Optimization of a Low Cost and Broadly Sensitive Genotyping Assay for HIV-1 Drug Resistance Surveillance and Monitoring in Resource-Limited Settings

Commercially available HIV-1 drug resistance (HIVDR) genotyping assays are expensive and have limitations in detecting non-B subtypes and circulating recombinant forms that are co-circulating in resource-limited settings (RLS). This study aimed to optimize a low cost and broadly sensitive in-house assay in detecting HIVDR mutations in the protease (PR) and reverse transcriptase (RT) regions of pol gene. The overall plasma genotyping sensitivity was 95.8% (N = 96). Compared to the original in-house assay and two commercially available genotyping systems, TRUGENE® and ViroSeq®, the optimized in-house assay showed a nucleotide sequence concordance of 99.3%, 99.6% and 99.1%, respectively. The optimized in-house assay was more sensitive in detecting mixture bases than the original in-house (N = 87, P<0.001) and TRUGENE® and ViroSeq® assays. When the optimized in-house assay was applied to genotype samples collected for HIVDR surveys (N = 230), all 72 (100%) plasma and 69 (95.8%) of the matched dried blood spots (DBS) in the Vietnam transmitted HIVDR survey were genotyped and nucleotide sequence concordance was 98.8%; Testing of treatment-experienced patient plasmas with viral load (VL) ≥ and <3 log10 copies/ml from the Nigeria and Malawi surveys yielded 100% (N = 46) and 78.6% (N = 14) genotyping rates, respectively. Furthermore, all 18 matched DBS stored at room temperature from the Nigeria survey were genotyped. Phylogenetic analysis of the 236 sequences revealed that 43.6% were CRF01_AE, 25.9% subtype C, 13.1% CRF02_AG, 5.1% subtype G, 4.2% subtype B, 2.5% subtype A, 2.1% each subtype F and unclassifiable, 0.4% each CRF06_CPX, CRF07_BC and CRF09_CPX

Parasitic crustaceans in fishes from some Philippine Lakes

Parasitic crustaceans are among the most harmful parasites of fishes. Certain species cause disease outbreaks and mortalities in aquaculture, facilities, and sometimes in natural systems, resulting in serious economic losses. Edible fishes from some Philippine lakes also show infestation by parasitic crustaceans. The branchiuran, Argulus indicus Weber, and the copepod, Lernaea cyprinacea Linnaeus, were recovered from the skin and base of the dorsal fin, respectively, of the mudfish Channa striata from Laguna de Bay. L. cyprinacea was also found on the white goby Glossogobius giurus in Naujan Lake. In La Mesa Reservoir, the gills of wild populations of tilapias Oreochromis niloticus and Tilapia zillii, white goby, and silvery theraponid Therapon plumbeus were infected with the copepod, Ergasilus philippinensis Velasquez. An isopod, Alitropus typus Edwards, was recovered from the buccal and gill cavities of several fishes from Lake Taal, namely; the mud gudgeon Ophiocara aporos, cardinal fish Apogon thermalis, silvery theraponid, and cage cultured Oreochromis niloticus. Previous reports and above finding indicate wide host specificity of the parasites. Of these four parasites, only Ergasilus philippinensis has not been reported to cause mass mortality in cultured fishes. Measures should be undertaken to prevent their introduction to other water bodies in which they do not yet occur

Some limnological features of the northern shore areas of Volcano Island, Lake Taal

Abstract only.Physico-chemical and biological features of the northern shore areas of Volcano Island, Lake Taal observed at monthly intervals from four stations during the period 1994 and 1996 indicate varied microhabitats inhabited by a variety of plants and animals. Physico-chemical characteristics of surface waters were: temperature, 28-35°C; dissolved oxygen content, 3.5-6.2 ppm; pH, 7.5-8.9; salinity, 0-24 ppt; and conductivity, 1.6-4.3 S cm-1. Substratum types were mainly sandy with pebbles or rocks or sandy-muddy. Characteristic submerged plants were the eelgrass Vallisneria gigantea and filamentous green algae. In the eelgrass region, atyid shrimps, mostly Ciridina gracilirostris, commonly occur. Snails such as Melanoides costellaris and Terebia granifera were the most abundant benthic animals collected. Other invertebrates identified from core samples were Corbicula manilensis, annelids, crustaceans and chironomid larvae

Fish in a man-made lake: what is there to eat? (Ecological studies in La Mesa Reservoir)

Abstract only.Since 1975, a number of ecological studies have been done in La Mesa Reservoir (also known as La Mesa Dam or La Mesa Lake). Eight species of fish are known to occur in the lake; of these species, one is stocked to control the proliferation of algae. The plankton community of the reservoir has been found to be remarkably diverse, with at least 62 species of zooplankton and possibly 70 species of phytoplankton. The high biological diversity is due to this lake being a protected area as it is Metro Manila's main source of drinking water. A confluence of several factors that preserve this condition of high aquatic biodiversity is possible: (1) Little perturbation in its water quality and its watershed occurs. (2) During high water levels, numerous coves and embayments and the moderate depths create a myriad of ecological niches and refuges for the aquatic biota. (3) Plankton diversity is likely enhanced by abundance of edible algal species (for herbivorous zooplankton) and only occasional moderate algal blooms. (4) Low fish predation tolerates large-sized species in the plankton, i.e., Filipinodiaptomus insulanus, a copepod endemic to only a few large areas in Luzon. (5) Nuisance algae are controlled by stocking of tilapia fry and the occasional use of algicide (CuSO4)

Metazoan parasites of Glossogobius giurus (Hamilton-Buchanan) from Naujan Lake, Oriental Mindoro, Philippines

Thirty-five specimens of Glossogobius giurus (TL = 10.8-23.4 cm, wt. = 8.8-66.3 g) collected from Naujan Lake, Oriental Mindoro from May 1991 to February 1992 were examined for metazoan parasites. The parasite species recovered (their organ location in the host, prevalence (%) and intensity of infection range and mean number of parasites per infected fish) were Neochasmus microvatus (Tubangui, 1928) Tubangui and Masilungan, 1944, (Digenea: Cryptogonimidae), stomach and intestine, 48.6, 1-279 (45.1); Opegaster minima (Tubangui, 1928) Yamaguti, 1934, (Digenea: Opecoelidae), stomach and intestine, 37.1, 1-33 (8.7); larval Diplostomulum sp. Hughes, 1929 (Digenea: Diplostomidae), eyes, 25.7, 1-5 (1.8); and Lernaea cyprinacea L. (Crustacea: Copepoda), skin and muscle, 8.6, 1-2 (13)

Protein-degrading bacteria in the sediments of caged and uncaged sites of Lake Taal, Batangas, Philippines

The populations of protein-degrading bacteria in the sediments of caged (Leviste, Laurel) and uncaged sites (Quiling, Talisay) in Lake Taal were determined by means of the most probable number (MPN) enumeration using nutrient broth containing 12% gelatin. Protein degradation was checked through the liquefaction of gelatin. Results showed that protein degraders in the caged site had MPN of 1.53 x 1010/g dry weight of sediment while the uncaged site had MPN of 6.95 x 109/g dry weight. The populations were 4.98% and 50.0% of the total aerobic heterotrophic bacteria in the sediment for the caged and uncaged sites, respectively. The results indicate that: (a) active protein-degrading bacteria exist in the lake which could readily degrade any proteinaceous feeds present; and (b) there is no big difference between the populations of protein-degrading bacteria in the caged and uncaged sites, the latter possibly being a caged area in the past. These protein-degrading bacteria were identified as probably Bacillus, Aeromonas and Burkholderia. Isolate B44, a Bacillus isolated from the caged site, was found to be the most rapid liquefier of gelatin (liquefaction in three hours)