Whole genome sequencing of Indonesian dengue virus isolates using next-generation sequencing

Indonesia is a tropical country and hyperendemic for dengue. The disease prevalently affected Indonesian and it caused high morbidity and substantial economic burden. This vector-borne viral disease is caused by infection of dengue viruses (DENVs), which are the member of Flaviviridae family. While most of dengue studies in Indonesia focused on the epidemiology, the clinical aspects, the vectors, and to certain extent the virology, there were still gaps in the DENVs genomic aspects. Considering their high mutation rate, the DENVs were known for their high genetic diversity and it might affect the characteristics of the viruses. Comprehensive DENV genomic data were thus important for many aspects of disease management, including virus surveillance, pathogenesis, diagnostics, antiviral drug design, and vaccine development. We established in this study a method for DENV whole genome sequencing using the advanced Next-Generation Sequencing (NGS) and Nextera XT DNA library preparation kit, coupled with simplified bioinformatic analysis methods. The Indonesian DENVs from four serotypes were isolated from patients’ sera, while library was prepared from enriched templates and sequenced using Illumina NGS. Our study highlighted the potential of a robust NGS method in producing whole genome sequence of DENVs, which would be important for future dengue studies

Chikungunya fever outbreak identified in North Bali, Indonesia

Background: Chikungunya virus (CHIKV) infections have been reported sporadically within the last 5 years in several areas of Indonesia including Bali. Most of the reports, however, have lacked laboratory confirmation. Method: A recent fever outbreak in a village in the North Bali area was investigated using extensive viral diagnostic testing including both molecular and serological approaches. Results and conclusions: Ten out of 15 acute febrile illness samples were confirmed to have CHIKV infection by real-time PCR or CHIKV-specific IgM enzyme-linked immunosorbent assay (ELISA). The outbreak strain belonged to the Asian genotype with highest homology to other CHIKV strains currently circulating in Indonesia. The results are of public health concern particularly because Bali is a popular tourist destination in Indonesia and thereby the potential to spread the virus to non-endemic areas is high

Hepatitis B virus genotypes/subgenotypes in voluntary blood donors in Makassar, South Sulawesi, Indonesia

<p>Abstract</p> <p>Background</p> <p>Hepatitis B virus (HBV) genotype appears to show varying geographic distribution. Molecular epidemiological study of HBV in particular areas in Indonesia is still limited. This study was aimed to identify the prevalence of HBV genotype/subgenotype and mutations in basal core promoter (BCP) region in voluntary blood donors in Makassar, one of the biggest cities in east part of Indonesia.</p> <p>A total of 214 hepatitis B surface antigen (HBsAg)-positive samples were enrolled in this study. HBV genotype/subgenotype was identified by genotype-specific PCR method or direct sequencing of pre-S region. Mutations in BCP were identified by direct sequencing of the corresponding region.</p> <p>Results</p> <p>HBV/B and HBV/C were detected in 61.21% and 25.23% of the samples, while mix of HBV/B and HBV/C was found in 12.62% of the samples. Based on pre-S region, among HBV/B and HBV/C, HBV/B3 (95.00%) and HBV/C1 (58.82%) were predominant. Interestingly, HBV/D was identified in two samples (22.165.07 and 22.252.07). Complete genome sequences of two HBV/D strains (22.165.07 and 22.252.07) demonstrated that both strains belong to HBV/D6, and the divergence between the two strains were 1.45%, while divergences of both 22.165.07 and 22.252.07 strains with reference strain (<ext-link ext-link-id="AM422939" ext-link-type="gen">AM422939</ext-link>/France) were 2.67%. A1762T/G1764A mutation was observed in 1.96% and 5.36%, whereas T1753V mutation was found in 2.94% and 1.79% of HBV/B and HBV/C, respectively.</p> <p>Conclusion</p> <p>HBV/B and HBV/C are dominant in Makassar, similar to most areas in Indonesia. Mutations in BCP which might be associated with severity of liver disease are less common.</p

Memory B cell localisation and cell fate potential

Memory B cells (Bmem) provide a unique layer of defence against pathogens and are an essential component of the immunological memory acquired by vaccination and infection. Long-lived Bmem are generated upon antigen encounter in the primary immune response. Following the resolution of primary response, a subpopulation of Bmem is retained in the lymph node draining the site of vaccine injection or pathogen entry. In this draining lymph node, resting Bmem occupy the subcapsular sinus (SCS) niche where they scan SCS macrophages for antigen. Booster immunisation reactivates Bmem to become either short-lived plasma cells (PC) or re-enter secondary germinal centers (GC) to increase their B cell receptor affinity and diversity to the immunising antigen. However, it is unclear whether Bmem retained in the draining lymph node after primary immunisation have different cellular phenotypes, transcriptional states, and cell fate potential compared to recirculating Bmem found in the non-draining lymph node. Here, the established SWHEL mouse model was used to track and characterise antigen-specific Bmem in the draining and non-draining lymph nodes. Using intravital two-photon microscopy to probe the cellular dynamics of Bmem under homeostatic conditions in vivo, this study found that recirculating Bmem in the non-draining lymph node have distinct localisation, dynamic, and behaviour compared to Bmem residing in the draining lymph node. Importantly, boosting in the draining lymph node reactivates Bmems that preferentially re-enter the GC, facilitating affinity maturation of the secondary antibody response. In contrast, boosting in the non-draining lymph node preferentially recalls the PC response. These differential memory recall responses are not dependent on persisting primary GC or memory CD4 T cells but can be altered by disrupting the SCS macrophages. Furthermore, transcriptomic profiling by single-cell RNA sequencing revealed that Bmem in the draining and non-draining lymph nodes occupy distinct cell states, suggesting their cell fate potentials may also be molecularly imprinted. This thesis thus highlights an additional layer of control over Bmem fate through their geographical positioning and suggests that the site of booster vaccinations can affect the Bmem cell fate choice and, thereby, the quality and quantity of the resulting secondary antibody response

High prevalence of hepatitis B virus genotype C/C1 in the Minangkabau ethnic group in Indonesia

<p>Abstract</p> <p>Background</p> <p>The Minangkabau is one of the major ethnic groups in Indonesia. Previous studies with a limited number of samples have shown a different prevalence of HBV/C in the Minangkabau compared to the Indonesian population in general. The aim of this study was to assess the HBV genotype distribution pattern and the prevalence of pre-S, T1753V and A1762T/G1764A mutations among the Minangkabau HBV carriers. The samples were collected from Padang, West Sumatera and from western Java. Mixed primers for specific genotypes were used to determine the HBV genotype. Pre-S or S genes were amplified, sequenced and aligned with reference sequences from GenBank to derive a phylogenetic tree for subgenotyping. Pre-S genes were also analyzed for mutations. The basal core promoter (BCP) region was amplified and directly sequenced to analyze T1753V and A1762T/G1764A mutations.</p> <p>Results</p> <p>The predominant HBV genotype among the Minangkabau HBV carriers (n=117) was C (72.6%) followed by B (24.8%) and co-infection with B and C (2.6%). The prevalence of pre-S mutations, including both the pre-S deletion and pre-S2 start codon mutation, was 41.0%, and the T1753V and A1762T/G1764A mutations were found in 51.9% and 71.2% respectively. HBV/C1 was the predominant HBV subgenotype in the Minangkabau HBV carriers, and was found in 66.2%, followed by B3, B7, C8, B2, B9, C2, and C10 (18.3%, 7.0%, 2.8%, 1.4%, 1.4%, 1.4%, and 1.4% respectively). From samples that were found to be co-infected with HBV B and C, two samples were successfully cloned and subgenotyped, including one with mixed subgenotypes of B3 and C1, and another one with mixed subgenotypes of B7, C1, putative intergenotypic of B/A, and C/A. Furthermore, three samples from donors of non-Minangkabau ethnicity from Padang were found to be infected with an intragenotypic recombination form, including a putative recombinant of B8/B3 and B9/B7.</p> <p>Conclusion</p> <p>HBV/C with subgenotype C1 was the predominant HBV genotype among HBV carriers of Minangkabau ethnicity. The prevalence of pre-S, A1762T/G1764A, and T1753V mutations was higher among the Minangkabau compared to Indonesian HBV carriers in general.</p

Zika Virus Seropositivity in 1–4-Year-Old Children, Indonesia, 2014

We assessed Zika virus seroprevalence among healthy 1–4-year-old children using a serum sample collection assembled in 2014 representing 30 urban sites across Indonesia. Of 662 samples, 9.1% were Zika virus seropositive, suggesting widespread recent Zika virus transmission and immunity. Larger studies are needed to better determine endemicity in Indonesia

Detection of central nervous system viral infections in adults in Manado, North Sulawesi, Indonesia.

Central nervous system (CNS) viral infections are important causes of morbidity and mortality worldwide but the systematic survey of patients admitted to hospitals with CNS infections in many countries, including Indonesia, is limited. To obtain more information regarding the causes of CNS infections in Indonesia, this study was performed to detect and identify viral agents associated with CNS infections amongst in-patients at a referral hospital in Manado, North Sulawesi, Indonesia. Adult patients admitted to R.D. Kandou General Hospital with presumed CNS infection were enrolled. Cerebrospinal fluid, serum, and throat swab samples were collected and tested using molecular, serological, and virus isolation assays. A confirmed viral etiology was established in three and a probable/possible in 11 out of 74 patients. The most common was herpes simplex virus 1 (7/74, 9.5%), followed by Epstein-Barr virus (2/74, 2.7%), cytomegalovirus (1/74, 1.4%), enterovirus D68 (1/74, 1.4%), rhinovirus A (1/74, 1.4%), dengue virus (1/64, 1.6%), and Japanese encephalitis virus (1/64, 1.6%). There were 20 fatal cases (27.0%) during hospitalization in which eight were associated with viral causes. We identified herpes simplex virus 1 as the most common cause of CNS infection among adults in North Sulawesi with most of the cases remaining undiagnosed. Our study highlights the challenges in establishing the etiology of viral CNS infections and the importance of using a wide range of molecular and serological detection methods to identify CNS viruses

Isolation and complete genome analysis of neurotropic dengue virus serotype 3 from the cerebrospinal fluid of an encephalitis patient

<div><p>Although neurological manifestations associated with dengue viruses (DENV) infection have been reported, there is very limited information on the genetic characteristics of neurotropic DENV. Here we describe the isolation and complete genome analysis of DENV serotype 3 (DENV-3) from cerebrospinal fluid of an encephalitis paediatric patient in Jakarta, Indonesia. Next-generation sequencing was employed to deduce the complete genome of the neurotropic DENV-3 isolate. Based on complete genome analysis, two unique and nine uncommon amino acid changes in the protein coding region were observed in the virus. A phylogenetic tree and molecular clock analysis revealed that the neurotropic virus was a member of Sumatran-Javan clade of DENV-3 genotype I and shared a common ancestor with other isolates from Jakarta around 1998. This is the first report of neurotropic DENV-3 complete genome analysis, providing detailed information on the genetic characteristics of this virus.</p></div

β-cell function is regulated by metabolic and epigenetic programming of islet-associated macrophages, involving Axl, Mertk, and TGFβ receptor signaling

Summary: We have exploited islet-associated macrophages (IAMs) as a model of resident macrophage function, focusing on more physiological conditions than the commonly used extremes of M1 (inflammation) versus M2 (tissue remodeling) polarization. Under steady state, murine IAMs are metabolically poised between aerobic glycolysis and oxidative phosphorylation, and thereby exert a brake on glucose-stimulated insulin secretion (GSIS). This is underpinned by epigenetic remodeling via the metabolically regulated histone demethylase Kdm5a. Conversely, GSIS is enhanced by engaging Axl receptors on IAMs, or by augmenting their oxidation of glucose. Following high-fat feeding, efferocytosis is stimulated in IAMs in conjunction with Mertk and TGFβ receptor signaling. This impairs GSIS and potentially contributes to β-cell failure in pre-diabetes. Thus, IAMs serve as relays in many more settings than currently appreciated, fine-tuning insulin secretion in response to dynamic changes in the external environment. Intervening in this nexus might represent a means of preserving β-cell function during metabolic disease

Mfold RNA structure prediction for the complete 3’UTR of DENV-3 prototype strain H87 (KU050695) and the neurotropic DENV-3 201610225 (KY863456).

<p>Stop codon (UAA) is indicated with red font in both RNA structure just upstream nucleotide 10268. Nucleotide insertion and changes in isolate 201610225 are indicated with yellow and red circles, respectively. The positions of the nucleotide changes are indicated according to 201610225 nucleotide numbering with H87 nucleotide numbering in parentheses. The two stem-loops (SLI and SLII), two dumbbells (DBI and DBII), and small hairpin 3’ stem-loop (SHP-3’SL) structures are shown.</p