SURVEILLANCE IN 2013 OF AVIAN INFLUENZA VIRUS FROM LIVE-BIRD MARKETS IN BANGKOK, THAILAND.

Live-bird markets have been implicated in transmission of avian influenza viruses, most recently of influenza A (H7N9) in China. Low pathogenic avian influenza (LPAI) viruses, such as H7N9, cause asymptomatic infections in poultry, and active surveillance is required to detect infection and to prevent transmission to humans. Although limited numbers of live birds for consumption are sold in Bangkok live bird markets (LBM), transmission of H7N9 in nearby China has prompted a program of active surveillance for avian influenza in Bangkok LBM to determine LPAI viruses. In November 2013, Bangkok One Health team organized avian influenza surveillance in all nine districts of Bangkok with LBMs. Oropharyngeal swabs (n = 834), sera (n = 375) and fresh feces (n = 420) were taken from 400 chickens, 20 ducks, 20 geese and 394 pet birds from 75/87 shops. Additionally, drinking water (n = 208) and waste water (n = 26) were collected. Samples were tested for influenza A viruses using RT-PCR. In addition, samples were inoculated in eggs and tested by hemagglutination (HA) and hemagglutination inhibition (HI) assays using H5N1- and H7N9-specific antigens. Sera were tested by HI assay using similar antigens. No sample was found positive for influenza A virus. These data provide evidence that avian influenza viruses, including LPAI viruses such as H7N9, were not circulating in Bangkok LBMs during the period surveyed.

Is Leopoldamys neilli (Rodentia, Muridae) a synonym of Leopoldamys herberti? A reply to Balakirev et al. (2013).

Recently, Balakirev et al. (2013) presented a taxonomic revision of the genus Leopoldamys based on phylogenetic analyses. They identified five main Leopoldamys genetic lineages and suggested to rename several of them. According to these authors, the genetic lineage previously thought to belong to L. edwardsi (lineage L1) should be assigned to L. revertens while L. neilli (lineage L2) should be considered as a junior synonym of L. herberti. Using molecular and morphological data from a large sampling of Leopoldamys specimens, the aim of the present study was to investigate the taxonomic status of L. herberti and L. neilli. This study reveals that, contrary to Balakirev et al.'s statement, both genetic lineages L1 and L2 occur in Nakhon Ratchasima Province, close to the type locality of L. herberti. We also show that the external measurements and color pattern of L. herberti are highly similar to those of L1 specimens but are not consistent with the morphology of L2 specimens. Therefore these results strongly suggest that L. herberti should be assigned to the genetic lineage L1. Consequently L. neilli should not be considered as a junior synonym of L. herberti and this study confirms that the appropriate name of the genetic lineage L2 is L. neilli. Moreover, as our results show that L. herberti should be assigned to the lineage L1, this name has nomenclatural priority over L. revertens, the species name suggested by Balakirev et al. (2013) for this lineage.

Combined mitochondrial and nuclear markers revealed a deep vicariant history for Leopoldamys neilli, a cave-dwelling rodent of Thailand.

BACKGROUND: Historical biogeography and evolutionary processes of cave taxa have been widely studied in temperate regions. However, Southeast Asian cave ecosystems remain largely unexplored despite their high scientific interest. Here we studied the phylogeography of Leopoldamys neilli, a cave-dwelling murine rodent living in limestone karsts of Thailand, and compared the molecular signature of mitochondrial and nuclear markers. METHODOLOGY/PRINCIPAL FINDINGS: We used a large sampling (n = 225) from 28 localities in Thailand and a combination of mitochondrial and nuclear markers with various evolutionary rates (two intronic regions and 12 microsatellites). The evolutionary history of L. neilli and the relative role of vicariance and dispersal were investigated using ancestral range reconstruction analysis and Approximate Bayesian computation (ABC). Both mitochondrial and nuclear markers support a large-scale population structure of four main groups (west, centre, north and northeast) and a strong finer structure within each of these groups. A deep genealogical divergence among geographically close lineages is observed and denotes a high population fragmentation. Our findings suggest that the current phylogeographic pattern of this species results from the fragmentation of a widespread ancestral population and that vicariance has played a significant role in the evolutionary history of L. neilli. These deep vicariant events that occurred during Plio-Pleistocene are related to the formation of the Central Plain of Thailand. Consequently, the western, central, northern and northeastern groups of populations were historically isolated and should be considered as four distinct Evolutionarily Significant Units (ESUs). CONCLUSIONS/SIGNIFICANCE: Our study confirms the benefit of using several independent genetic markers to obtain a comprehensive and reliable picture of L. neilli evolutionary history at different levels of resolution. The complex genetic structure of Leopoldamys neilli is supported by congruent mitochondrial and nuclear markers and has been influenced by the geological history of Thailand during Plio-Pleistocene.