The molecular epidemiological study of hepatitis B virus (HBV) in Indonesia is still limited. This study was aimed to identify the prevalence of HBV pre-S deletion/insertion mutations, and to assess the association of pre-S deletion mutation with liver disease progression in Indonesia. Pre-S mutations were identified by direct sequencing. Of the 265 subjects, 32 samples (12.1%) harbored pre-S deletion/insertion mutations. The prevalence of those pre-S mutations was 2.7% (2/75), 12.9% (8/62), 16.7% (11/66), and 17.7% (11/62) in asymptomatic carrier, chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma groups, respectively. Statistical analysis showed significant difference among them (P = 0.024). In HBV genotype B (HBV/B), pre-S1, pre-S1/S2, and pre-S2 deletion mutations were detected respectively in 3 (17.6%), 4 (23.5%), and 9 (52.9%) of 17 samples. On the other hand, in HBV/C, 12 of 15 samples (80.0%) showed a pre-S2 deletion mutation, and only 2 samples (13.3%) demonstrated a pre-S1/S2 deletion mutation. These results suggest that in HBV/B deletion mutation tends to occur in pre-S1 or pre-S1/S2 region, while in HBV/C the deletion mutation usually occurs in the pre-S2 region. Analysis of complete genome of four viruses confirmed that 3 isolates were classified into HBV/B3, and 1 isolate was HBV/C1. However, SimPlot and BootScan analyses showed that isolate 08.10.002 was an intragenotypic recombinant between HBV/B3 and HBV/B4. As conclusion, the prevalence of HBV pre-S mutations was relatively low in Indonesian patients compared to those from Taiwan, Japan, and other Asian countries. There was a weak association between pre-S deletion mutation and progressive liver disease.

Margalefidinium polykrikoides , an unarmored dinoflagellate, was suspected to be the causative agent of the harmful algal blooms – associated with massive fish mortalities – that have occurred continually in Lampung Bay, Indonesia, since the first bloom event in October 2012. In this study, after examination of the morphology of putative M. polykrikoides -like cysts sampled in bottom sediments, cyst bed distribution of this harmful species was explored in the inner bay. Sediment samples showed that resting cysts, including several morphotypes previously reported as M. polykrikoides , were most abundant on the northern coast of Lampung Bay, ranging from 20.6 to 645.6 cysts g -1 dry sediment. Molecular phylogeny inferred from LSU rDNA revealed that the so-called Mediterranean ribotype was detected in the sediment while M. polykrikoides motile cells, four-cell chain forming in bloom conditions, belonged to the American-Malaysian ribotype. Moreover, hyaline cysts, exclusively in the form of four-cell chains, were also recorded. Overall, these results unequivocally show that the species M. polykrikoides is abundantly present, in the form of vegetative cells, hyaline and resting cysts in an Indonesian area.

Abstract. Abinawanto, Intan MDB, Wardhana W, Bowolaksono A. 2019. DNA barcoding reveals species diversity of mantis shrimp larvae (stomatopods) from Banten Bay, Indonesia. Biodiversitas 20: 1758-1763. Larvae of stomatopods can be morphologically identified by linking between larval and adult form, but it's difficult applied in the laboratory because of requirement of condition to rearing larvae collected either from plankton, or spawning adults in the laboratory. Molecular methods are the alternative approach to gather accurate taxonomic identification. One of molecular methods is DNA barcoding based upon sequence diversity in cytochrome c oxidase subunit 1 (COI). Research on stomatopod larvae diversity and distribution at six stations in Banten Bay has been studied from October 2013 to March 2014. This study was conducted to identify the diversity of stomatopod larvae through DNA barcoding and also to examine the distribution of stomatopod larvae in Banten Bay. DNA barcoding was used to identify mantis shrimp larvae in Banten Bay, Indonesia. Partial mitochondrial COI were obtained for 37 larvae, revealing five distinct molecular operational taxonomic units (MOTUs). All MOTUs distinctively fell into Squillidea clade. Two Molecular Operational Taxonomic Units, MOTUs were successfully identified to species level (i.e. Anchisquilla fasciata), while three others remained identified to genus level (i.e. Stomatopoda spp). The intraspecific variation of COI ranged from 0% to 3.1% (Kimura 2-parameter distance), whereas interspecific divergence ranged from 5.9% to 20.4%. These results imply that COI genes are suitable for species identification of stomatopod larvae in this area, though the number of unidentified species was higher than the identified ones. This is likely because of the limited database in GenBank. In addition, the two identified species represents new records for this area, suggesting that the mantis shrimp in the area have been underestimated based on traditional biodiversity measures. We recommend to develop a taxonomically-comprehensive DNA barcoding database to improve the accuracy and feasibility of using DNA barcoding for species identification of Indonesia mantis shrimps.

Pre-S2 start codon mutation was higher in Indonesian patients compared to other Asian countries, and its prevalence was associated with advanced liver disease, particularly in HBeAg⁺ patients.

The percentage of HBeAg(-) patients is high in Indonesia, and most of the HBeAg(-) patients had been seroconverted. The A1896 mutation was most likely the major cause of HBeAg loss. The T1762/A1764 mutation alone was associated with lower viral loads in HBeAg(+) patients, but not in HBeAg(-) patients.