotyping was performed by reverse transcriptase polymerase chain reaction, followed by sequencing of the VP4, VP7, and NSP4 genes of representative strains. Phylogenetic analysis was performed to investigate their relationship with globally circulating strains. Conservational analysis, immunoinformatics, and epitope mapping in comparison to vaccine strains were also performed. The sequence analyses showed that differences of multiple amino acid residues existed between the VP4, VP7, and NSP4 antigenic regions of the vaccine strains and the Indonesian isolates. However, many predicted conserved epitopes with higher antigenicity were observed in the vaccine and Indonesian strains, conferring the importance of these epitopes. The identified epitopes showed a higher potential of rotavirus vaccine to be employed in Indonesia. It could also be helpful to inform the design of a peptide vaccine based on the conserved regions and epitopes in the viral proteins.

Norovirus and rotavirus infections in children less than five years of age hospitalized with acute gastroenteritis in Indonesia.

Rotaviruses and noroviruses are the most important viral causes of acute gastroenteritis in children. While previous studies of acute gastroenteritis in Indonesia mainly focused on rotavirus, here, we investigated the burden and epidemiology of norovirus and rotavirus disease. Children less than five years of age hospitalized with acute gastroenteritis were enrolled in this study from January to December 2015 at three participating hospitals. Rotavirus was detected by enzyme immunoassay (EIA), followed by genotyping by reverse transcription PCR (RT-PCR). Norovirus genogroups were determined by TaqMan-based quantitative RT-PCR. Among 406 enrolled children, 75 (18.47%), 223 (54.93%) and 29 (7.14%) cases were positive for norovirus, rotavirus and both viruses (mixed infections), respectively. Most cases clinically presented with fever, diarrhea, vomiting and some degree of dehydration. The majority (n = 69/75 [92%]) of the noroviruses identified belonged to genogroup II, and several genotypes were identified by sequencing a subset of samples. Among 35 samples tested for rotavirus genotype, the most prevalent genotype was G3P[8] (n = 30/35 [85.6%]). Our study suggests that the burden of norovirus diseases in Indonesian children should not be underestimated. It also shows the emergence of rotavirus genotype G3P[8] in Indonesia.

Immunity against hepatitis E virus infection: Implications for therapy and vaccine development.

Hepatitis E virus (HEV) is the leading cause of acute viral hepatitis worldwide and an emerging cause of chronic infection in immunocompromised patients. As with viral infections in general, immune responses are critical to determine the outcome of HEV infection. Accumulating studies in cell culture, animal models and patients have improved our understanding of HEV immunopathogenesis and informed the development of new antiviral therapies and effective vaccines. In this review, we discuss the recent progress on innate and adaptive immunity in HEV infection, and the implications for the devolopment of effective vaccines and immune-based therapies.

The global burden of hepatitis E outbreaks: a systematic review.

Hepatitis E virus (HEV) is responsible for repeated water-borne outbreaks since the past century, representing an emerging issue in public health. However, the global burden of HEV outbreak has not been comprehensively described. We performed a systematic review of confirmed HEV outbreaks based on published literatures. HEV outbreaks have mainly been reported from Asian and African countries, and only a few from European and American countries. India represents a country with the highest number of reported HEV outbreaks. HEV genotypes 1 and 2 were responsible for most of the large outbreaks in developing countries. During the outbreaks in developing countries, a significantly higher case fatality rate was observed in pregnant women. In fact, outbreaks have occurred both in open and closed populations. The control measures mainly depend upon improvement of sanitation and hygiene. This study highlights that HEV outbreak is not new, yet it is a continuous global health problem.

Inhibitory receptor molecules in chronic hepatitis B and C infections: novel targets for immunotherapy?

Chronic HBV and HCV infections are the leading cause of liver-related morbidity and mortality. For effective antiviral immunity, virus-specific T cells are required, but these cells have been shown to be weak or absent in chronic HBV and HCV patients. One of the mechanisms that underlies the impaired T-cell response is the result of the continuously high viral load that causes HBV-specific and HCV-specific T cells to become exhausted, which is characterized by impaired proliferation, cytokine production and cytotoxic activity of T cells as well as high susceptibility to apoptosis. In vitro studies from chronic HBV and HCV patients as well as in vivo studies in animal models demonstrated a reversible state of T-cell exhaustion, which can be manipulated to reinvigorate the specific antiviral immune responses. In chronic HCV infection, this concept has been explored in clinical trials by administration of specific antibody to block the inhibitory pathways. The manipulation of inhibitory receptors is a promising and potential strategy for immunotherapeutic interventions in chronic HBV and HCV patients to facilitate complete elimination of the viruses or sustained viral control.

The recent re-emergence of human monkeypox: Would it become endemic beyond Africa?

Viral outbreaks still become global health challenges, for instance, influenza A viruses, Japanese encephalitis, Ebola virus, Yellow fever, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since 7 May 2022, another outbreak of monkeypox also has been reported in European countries and the United States. Meanwhile, the monkeypox virus is previously endemic only in the western and central parts of Africa. Monkeypox is a zoonotic disease, although the primary animal reservoir remains unknown. This article concisely reviews the monkeypox virus, its transmission, pathogenesis, and clinical manifestation, its changing global epidemiology before and during the current outbreak, and possible driving factors of the recent outbreak. Furthermore, we also discuss whether the monkeypox virus would become endemic beyond Africa. Even though the available data suggests that human-to-human transmission is currently happening and unconnected clusters exist, many efforts have been made to tackle this outbreak, such as active case detection, contact tracing, isolation, and postexposure vaccination.

Understanding the Biology and Immune Pathogenesis of Chikungunya Virus Infection for Diagnostic and Vaccine Development.

Chikungunya virus, the causative agent of chikungunya fever, is generally characterized by the sudden onset of symptoms, including fever, rash, myalgia, and headache. In some patients, acute chikungunya virus infection progresses to severe and chronic arthralgia that persists for years. Chikungunya infection is more commonly identified in tropical and subtropical regions. However, recent expansions and epidemics in the temperate regions have raised concerns about the future public health impact of chikungunya diseases. Several underlying factors have likely contributed to the recent re-emergence of chikungunya infection, including urbanization, human travel, viral adaptation to mosquito vectors, lack of effective control measures, and the spread of mosquito vectors to new regions. However, the true burden of chikungunya disease is most likely to be underestimated, particularly in developing countries, due to the lack of standard diagnostic assays and clinical manifestations overlapping with those of other endemic viral infections in the regions. Additionally, there have been no chikungunya vaccines available to prevent the infection. Thus, it is important to update our understanding of the immunopathogenesis of chikungunya infection, its clinical manifestations, the diagnosis, and the development of chikungunya vaccines.

The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis.

An in-depth analysis of first-wave SARS-CoV-2 genome is required to identify various mutations that significantly affect viral fitness. In the present study, we performed a comprehensive in silico mutational analysis of 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), and spike (S) proteins with the aim of gaining important insights into first-wave virus mutations and their functional and structural impact on SARS-CoV-2 proteins. Our integrated analysis gathered 6000 SARS-CoV-2 sequences and identified 92 mutations in S, 37 in RdRp, and 11 in 3CLpro regions. The impact of these mutations was also investigated using various in silico approaches. Among these, 32 mutations in S, 15 in RdRp, and 3 in 3CLpro proteins were found to be deleterious in nature and could alter the structural and functional behavior of the encoded proteins. The D614G mutation in spike and the P323Lmutation in RdRp are the globally dominant variants with a high frequency. Most of the identified mutations were also found in the binding moiety of the viral proteins which determine their critical involvement in host-pathogen interactions and may represent drug targets. Furthermore, potential CD4+ and CD8+ T cell epitopes were predicted, and their overlap with genetic variations was explored. This study also highlights several hot spots in which HLA and drug selective pressure overlap. The findings of the current study may allow a better understanding of COVID-19 diagnostics, vaccines, and therapeutics.

Interleukin 15 upregulates the expression of PD-1 and TIM-3 on CD4+ and CD8+ T cells.

Virus-specific T cell-mediated immunity is severely impaired in chronic hepatitis B virus (HBV) patients. HBV-specific T cells in chronic HBV patients show a low ability to produce cytokines and to exert their cytotoxic activity. A prominent characteristic of these exhausted T cells is overexpression of inhibitory receptor molecules which negatively regulate T cell function. In this study, we examined in vitro regulation of two inhibitory receptor expressions, programmed death 1 (PD-1) and T cell immunoglobulin mucin domain-containing molecule 3 (TIM-3). Peripheral blood mononuclear cells (PBMCs) obtained from healthy individuals were in vitro stimulated with a panel of cytokines. PD-1 and TIM-3 expression levels on CD4+ and CD8+ T cells were examined at days 2 and 7 post stimulation. We demonstrated that PD-1 and TIM-3 were induced via polyclonal (anti-CD3) and cytokine (interleukin 15 [IL-15]) stimulations. Noteworthy, there was a significantly increased induction of TIM-3 on CD8+ T cells as compared to CD4+ T cells. Our study thus contributes to further understanding the regulation of T cell exhaustion markers PD-1 and TIM-3.