Pooling sputum samples for Xpert® MTB/RIF and Xpert® Ultra testing for TB diagnosis

Background The use of molecular amplification as-says for TB diagnosis is limited by their costs and cartridge stocks. Pooling multiple samples to test them together is reported to have similar accuracy to individual testing and to save costs. Methods Two surveys of individuals with presumptive TB were conducted to assess the performance of pooled testing using Xpert® MTB/RIF (MTB/RIF) and Xpert® Ultra (Ultra). Results A total of 500 individuals were tested using MTB/RIF, with 72 (14.4%) being MTB-positive. The samples were tested in 125 pools, with 50 pools having 1 MTB-positive and 75 only MTB-negative samples: 46/50 (92%, 95% CI 80.8–97.8) MTB-positive pools tested MTB-positive and 71/75 (94.7%, 95% CI 86.9–98.5) MTB-negative pools tested MTB-negative in the pooled test (agreement: 93.6%, κ = 0.867). Five hundred additional samples were tested using Ultra, with 60 (12%) being MTB-positive. Samples were tested in 125 pools, with 42 having 1 MTB-positive and 83 only MTB-negative samples: 35/42 (83.6%, 95% CI 68.6–93.0) MTB-positive pools tested MTB-positive and 82/83 (98.8%, 95% CI 93.5–100.0) MTB-negative pools tested MTB-negative in the pooled test (agreement: 93.6%, κ = 0.851; P > 0.1 between individual and pooled testing). Pooled testing saved 35% (MTB/RIF) and 46% (Ultra) of cartridges. Conclusions Pooled and individual testing has a high level of agreement and improves testing efficiency

Designing freshwater protected areas (FPAs) for indiscriminate fisheries

Freshwater protected areas (FPAs) are increasingly important for biodiversity conservation, given the intensive use of these systems for water, energy and food production. However, the fisheries benefits of FPAs are not well understood, particularly for indiscriminate fisheries typical of tropical systems. Here we report the results of a model that tests the fisheries effects of no-take protected areas in conditions unique to indiscriminate riverine/floodplain systems. The model has a generalized form applicable to a wide range of systems. We report the results of the general model, as well as those from a specialized form parameterized for the Tonle Sap lake, Cambodia. Both the general and Tonle Sap versions of the model show that FPAs can pay important fisheries benefits, especially where it is difficult to control fishing mortality through gear restrictions or other means. The harvest and profit benefit response curves have similar shapes, with additional FPAs paying high dividends at less than approximately 50% FPA coverage, and then truncating and declining thereafter. In the specific setting of the Tonle Sap of Cambodia, FPAs would pay a large increase in harvest because current FPA coverage is low. It may be counterintuitive to community fisheries managers in Cambodia that the best way to increase harvest is to restrict fishing, but at very high levels of fishing effort, reducing effort or area fished will improve both harvest and profit. In Cambodia, it may make sense to maximize harvest rather than profit because fishers living in poverty need to maximize protein offtake, but the benefits of FPAs remain. Similar considerations may apply in many freshwater and indiscriminate fisheries

Designing freshwater protected areas (FPAs) for indiscriminate fisheries

Freshwater protected areas (FPAs) are increasingly important for biodiversity conservation, given the intensive use of these systems for water, energy and food production. However, the fisheries benefits of FPAs are not well understood, particularly for indiscriminate fisheries typical of tropical systems. Here we report the results of a model that tests the fisheries effects of no-take protected areas in conditions unique to indiscriminate riverine/floodplain systems. The model has a generalized form applicable to a wide range of systems. We report the results of the general model, as well as those from a specialized form parameterized for the Tonle Sap lake, Cambodia. Both the general and Tonle Sap versions of the model show that FPAs can pay important fisheries benefits, especially where it is difficult to control fishing mortality through gear restrictions or other means. The harvest and profit benefit response curves have similar shapes, with additional FPAs paying high dividends at less than approximately 50% FPA coverage, and then truncating and declining thereafter. In the specific setting of the Tonle Sap of Cambodia, FPAs would pay a large increase in harvest because current FPA coverage is low. It may be counterintuitive to community fisheries managers in Cambodia that the best way to increase harvest is to restrict fishing, but at very high levels of fishing effort, reducing effort or area fished will improve both harvest and profit. In Cambodia, it may make sense to maximize harvest rather than profit because fishers living in poverty need to maximize protein offtake, but the benefits of FPAs remain. Similar considerations may apply in many freshwater and indiscriminate fisheries

Conservation of reef corals in the South China Sea based on species and evolutionary diversity

The South China Sea in the Central Indo-Pacific is a large semi-enclosed marine region that supports an extraordinary diversity of coral reef organisms (including stony corals), which varies spatially across the region. While one-third of the world’s reef corals are known to face heightened extinction risk from global climate and local impacts, prospects for the coral fauna in the South China Sea region amidst these threats remain poorly understood. In this study, we analyse coral species richness, rarity, and phylogenetic diversity among 16 reef areas in the region to estimate changes in species and evolutionary diversity during projected anthropogenic extinctions. Our results show that richness, rarity, and phylogenetic diversity differ considerably among reef areas in the region, and that their outcomes following projected extinctions cannot be predicted by species diversity alone. Although relative rarity and threat levels are high in species-rich areas such as West Malaysia and the Philippines, areas with fewer species such as northern Vietnam and Paracel Islands stand to lose disproportionately large amounts of phylogenetic diversity. Our study quantifies various biodiversity components of each reef area to inform conservation planners and better direct sparse resources to areas where they are needed most. It also provides a critical biological foundation for targeting reefs that should be included in a regional network of marine protected areas in the South China Sea. © 2016, Springer Science+Business Media Dordrecht

P1 Laos bats Astrovirus Data_2019Aug16_1656

Data pertaining to bats sampled in Lao PDR for which Astrovirus family testing was performe

Genetic diversity of coronaviruses in bats in Lao PDR and Cambodia

South-East Asia is a hot spot for emerging zoonotic diseases, and bats have been recognized as hosts for a large number of zoonotic viruses such as Severe Acute Respiratory Syndrome (SARS), responsible for acute respiratory syndrome outbreaks. Thus, it is important to expand our knowledge of the presence of viruses in bats which could represent a risk to humans. Coronaviruses (CoVs) have been reported in bat species from Thailand, China, Indonesia, Taiwan and the Philippines. However no such work was conducted in Cambodia or Lao PDR. Between 2010 and 2013, 1965 bats were therefore sampled at interfaces with human populations in these two countries. They were tested for the presence of coronavirus by consensus reverse transcription-PCR assay. A total of 93 samples (4.7%) from 17 genera of bats tested positive. Sequence analysis revealed the presence of potentially 37 and 56 coronavirus belonging to alpha-coronavirus (αCoV) and beta-CoV (βCoV), respectively. The βCoVs group is known to include some coronaviruses highly pathogenic to human, such as SARS-CoV and MERS-CoV. All coronavirus sequences generated from frugivorous bats (family Pteropodidae) (n = 55) clustered with other bat βCoVs of lineage D, whereas one coronavirus from Pipistrellus coromandra fell in the lineage C of βCoVs which also includes the MERS-CoV. αCoVs were all detected in various genera of insectivorous bats and clustered with diverse bat αCoV sequences previously published. A closely related strain of PEDV, responsible for severe diarrhea in pigs (PEDV-CoV), was detected in 2 Myotis bats. We highlighted the presence and the high diversity of coronaviruses circulating in bats from Cambodia and Lao PDR. Three new bat genera and species were newly identified as host of coronaviruses, namely Macroglossus sp., Megaerops niphanae and Myotis horsfieldii

P1 Cambodia bats Astrovirus data_2019Aug16_1658

Data pertaining to bats sampled in Cambodia for which Astrovirus family testing was performe

Data from: Diversity of bat astroviruses in Lao PDR and Cambodia

Astroviruses are known to infect humans and a wide range of animal species, and can cause gastroenteritis in their hosts. Recent studies have reported astroviruses in bats in Europe and in several locations in China. We sampled 1876 bats from 17 genera at 45 sites from 14 and 13 provinces in Cambodia and Lao PDR respectively, and tested them for astroviruses. Our study revealed a high diversity of astroviruses among various Yangochiroptera and Yinpterochiroptera bats. Evidence for varying degrees of host restriction for astroviruses in bats was found. Furthermore, additional Pteropodid hosts were detected. The astroviruses formed distinct phylogenetic clusters within the genus Mamastrovirus, most closely related to other known bat astroviruses. The astrovirus sequences were found to be highly saturated indicating that phylogenetic relationships should be interpreted carefully. An astrovirus clustering in a group with other viruses from diverse hosts, including from ungulates and porcupines, was found in a Rousettus bat. These findings suggest that diverse astroviruses can be found in many species of mammals, including bats

Data from: Genetic diversity of coronaviruses in bats in Lao PDR and Cambodia

South-East Asia is a hot spot for emerging zoonotic diseases, and bats have been recognized as hosts for a large number of zoonotic viruses such as Severe Acute Respiratory Syndrome (SARS), responsible for acute respiratory syndrome outbreaks. Thus, it is important to expand our knowledge of the presence of viruses in bats which could represent a risk to humans. Coronaviruses (CoVs) have been reported in bat species from Thailand, China, Indonesia, Taiwan and the Philippines. However no such work was conducted in Cambodia or Lao PDR. Between 2010 and 2013, 1965 bats were therefore sampled at interfaces with human populations in these two countries. They were tested for the presence of coronavirus by consensus reverse transcription-PCR assay. A total of 93 samples (4.7%) from 17 genera of bats tested positive. Sequence analysis revealed the presence of potentially 37 and 56 coronavirus belonging to alpha-coronavirus (αCoV) and beta-CoV (βCoV), respectively. The βCoVs group is known to include some coronaviruses highly pathogenic to human, such as SARS-CoV and MERS-CoV. All coronavirus sequences generated from frugivorous bats (family Pteropodidae) (n=55) clustered with other bat βCoVs of lineage D, whereas one coronavirus from Pipistrellus coromandra fell in the lineage C of βCoVs which also includes the MERS-CoV. αCoVs were all detected in various genera of insectivorous bats and clustered with diverse bat αCoV sequences previously published. A closely related strain of PEDV, responsible for severe diarrhea in pigs (PEDV-CoV), was detected in 2 Myotis bats. We highlighted the presence and the high diversity of coronaviruses circulating in bats from Cambodia and Lao PDR. Three new bat genera and species were newly identified as host of coronaviruses, namely Macroglossus sp., Megaerops niphanae and Myotis horsfieldii