Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia.

BACKGROUND: Dengue virus (DENV) infects hundreds of thousands of people annually in Indonesia. However, DENV sequence data from the country are limited, as samples from outbreaks must be shipped across long-distances to suitably equipped laboratories to be sequenced. This approach is time-consuming, expensive, and frequently results in failure due to low viral load or degradation of the RNA genome. METHODS: We evaluated a method designed to address this challenge, using the 'Primal Scheme' multiplex PCR tiling approach to rapidly generate short, overlapping amplicons covering the complete DENV coding-region, and sequencing the amplicons on the portable Nanopore MinION device. The resulting sequence data was assessed in terms of genome coverage, consensus sequence accuracy and by phylogenetic analysis. RESULTS: The multiplex approach proved capable of producing near complete coding-region coverage from all samples tested ([Formula: see text] = 99.96%, n = 18), 61% of which could not be fully amplified using the current, long-amplicon PCR, approach. Nanopore-generated consensus sequences were found to be between 99.17-99.92% identical to those produced by high-coverage Illumina sequencing. Consensus accuracy could be improved by masking regions below 20X coverage depth (99.69-99.92%). However, coding-region coverage was reduced at this depth ([Formula: see text] = 93.48%). Nanopore and Illumina consensus sequences generated from the same samples formed monophyletic clades on phylogenetic analysis, and Indonesian consensus sequences accurately clustered by geographical origin. CONCLUSION: The multiplex, short-amplicon approach proved superior for amplifying DENV genomes from clinical samples, particularly when the virus was present at low concentrations. The accuracy of Nanopore-generated consensus sequences from these amplicons was sufficient for identifying the geographic origin of the samples, demonstrating that the approach can be a useful tool for identifying and monitoring DENV clades circulating in low-resource settings across Indonesia. However, the inaccuracies in Nanopore-generated consensus sequences mean that the approach may not be appropriate for higher resolution transmission studies, particularly when more accurate sequencing technologies are available.

Scrub typhus in Indonesia: A cross-sectional analysis of archived fever studies samples.

BACKGROUND: Scrub typhus is an understudied vector-borne bacterial infection. METHODS: We tested archived fever samples for scrub typhus seropositivity to begin charting its geographic distribution in Indonesia. We analysed 1033 serum samples from three sites. IgM and IgG enzyme-linked immunosorbent assay (ELISA) against Orientia tsutsugamushi was performed using Karp, Kato, Gilliam, TA 716 antigens. To determine the cutoff in the absence of a presumed unexposed population and gold standard tests, we identified the visual inflection point, performed change point analysis, and used finite mixture models. RESULTS: The optical density cutoff values used for IgM and IgG were 0.49 and 0.13, respectively. Across all sites, IgM seropositivity was 4.6% (95% CI: 3.4 to 6.0%) while IgG seropositivity was 4.4% (95% CI: 3.3 to 5.8%). The overall seropositivity across sites was 8.8% (95% CI: 8.1 to 11.7%). The overall seropositivity for Jambi, Denpasar, Tabanan were 9.7% (95% CI: 7.0 to 13.3%), 8.0% (95% CI: 5.7 to 11.0%), 9.0% (95% CI: 6.1 to 13.0%), respectively. CONCLUSIONS: We conclude that O. tsutsugamushi exposure in humans occurred at all sites analysed and could be the cause of illness in some cases. Though it was not the main cause of acute fever in these locations, it is still important to consider scrub typhus in cases not responding to beta-lactam antibiotics. Future seroprevalence surveys and testing for scrub typhus in acute febrile illness studies will be essential to understand its distribution and burden in Indonesia.

Significant increase in anti-SARS-CoV-2 antibodies after administration of heterologous mRNA-based vaccine booster in individuals receiving two doses of inactivated COVID-19 vaccine: A single-center study in healthcare workers in Jakarta, Indonesia.

BACKGROUND: Vaccine plays an important role in breaking SARS-CoV-2 transmission and accelerating the path to pandemic recovery. Currently, there is still limited data on heterologous COVID-19 booster vaccination efficacy and effectiveness in Indonesia. METHODS: Antibody response was retrospectively analyzed from 156 serum collected from healthcare workers that have received mRNA-1273 vaccine as the booster against SARS-CoV-2. These individuals had previously received the full two doses of inactivated anti-SARS-CoV-2 vaccine. Serological analysis was performed to measure total antibody, as well as IgA and IgG antibodies specific to spike (S) protein using ECLIA and ELISA methods. RESULTS: A significant increase in total, IgA, and IgG antibody titers was reported in vaccine receiving a third heterologous booster dose of mRNA-based COVID-19 vaccine following two doses of inactivated type. CONCLUSION: The third heterologous booster dose of vaccine may be beneficial to individuals with or without previous history of SARS-CoV-2 infection.

Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center study.

We determined the prevalence and epidemiological characteristics of COVID-19 in Jakarta and neighboring areas, Indonesia from March 2020 to February 2021, based on nasopharyngeal/oropharyngeal (NP/OP) swab specimens that were tested at the Eijkman Institute for Molecular Biology, Jakarta. NP/OP swab specimens were collected from COVID-19 suspects or individuals in contact tracing programs from primary healthcare centers (PHC) and hospitals. The specimens were screened for the SARS-CoV-2 by qRT-PCR. Demography data and clinical symptoms were collected using national standardized laboratory form. Of 64,364 specimens, 10,130 (15.7%) were confirmed positive for SARS-CoV-2, with the peak prevalence of infection in March 2020 (26.3%) follow by in January 2021 (23.9%) and February 2021 (21.8%). We found that the positivity rate of the specimens from Jakarta, West Java, and Banten was 16.3%, 13.3%, and 16.8%, respectively. Positivity rate was higher in specimens from hospitals (16.9%) than PHC (9.4%). Of the positive specimens, 29.6% were from individuals aged >60 years old, followed by individuals aged 41-60 years old (24.2%). Among symptomatic cases of SARS-CoV-2, the most common symptoms were cough, fever, and a combination of both cough & fever. In conclusion, this study illustrates the prevalence and epidemiological characteristics from one COVID-19 diagnostic center in Jakarta and neighbouring areas in Indonesia.

Whole-Genome Sequencing of SARS-CoV-2 Infection in a Cluster of Immunocompromised Children in Indonesia.

Background: Thus far, Indonesia has recorded over 4,000,000 confirmed COVID-19 cases and 144,000 fatalities; 12.8% of cases have been in children under 18 years. Whole-genome viral sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been demonstrated to help differentiate hospital-acquired infection from community-acquired coronavirus disease 2019 (COVID-19) infection. Our study highlighted the use of WGS to investigate the origin of infection among pediatric oncology patients in Jakarta. The aim of our study was to evaluate clinical and laboratory characteristics and also the efficacy of using WGS to confirm hospital-acquired COVID-19 infection in a cluster of immunocompromised children within a single ward of a tertiary hospital in metropolitan Jakarta based on quasispecies, viral load, and admission dates. Method: Real-time reverse-transcription polymerase chain reaction (RT-PCR) from nasopharyngeal (NP) swabs was used to diagnose the patients and also guardians and healthcare workers (HCWs) in the ward, followed by WGS of RT-PCR positive cases to establish their phylogenetic relationships. Result: Using WGS, we showed that SARS-CoV-2 transmission in a cluster of children with underlying malignancy was characterized by high similarity of whole virus genome, which suggests nosocomial transmission.

Neurological Disease Associated with Chikungunya in Indonesia.

Chikungunya virus (CHIKV) is recognized but rarely considered as a cause of central nervous system infection in endemic areas. A total of 244 patients with acute meningoencephalitis in Indonesia were retrospectively tested to identify whether any CHIKV infection was associated with neurological manifestations, especially in provinces known for CHIKV endemicity. Cerebrospinal fluid (CSF) and blood specimens were tested using CHIKV-specific real-time reverse transcription polymerase chain reaction and IgM ELISA, alongside a panel of neurotropic viruses. We report four cases of suspected or confirmed CHIKV-associated neurological disease, including CHIKV RNA detection in CSF of one patient and in acute serum of another, and CHIKV IgM in CSF of three patients and in serum of a fourth. In conclusion, CHIKV should be considered as a cause of neurologic disease in endemic areas and especially during outbreaks, in addition to the more common arboviral diseases such as dengue and Japanese encephalitis viruses.

Hypnozoite depletion in successive Plasmodium vivax relapses.

Genotyping Plasmodium vivax relapses can provide insights into hypnozoite biology. We performed targeted amplicon sequencing of 127 relapses occurring in Indonesian soldiers returning to malaria-free Java after yearlong deployment in malarious Eastern Indonesia. Hepatic carriage of multiple hypnozoite clones was evident in three-quarters of soldiers with two successive relapses, yet the majority of relapse episodes only displayed one clonal population. The number of clones detected in relapse episodes decreased over time and through successive relapses, especially in individuals who received hypnozoiticidal therapy. Interrogating the multiplicity of infection in this P. vivax relapse cohort reveals evidence of independent activation and slow depletion of hypnozoites over many months by multiple possible mechanisms, including parasite senescence and host immunity.

COVID-19 prevalence among healthcare workers in Jakarta and neighbouring areas in Indonesia during early 2020 pandemic.

BACKGROUND: The COVID-19 disease has overwhelmed and disrupted healthcare services worldwide, particularly healthcare workers (HCW). HCW are essential workers performing any job in a healthcare setting who are potentially directly or indirectly exposed to infectious materials. Our retrospective cohort study aimed to determine the prevalence of COVID-19 infections among HCW in Jakarta and neighbouring areas during the first three months of the pandemic. METHODS: Nasopharyngeal/oropharyngeal swab specimens from HCW working at private and public hospitals in Jakarta and neighbouring areas were screened for SARS-CoV-2 between March and May 2020. Data on demography, clinical symptoms, contact history, and personal protective equipment (PPE) use were collected using standardised forms. RESULTS: Among 1201 specimens, 7.9% were confirmed positive for SARS-CoV-2 with the majority coming from medical doctors (48.4%) and nurses (44.2%). 64.2% of the positive cases reported to have contact with suspect/confirmed COVID-19 cases, including 32 (52.2%) with patient and 3 (6.6%) with co-worker. The symptomatic HCW had a significantly lower median Ct value as compared to their asymptomatic counterpart (p < .001). Tendency to have a higher prevalence of pneumonia was observed in the age group of 40 - 49 and ≥50 years old. CONCLUSION: Our findings highlighted the necessity to implement proper preventive and surveillance strategies for this high-risk population including adherence to strict PPE protocol and appropriate training.Key MessageHealthcare workers (HCW), defined as those handling any job in a healthcare setting, are at the frontline of risk of infection as SARS-CoV-2 is easily transmitted through airborne droplets and direct contact with contaminated surfaces. The aim of our study is to attain a more comprehensive and accurate picture of the impact of COVID-19 on HCW during the earlier phase of the outbreak in Indonesia to develop effective strategies that protect the health and safety of this workforce. Our findings highlighted that COVID-19 infections in HCW were mostly acquired in healthcare settings, with significant consequences of pneumonia and hospitalisation occurring across all age groups.

Characteristics of children with confirmed SARS-CoV-2 infection in Indonesia.

Objective: COVID-19 in children poses a significant challenge due to the atypical/asymptomatic presentations. The study is aimed to help understand clinical characteristics in Indonesian children for better management and control of transmission. Methods: clinical characteristics of children with confirmed COVID-19 were retrospectively analysed from the database dating from March to November 2020. Results: the study revealed a high prevalence (67.3%) of asymptomatic cases from contact tracing population. The most common symptoms in children with confirmed COVID-19 were cough and fatigue. Among symptomatic patients, 14/21 (66.7%) had either radiological and/or clinical evidence of pneumonia. Conclusion: children with respiratory symptoms especially those with contact history should be screened for possible COVID-19 infection regardless of disease severity.

Convalescent plasma therapy in patients with moderate-to-severe COVID-19: A study from Indonesia for clinical research in low- and middle-income countries.

BACKGROUND: We explored the outcome of convalescent plasma (CP) treatment in patients with moderate and severe coronavirus disease 2019 (COVID-19) and investigated variables for the design of further trials in Indonesia. METHODS: Hospitalised patients with moderate (n = 5) and severe (n = 5) COVID-19 were recruited and transfused with CP from donors who recovered from mild (n = 5), moderate (n = 5), or severe (n = 1) COVID-19. Neutralising antibodies (NAbs) to the virus were measured at the end of the study using a surrogate virus neutralisation test as an alternative to the plaque reduction assay. Clinical improvement was assessed based on the modified World Health Organization Research and Development Blueprint six-point scale, Brixia Chest-X-Ray scoring, and laboratory parameters. The study was registered at ClinicalTrials.gov (NCT04407208). FINDINGS: CP transfusion in three doses of 3 mL/kg of recipient body weight at 2-day intervals was well tolerated. Good clinical improvement was achieved in all patients with moderate disease and in two patients with severe disease. Most patients at baseline had detectable NAbs with median inhibition rates comparable to those of the donors (90·91% vs. 86·31%; p = 0·379). This could be due to the unavailability of pre-donation NAb testing and postponed CP administration that required communal consent. INTERPRETATION: This study highlights the safety of CP therapy. Although improvements were observed, we could not conclude that the outcomes were solely due to CP treatment. Further randomised controlled trials that cover different disease stages with pre-donation NAb measurements using locally applicable strategies are warranted. FUNDING: The study was supported by PT Bio Farma, Indonesia.

Japanese encephalitis virus infection in non-encephalitic acute febrile illness patients.

Although Japanese encephalitis virus (JEV) is considered endemic in Indonesia, there are only limited reports of JEV infection from a small number of geographic areas within the country with the majority of these being neuroinvasive disease cases. Here, we report cases of JEV infection in non-encephalitic acute febrile illness patients from Bali, Indonesia. Paired admission (S1) and discharge (S2) serum specimens from 144 acute febrile illness patients (without evidence of acute dengue virus infection) were retrospectively tested for anti-JEV IgM antibody and confirmed by plaque reduction neutralization test (PRNT) for JEV infection. Twenty-six (18.1%) patients were anti-JEV IgM-positive or equivocal in their S2 specimens, of which 5 (3.5%) and 8 (5.6%) patients met the criteria for confirmed and probable JEV infection, respectively, based on PRNT results. Notably, these non-encephalitic JE cases were less likely to have thrombocytopenia, leukopenia, and lower hematocrit compared with confirmed dengue cases of the same cohort. These findings highlight the need to consider JEV in the diagnostic algorithm for acute febrile illnesses in endemic areas and suggest that JEV as a cause of non-encephalitic disease has likely been underestimated in Indonesia.

An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia.

BACKGROUND: Chikungunya virus (CHIKV) is an important emerging and re-emerging public health problem worldwide. In Indonesia, where the virus is endemic, epidemiological information from outside of the main islands of Java and Bali is limited. METHODOLOGY/PRINCIPAL FINDINGS: Four hundred and seventy nine acutely febrile patients presenting between September 2017-2019 were recruited from three city hospitals situated in Ambon, Maluku; Banjarmasin, Kalimantan; and Batam, Batam Island as part of a multi-site observational study. CHIKV RNA was detected in a single serum sample while a separate sample was IgM positive. IgG seroprevalence was also low across all three sites, ranging from 1.4-3.2%. The single RT-PCR positive sample from this study and 24 archived samples collected during other recent outbreaks throughout Indonesia were subjected to complete coding region sequencing to assess the genetic diversity of Indonesian strains. Phylogenetic analysis revealed all to be of a single clade, which was distinct from CHIKV strains recently reported from neighbouring regions including the Philippines and the Pacific Islands. CONCLUSIONS/SIGNIFICANCE: Chikungunya virus strains from recent outbreaks across Indonesia all belong to a single clade. However, low-level seroprevalence and molecular detection of CHIKV across the three study sites appears to contrast with the generally high seroprevalences that have been reported for non-outbreak settings in Java and Bali, and may account for the relative lack of CHIKV epidemiological data from other regions of Indonesia.

Rickettsia felis identified in two fatal cases of acute meningoencephalitis.

BACKGROUND: Rickettsia felis has recently emerged worldwide as a cause of human illness. Typically causing mild, undifferentiated fever, it has been implicated in several cases of non-fatal neurological disease in Mexico and Sweden. Its distribution and pathogenicity in Southeast Asia is poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: We retroactively tested cerebrospinal fluid (CSF) or sera from 64 adult patients admitted to hospital in North Sulawesi, Indonesia with acute neurological disease. Rickettsia felis DNA was identified in the CSF of two fatal cases of meningoencephalitis using multi-locus sequence typing semi-nested PCR followed by Sanger sequencing. DNA from both cases had 100% sequence homologies to the R. felis reference strain URRWXCal2 for the 17-kDa and ompB genes, and 99.91% to gltA. CONCLUSION/SIGNIFICANCE: The identification of R. felis in the CSF of two fatal cases of meningoencephalitis in Indonesia suggests the distribution and pathogenicity of this emerging vector-borne bacteria might be greater than generally recognized. Typically Rickettsia are susceptible to the tetracyclines and greater knowledge of R. felis endemicity in Indonesia should lead to better management of some acute neurological cases.

Distinct Dengue Disease Epidemiology, Clinical, and Diagnosis Features in Western, Central, and Eastern Regions of Indonesia, 2017-2019.

The people of Indonesia have been afflicted by dengue, a mosquito-borne viral disease, for over 5 decades. The country is the world's largest archipelago with diverse geographic, climatic, and demographic conditions that may impact the dynamics of disease transmissions. A dengue epidemiology study was launched by us to compare and understand the dynamics of dengue and other arboviral diseases in three cities representing western, central, and eastern Indonesia, namely, Batam, Banjarmasin, and Ambon, respectively. A total of 732 febrile patients were recruited with dengue-like illness during September 2017-2019 and an analysis of their demographic, clinical, and virological features was performed. The seasonal patterns of dengue-like illness were found to be different in the three regions. Among all patients, 271 (37.0%) were virologically confirmed dengue, while 152 (20.8%) patients were diagnosed with probable dengue, giving a total number of 423 (57.8%) dengue patients. Patients' age and clinical manifestations also differed between cities. Mostly, mild dengue fever was observed in Batam, while more severe cases were prominent in Ambon. While all dengue virus (DENV) serotypes were detected, distinct serotypes dominated in different locations: DENV-1 in Batam and Ambon, and DENV-3 in Banjarmasin. We also assessed the diagnostic features in the study sites, which revealed different patterns of diagnostic agreements, particularly in Ambon. To detect the possibility of infection with other arboviruses, further testing on 461 DENV RT-PCR-negative samples was performed using pan-flavivirus and -alphavirus RT-PCRs; however, only one chikungunya infection was detected in Ambon. A diverse dengue epidemiology in western, central, and eastern Indonesia was observed, which is likely to be influenced by local geographic, climatic, and demographic conditions, as well as differences in the quality of healthcare providers and facilities. Our study adds a new understanding on dengue epidemiology in Indonesia.

Absence of Evidence of Zika Virus Infection in Cord Blood and Urine from Newborns with Congenital Abnormalities, Indonesia.

Zika virus (ZIKV) has recently been confirmed as endemic in Indonesia, but no congenital anomalies (CA) related to ZIKV infection have been reported. We performed molecular and serological testing for ZIKV and other flaviviruses on cord serum and urine samples collected in October 2016 to April 2017 during a prospective, cross-sectional study of neonates in Jakarta, Indonesia. Of a total of 429 neonates, 53 had CA, including 14 with microcephaly. These 53, and 113 neonate controls without evidence of CA, were tested by ZIKV-specific real-time reverse transcription polymerase chain reaction (RT-PCR), pan-flavivirus RT-PCR, anti-ZIKV and anti-DENV IgM ELISA, and plaque reduction neutralization test. There was no evidence of ZIKV infection among neonates in either the CA or non-CA cohorts, except in three cases with low titers of anti-ZIKV neutralizing antibodies. Further routine evaluation throughout Indonesia of pregnant women and their newborns for exposure to ZIKV should be a high priority for determining risk.

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.

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.

Genomic characterization of Zika virus isolated from Indonesia.

Zika virus (ZIKV) JMB-185 strain was isolated from a febrile patient in Jambi, Indonesia in 2014. To understand its genetic characteristics, we performed whole genome sequencing using the Ion Torrent PGM platform on the supernatant of the first passage. The phylogenetic analysis showed that the isolate was not closely related to the Brazilian ZIKV associated with microcephaly or isolates from the recent Singapore Zika outbreak. Molecular evolution analysis indicated that JMB-185 strain may have been circulating in the Southeast Asia region, including Indonesia since 2000. We observed high nucleotide sequence identity between Indonesia, Thailand, Singapore, and American strains although unique amino acid substitutions were also observed. This report provides information on the genomic characteristics of Indonesian ZIKV which may be used for further studies.