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Virology Journal Biomed Central Virology Journal BioMed Central Research Open Access Genetic analysis of Thailand hantavirus in Bandicota indica trapped in Thailand Jean-Pierre Hugot1,2, Angelina Plyusnina3, Vincent Herbreteau2, Kirill Nemirov4, Juha Laakkonen5, Åke Lundkvist4, Yupin Supputamongkol6, Heikki Henttonen5 and Alexander Plyusnin*3,4 Address: 1OSEB, UMR 5202 du CNRS, Muséum National d'Histoire naturelle, Paris, France, 2Institut de Recherche pour le Développement, Paris, France, 3Department of Virology, Haartman Institute, University of Helsinki, Finland, 4Swedish Institute for Infectious Disease Control, Stockholm, Sweden, 5Finnish Forest Research Institute, Vantaa, Finland and 6Siriraj Hospital, Bangkok, Thailand Email: Jean-Pierre Hugot - [email protected]; Angelina Plyusnina - [email protected]; Vincent Herbreteau - [email protected]; Kirill Nemirov - [email protected]; Juha Laakkonen - [email protected]; Åke Lundkvist - [email protected]; Yupin Supputamongkol - [email protected]; Heikki Henttonen - [email protected]; Alexander Plyusnin* - [email protected] * Corresponding author Published: 05 September 2006 Received: 10 July 2006 Accepted: 05 September 2006 Virology Journal 2006, 3:72 doi:10.1186/1743-422X-3-72 This article is available from: http://www.virologyj.com/content/3/1/72 © 2006 Hugot et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Sixty one tissue samples from several rodent species trapped in five provinces of Thailand were examined for the presence of hantaviral markers by enzyme-immunoassay and immunoblotting. Four samples, all from the great bandicoot rat Bandicota indica, were confirmed positive for the hantaviral N-antigen. Two of them were trapped in Nakhon Pathom province, the other two in Nakhon Ratchasima province, approximately 250 km from the other trapping site. When analysed by RT-nested PCR, all four rodents were found positive for the hantaviral S- and M-segment nucleotide sequences. Genetic analysis revealed that the four newly described wild-type strains belong to Thailand hantavirus. On the phylogenetic trees they formed a well-supported cluster within the group of Murinae-associated hantaviruses and shared a recent common ancestor with Seoul virus. Background species are recognized [3-5]. The first group is associated Hantaviruses (genus Hantavirus, family Bunyaviridae) are with Murinae rodents (mice and rats of the Old World). robo (from rodent-borne) viruses that cause hemorrhagic The hantaviruses that belonged to the second group are fever with renal syndrome (HFRS) in Eurasia and hantavi- carried by Sigmodontinae rodents (mice and rats of the rus (cardio)pulmonary syndrome (HPS) in the Americas New World). The third group is associated with Arvicoli- [1-3]. In nature, hantaviruses are carried by rodents of nae rodents (voles and lemmings of the north hemi- family Muridae, and each hantavirus species is predomi- sphere) and includes viruses from Europe, Asia and North nantly associated with a unique rodent host species. America. In addition to these three groups, the list of Transmission of the virus to humans occurs by inhalation hantaviral species includes Thottapalayam, so far the only of virus-infected aerosols from excreta of persistently hantavirus found in association with a shrew, Suncus muri- infected animals. Currently three groups of hantavirus nus [6]. Page 1 of 9 (page number not for citation purposes) Virology Journal 2006, 3:72 http://www.virologyj.com/content/3/1/72 Since hantaviruses have been isolated from Murinae recommendations [15]. Animals were collected early in rodents in North Asia and Europe, the association with the morning and transferred to a field laboratory. Geo- this particular group of hosts questions the presence of graphical coordinates of the trapping places were system- hantaviruses in other parts of the World, and particularly atically recorded. Species identification was done using a in South East Asia from where murine rodents are consid- regional taxonomic identification key [7]. Animals were ered to originate and where more than 35 species of Muri- measured, weighted and pictured. Serum samples and nae rodents are living [7]. Several hantaviruses have been organs were stored in cryovials at -70°C. recorded from South-East Asia, particularly: THAIV dis- covered in 1994 [8] in Thailand from a great bandicoot Screening of rodent samples rat, Bandicota indica; and several hantavirus like isolated in Rodent lung tissue samples were screened by immunob- Cambodia from Rattus rattus and R. norvegicus [9]. Also, lotting, for the presence of hantaviral N-antigen as serological surveys carried out to detect evidence of hanta- described earlier [16]. In brief, small chips of tissue virus in human populations or in wild rodents, revealed (approximately 100 mg) were placed into 500 mkl of Lae- positive samples in Thailand and Cambodia [9-12]. From mmli sample buffer and homogenized by sonication. these preliminary results and after confirmation of a first Aliquots of 10 mkl were separated by electrophoresis in human case in Thailand [13] several questions arise: What 10% sodium dodecyl sulphate-polyacrylamide gels and is the genetic diversity of the hantaviruses in South-East blotted with rabbit polyclonal antibody raised against Asia? What are the relationships of the South Asian hanta- Dobrava virus. Goat anti-rabbit antibodies conjugated viruses with the others? What is the real importance of with the horse radish peroxidase (Dako, Glostrup, Den- hantaviruses for human health in this part of the World? mark) were used as secondary antibodies. A confirmatory The answers to these questions clearly deal with the hanta- immunoblotting was performed with the rat anti-SEOV virus biodiversity and phylogeny [4,5,14]. They also sup- antiserum [17]; in this case, rabbit anti-rat antibodies con- pose that coordinated investigations might relate the jugated with the horseraddish peroxidase (Dako, Glos- distribution of the hantaviruses in human populations trup, Denmark) were used as secondary antibodies. and in different rodent species. RNA isolation, reverse transcription (RT)-polymerase The first aim of this study was to examine a set of tissue chain reaction (PCR) and sequencing samples from several rodent species trapped in Thailand, RNA was purified from N antigen- positive samples with for the presence of hantaviral markers. Since the hantavi- the TriPure reagent (Behringer Maannheim) following the ral N-protein antigen was detected in samples from B. manufacturer's instructions. Approximately 100 mg- piece indica, it was decided to attempt a recovery of viral of each lung tissue sample was ground in 1 ml of the genome sequences (S and M segments) from the antigen- TriPure reagent and subjected to RNA extraction. RT-PCR positive tissue samples and to perform a (phylo)genetic of the entire hantaviral S segment was performed essen- analysis using these new data. So far, no complete THAIV tially as described previously [18,19]. Partial sequences of S-sequence has been described in the literature [1] but the S segment (nt 389–946) and the M segment (nt 2021– while this work was in progress a complete THAIV S- 2303) from wild-type THAIV strains were obtained by RT- sequence was deposited to Genbank. This sequence nested PCRs (sequences of primers are available upon belongs to a cell culture isolate 741, originating from request). PCR-amplicons were gel-purified using Thailand. Thus, our data presented an opportunity to QIAquick Gel Extraction -kit (QIAGEN). PCR-amplicon compare the newly recovered sequences of the wild-type containing the entire S-sequences was cloned using the THAIV strains with that of a regular THAI isolate. pGEM-T cloning kit (Promega) and the plasmids were purified with the QIAprep kit (QIAgen). PCR-amplicons Materials and methods containing the partial S- and M-sequences were gel-puri- Trapping/collection fied using QIAquick Gel Extraction -kit (QIAGEN). The Rodents were collected since 2004 during several field plasmids and PCR-amplicons were sequenced automati- studies in the following provinces of Thailand: Nakhon cally using either ABI PRISM™ Dye Terminator or ABI Ratchasima, Sakhon Nakhon, Phrae, Nakhon Pathom PRISM™ M13F and M13R Dye Primer sequencing kits and Loei. Trapping was focused on species living in prox- (Perkin Elmer/ABI, NJ). Multiple nucleotide and amino imity to humans: domestic and peridomestic species, Rat- sequence alignments were prepared manually using tus exulans, R. rattus, R. norvegicus, and the main wild SeqApp 1.9a169 sequence editing program. Hantavirus species occurring in agricultural areas, Bandicota indica sequences used for comparison were recovered from the and B. savilei. The study was conducted in agricultural Gene Bank. areas including rice-growing rural villages either in sea- sonally flooded or non-flooded lands. Trapping and processing were performed according to established safety Page 2 of 9 (page number not for citation purposes) Virology Journal 2006, 3:72 http://www.virologyj.com/content/3/1/72 Phylogenetic analysis Other three sequences differed at 3–7 positions, i.e. To infer phylogenies, the PHYLIP program package [20] shown 1.1–2.4% diversity. Notably, all but one mutation was used first.
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