Hendra Wibawa

Disease Investigation Center Wates, Yogyakarta, Indonesia

Highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b viruses were isolated from domestic ducks in South Kalimantan, Indonesia, during April 2022. The viruses were genetically similar to those detected in East Asia during 2021-2022. Molecular surveillance of wild birds is needed to detect potential pandemic threats from avian influenza virus.

During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike...

Background The SARS-CoV-2 Omicron variant has replaced the previously dominant Delta variant because of high transmissibility. However, studies on the impact of the Omicron variant on the severity of COVID-19 are still limited in developing countries. Our study aimed to determine the prognostic factors for the outcomes of patients infected with SAR...

Foot-and-mouth disease (FMD) is a contagious disease affecting cloven-hoofed animals, which has been well-documented as one of the major animal diseases that causes severe economic loss in livestock sectors. The disease is endemic in many countries, particularly in Asia and Africa. Indonesia has been declared a disease-free country since 1986, and...

Highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b viruses were detected and isolated from domestic ducks in South Kalimantan, Indonesia during April 2022. The viruses were genetically similar to clade 2.3.4.4b H5N1 viruses recently detected in East Asia from 2021-2022. Further investigation is necessary to determine the source of virus incur...

Anthrax is a worldwide distributing zoonotic disease, caused by Bacillus anthracis , which occurs sporadically in Indonesia, particularly in the provinces of East Java, Central Java, and Yogyakarta, which are the working areas of the Disease Investigation Center (DIC) Wates. Penicillin has been the primary antimicrobial treatment recommended for an...

From 2019 until 2022, some villages in Gunungkidul had anthrax outbreaks twice and infected some people. These facts raise the question: Do the farmers know enough about anthrax and its risk? This study aims to identify the association between farmers’ knowledge of anthrax from the anthrax outbreak village in Gunungkidul regency and their decision...

During 2022, outbreaks of foot-and-mouth disease (FMD) were reported across the islands of Indonesia, a country that had previously maintained an FMD-free (without vaccination) status since 1990. This report describes the near-complete genome sequence of a representative FMD virus collected from these cases belonging to the O/ME-SA/Ind-2001e lineag...

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a newly emerging virus well known as the major cause of the worldwide pandemic due to Coronavirus Disease 2019(COVID-19). Major breakthroughs in the Next Generation Sequencing (NGS) field were elucidated following the first release of a full-length SARS-CoV-2 genome on 10 January 2020,...

Background The SARS-CoV-2 Omicron variant has replaced the previously dominant Delta variant because of high transmissibility. It is responsible for the current increase in the COVID-19 infectivity rate worldwide. However, studies on the impact of the Omicron variant on the severity of COVID-19 are still limited in developing countries. Here, we co...

Wet markets sell fresh food and are a global phenomenon. They are important for food security in many regions worldwide but have come under scrutiny due to their potential role in the emergence of infectious diseases. The sale of live wildlife has been highlighted as a particular risk, and the World Health Organisation has called for the banning of...

Background: Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) has been responsible for the current increase in Coronavirus disease 2019 (COVID-19) infectivity rate worldwide. We compared the impact of the Delta variant and non-Delta variant on the COVID-19 outcomes in patients from Yogyakarta and Central Java pr...

Background: SARS-CoV-2 Delta variant (B.1.617.2) has been responsible for the current increase in COVID-19 infectivity rate worldwide. We compared the impact of the Delta variant and non-Delta variant on the COVID-19 outcomes in patients from Yogyakarta and Central Java provinces, Indonesia. Methods: In this cross-sectional study, we ascertained 1...

Background: The outcome of SARS-CoV-2 infection is determined by multiple factors, including the viral, host genetics, age, and comorbidities. This study investigated the association between prognostic factors and disease outcomes of patients infected by SARS-CoV-2 with multiple S protein mutations. Methods: Fifty-one COVID-19 patients were recrui...

Background and Aim: Anthrax is a non-contagious infectious disease caused by Bacillus anthracis. The bacteria form spores that are resistant to extreme conditions and can contaminate the environment for decades. This study aimed to detect and characterize B. anthracis found in endemic areas of anthrax in Yogyakarta and Central Java province, Indone...

Background: SARS-CoV-2 Delta variant (B.1.617.2) has been responsible for the current increase in COVID-19 infectivity rate worldwide. We compared the impact of the Delta variant and non-Delta variant on the COVID-19 outcomes in patients from Yogyakarta and Central Java provinces, Indonesia. Methods: We ascertained 161 patients, 69 with the Delta v...

Wet markets are important for food security in many regions worldwide but have come under scrutiny due to their potential role in the emergence of infectious diseases. The sale of live wildlife has been highlighted as a particular risk, and the World Health Organisation has called for the banning of live, wild-caught mammalian species in markets un...

Background: Recent studies focusing on the association of SARS-CoV-2 variants of concern (VOC) on COVID-19 outcomes have been reported. However, studies of the impact of multiple mutations within the spike (S) protein of SARS-CoV-2 on COVID-19 illness are limited. This study determined the association between multiple mutations within the S protein...

Objective: A phylogenetic study was carried out on the avian influenza virus (AIV) isolated from a disease outbreak in Sidenreng Rappang Regency, South Sulawesi, Indonesia, in 2018. Material and methods: Oropharyngeal swabs and organ samples were obtained from ducks that showed clinical symptoms: torticollis, fascial edema, neurological disorder...

Background: Transmission within families and multiple spike protein mutations have been associated with the rapid transmission of SARS-CoV-2. We aimed to: 1) describe full genome characterization of SARS-CoV-2 and correlate the sequences with epidemiological data within family clusters, and 2) conduct phylogenetic analysis of all samples from Yogya...

Background and aim: Classical swine fever (CSF) is one of the primary diseases in animals in Indonesia, particularly areas that supply pig meat to the country, such as Karanganyar district, Central Java. The government has tried to prevent and control the disease by vaccination, but it has not yet given effective results. Therefore, another attemp...

Background: Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were: 1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; 2)...

Swine could play a role as a “mixing vessel” for avian and human influenza viruses and should, therefore, be thought of playing an intermediate role in the emergence of pandemic influenza strains. The aim of this study was to identify risk factors for Swine influenza virus (SIV) seropositivity at the farm level in West Java and Banten provinces, In...

Background: Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were 1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; 2) t...

Background and aim: In Indonesia, highly pathogenic avian influenza (HPAI) H5N1 outbreaks in poultry are still reported. The disease causes a decrease in egg production and an increase in mortality; this has an impact on the economic losses of farmers. Several studies have considered that ducks play a role in the HPAI endemicity in the country; ho...

In July 2016, an avian influenza outbreak in duck farms in Yogyakarta province was reported to Disease Investigation Center (DIC) Wates, Indonesia with approximately 1,000 ducks death or culled. In this study, two avian influenza (AI) virus subtypes, A/duck/Bantul/04161291‐OR/2016 (H5N1) and A/duck/Bantul/04161291‐OP/2016 (H9N2) isolated from ducks...

Background and Aim: A previous study divided Indonesian bovine viral diarrhea virus (BVDV)-1 into subgenotypes BVDV-1a to BVDV-1d based on the partial NS5B gene using strain Bega as reference for BVDV-1a. In fact, it is clustered into BVDV-1c with strain Bega-like Australia. BVDV genotyping has been done on isolates from Jakarta, West and Central J...

Highly pathogenic avian influenza (HPAI) A(H5N1) viruses have been circulating since 2003 in Indonesia, with major impacts on poultry health, severe economic losses, and 168 fatal laboratory-confirmed human cases. We performed phylogenetic analysis on 39 full-genome H5N1 virus samples collected during outbreaks among poultry in 2015–2016 in West Ja...

The Eurasian lineage of highly pathogenic avian influenza (HPAI) H5N1 virus has caused poultry outbreaks in many countries across Asia, Europe and Africa. In Indonesia, HPAI (H5N1) virus belonging to clade 2.1 was identified in the initial outbreaks in 2003 (1) and it continued to evolve resulting in different sub-lineages and the major dominance o...

Highly pathogenic avian influenza virus (HPAIV) H5N1 has been reported in Asia, including Indonesia since 2003. Although several risk factors related to the HPAIV outbreaks in poultry in Indonesia have been identified, little is known of the contact structure of farms of different poultry production types (backyard chickens, broilers, layers, and d...

Indonesia came to prominence in the Global Outbreak Alert and Response Network (“GOARN”) on account of a series of human spillover cases of Avian Influenza (AI) H5N1 in 2005. Since then, the Government of Indonesia (“GOI”) has implemented effective control disease measures, and spillover events from poultry to humans are now uncommon. However, the...

H5N1 highly pathogenic avian influenza (HPAI) virus causes high mortality of infected birds, with infection in multiple organs, including in feathers. Feathers have been proposed as samples for diagnosis of HPAI infection in birds, and this study is part of a broader investigation validating the use of feathers for diagnostic purposes. To understan...

Oropharyngeal and cloacal swabs have been widely used for the detection of H5N1 highly pathogenic avian Influenza A virus (HPAI virus) in birds. Previous studies have shown that the feather calamus is a site of H5N1 virus replication and therefore has potential for diagnosis of avian influenza. However, studies characterizing the value of feathers...

After reports of unusually high mortality rates among ducks on farms in Java Island, Indonesia, in September 2012, influenza A(H5N1) viruses were detected and characterized. Sequence analyses revealed all genes clustered with contemporary clade 2.3.2.1 viruses, rather than enzootic clade 2.1.3 viruses, indicating the introduction of an exotic H5N1...

A–G. Phylogenetic tree of PB2, PB1, PA, NP, NA, M, NS (A = PB2; B = PB1; C = PA; D = NP; E = NA; F = M; G = NS). The phylogenetic tree was generated in MEGA version 4, using neighbor-joining analysis with 1000 bootstrap replicates using the Kimura-2 parameter model. Viruses characterized in this study are indicated with a bar showing samples collec...

Phylogenetic tree of PB2, PB1, PA, NP, NA, M, NS (A = PB2; B = PB1; C = PA; D = NP; E = NA; F = M; G = NS). From bird samples collected in Indonesia during September–November 2012.

Ducks are important maintenance hosts for avian influenza, including H5N1 highly pathogenic avian influenza viruses. A previous study indicated that persistence of H5N1 viruses in ducks after the development of humoral immunity may drive viral evolution following immune selection. As H5N1 HPAI is endemic in Indonesia, this mechanism may be importan...

To determine the pathobiology of Indonesian H5N1 highly pathogenic avian influenza, two viruses representing clades 2.1.1 and 2.1.3 were inoculated into broiler chickens and Pekin ducks via the eyes, nostrils and oropharynx. In chickens, both viruses produced fulminant disease; tissue tropism was broad but predominantly endothelial and viral loads...

The Eurasian lineage of H5N1 viruses continue to cause highly pathogenic avian influenza (HPAI) in poultry in some countries in Asia and Africa. In Indonesia, H5N1 clade 2.1 viruses have been known to cause all H5N1 HPAI outbreaks in which 2.1.3 clade viruses have predominantly circulated in poultry in this country since 2005. Most H5N1 HPAI outbre...

Ducks are considered to play an important role in the transmission and maintenance of the Highly Pathogenic Avian Influenza (HPAI) virus. However, there is limited information on duck management practices in countries where HPAI is endemic. A cross-sectional questionnaire survey was conducted on 96 ‘stationary’ smallholder duck farms in Indonesia t...

Background Chicken red blood cells (RBCs) are commonly used in hemagglutination inhibition (HI) tests to measure hemagglutinating antibodies against influenza viruses. The use of horse RBCs in the HI test can reportedly increase its sensitivity when testing human sera for avian influenza antibodies. This study aims to compare the proportion of posi...

SUMMARYA prospective longitudinal study was conducted on 96 smallholder duck farms in Indonesia over a period of 14 months in 2007 and 2008 to monitor bird- and flock-level incidence rates of H5 highly pathogenic avian influenza (HPAI) infection in duck flocks, and to identify risk factors associated with these flocks becoming H5 seropositive. Floc...

Background: Indonesia is one of the countries most severely affected by H5N1 highly pathogenic avian influenza (HPAI) virus in terms of poultry and human health. However, there is little information on the diversity of H5N1 viruses circulating in backyard farms, where chickens and ducks often intermingle. In this study, H5N1 virus infection occurri...

Indonesia is one of the countries most severely affected by H5N1 highly pathogenic avian influenza (HPAI) virus in terms of poultry and human health. However, there is little information on the diversity of H5N1 viruses circulating in backyard farms, where chickens and ducks often intermingle. In this study, H5N1 virus infection occurring in 96 sma...

In Java, Indonesia, during March 2007-March 2008, 96 farms with scavenging ducks that were not vaccinated against highly pathogenic avian influenza (HPAI) were monitored bimonthly. Bird-level (prevalence among individual birds) H5 seroprevalence was 2.6% for ducks and 0.5% for chickens in contact with ducks. At least 1 seropositive bird was detecte...

Avian Pathology Publication details, including instructions for authors and subscription information: Infection studies with two highly pathogenic avian influenza strains (Vietnamese and Indonesian) in Pekin ducks (Anas platyrhynchos), with particular reference to clinical disease, tissue tropism and viral shedding W.(2009)'Infection studies with t...

Pekin ducks were infected by the mucosal route (oral, nasal, ocular) with one of two strains of Eurasian lineage H5N1 highly pathogenic avian influenza virus: A/Muscovy duck/Vietnam/453/2004 and A/duck/Indramayu/BBVW/109/2006 (from Indonesia). Ducks were killed humanely on days 1, 2, 3, 5 and 7 after challenge, or whenever morbidity was severe enou...

The current study evaluated the test characteristics of 2 commercially available rapid antigen tests for highly pathogenic avian influenza. Diagnostic specimens were collected from free-ranging village chickens in Indonesia. A total of 174 healthy, sick, and dead birds were included in the study. The relative diagnostic test sensitivity and the rel...

Jembrana disease is a disease which specifically attack Bali cattle. The causative agent of disease is a virus from family of Lentiviridaeand subfamily of Retroviridae. Development of DNA vaccine candidate, psDNA-CA, was produced by inserting the gag-ca gene which code the capsid (CA) antigen of the virus to an eukaryotic expression vector, pcDNA3....

The resistance of cotton rats, Sigmodon hispidus to Nippostrongylus brasiliensis infection was examined and compared the response to that of the susceptible Indian soft-furred rat, Millardia meltada. After a primary infection with infective third-stage N. brasiliensis larvae (L3), the number of eggs in feces and adult worm recovery rates from the s...

The resistance of cotton rats, Sigmodon hispidus to Nippostrongylus brasiliensis infection was examined and compared the response to that of the susceptible Indian soft-furred rat, Millardia meltada. After a primary infection with infective third-stage N. bra-siliensis larvae (L 3), the number of eggs in feces and adult worm recovery rates from the...