Publications by authors named "Laurent Gavotte"

26 Publications

  • Page 1 of 1

Understanding the origin of COVID-19 requires to change the paradigm on zoonotic emergence from the spillover model to the viral circulation model.

Infect Genet Evol 2021 Mar 17:104812. Epub 2021 Mar 17.

IHU-Méditerranée Infection and CNRS, Marseille, France.

While the COVID-19 pandemic continues to spread with currently more than 117 million cumulated cases and 2.6 million deaths worldwide as per March 2021, its origin is still debated. Although several hypotheses have been proposed, there is still no clear explanation about how its causative agent, SARS-CoV-2, emerged in human populations. Today, scientifically-valid facts that deserve to be debated still coexist with unverified statements blurring thus the knowledge on the origin of COVID-19. Our retrospective analysis of scientific data supports the hypothesis that SARS-CoV-2 is indeed a naturally occurring virus. However, the spillover model considered today as the main explanation to zoonotic emergence does not match the virus dynamics and somehow misguided the way researches were conducted. We conclude this review by proposing a change of paradigm and model and introduce the circulation model for explaining the various aspects of the dynamic of SARS-CoV-2 emergence in humans.
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http://dx.doi.org/10.1016/j.meegid.2021.104812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7969828PMC
March 2021

Evaluation of fecal immunoassays for canine Echinococcus infection in China.

PLoS Negl Trop Dis 2021 Mar 15;15(3):e0008690. Epub 2021 Mar 15.

Cirad, UMR 17, Intertryp, Campus international de Baillarguet, Montpellier Cedex 5, France.

Human echinococcosis is present worldwide but it is in China that disease prevalence is the highest. In western China, especially in the Tibetan Plateau, the burden of echinococcosis is the most important. Dogs are a major definitive host of Echinococcus and monitoring the presence of Echinococcus worms in dogs is therefore essential to efficiently control the disease. Detection kits based on three different technologies including sandwich ELISA, (indirect) ELISA, and gold immunodiffusion, are currently marketed and used in China. The objective of this work was to assess the efficacy of these kits, in particular with respect to sensitivity and specificity. Four fecal antigen detection kits for canine infection reflecting the three technologies were obtained from companies and tested in parallel on 220 fecal samples. The results indicate that the performance is lower than expected, in particular in terms of sensitivity. The best results were obtained with the sandwich ELISA technology. The gold immunofiltration yielded the poorest results. In all cases, further development is needed to improve the performance of these kits which are key components for the control of echinococcosis.
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http://dx.doi.org/10.1371/journal.pntd.0008690DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7993806PMC
March 2021

Indices and Risk of Dengue Transmission: A Lack of Correlation.

Front Public Health 2020 24;8:328. Epub 2020 Jul 24.

Université de Montpellier, Montpellier, France.

Dengue is present in 128 countries worldwide and is still expanding. There is currently no treatment or universally approved vaccine available. Therefore, prevention and control of mosquito vectors remain the most efficient ways of managing the risk of dengue outbreaks. The indices have been developed as quantitative indicators of the risk of dengue outbreaks. However, conflictual data are circulating about their reliability. We report in this article the first extensive study on indices, covering 78 locations of differing environmental and socio-economic conditions, climate, and population density across Indonesia, from West Sumatra to Papua. A total of 65,876 mosquito larvae and pupae were collected for the study. A correlation was found between incidence and human population density. No correlation was found between the incidence of dengue and the indices.
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http://dx.doi.org/10.3389/fpubh.2020.00328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393615PMC
July 2020

Pseudoscorpion Wolbachia symbionts: diversity and evidence for a new supergroup S.

BMC Microbiol 2020 06 30;20(1):188. Epub 2020 Jun 30.

ISEM, University of Montpellier, Montpellier, France.

Background: Wolbachia are the most widely spread endosymbiotic bacteria, present in a wide variety of insects and two families of nematodes. As of now, however, relatively little genomic data has been available. The Wolbachia symbiont can be parasitic, as described for many arthropod systems, an obligate mutualist, as in filarial nematodes or a combination of both in some organisms. They are currently classified into 16 monophyletic lineage groups ("supergroups"). Although the nature of these symbioses remains largely unknown, expanded Wolbachia genomic data will contribute to understanding their diverse symbiotic mechanisms and evolution.

Results: This report focuses on Wolbachia infections in three pseudoscorpion species infected by two distinct groups of Wolbachia strains, based upon multi-locus phylogenies. Geogarypus minor harbours wGmin and Chthonius ischnocheles harbours wCisc, both closely related to supergroup H, while Atemnus politus harbours wApol, a member of a novel supergroup S along with Wolbachia from the pseudoscorpion Cordylochernes scorpioides (wCsco). Wolbachia supergroup S is most closely related to Wolbachia supergroups C and F. Using target enrichment by hybridization with Wolbachia-specific biotinylated probes to capture large fragments of Wolbachia DNA, we produced two draft genomes of wApol. Annotation of wApol highlights presence of a biotin operon, which is incomplete in many sequenced Wolbachia genomes.

Conclusions: The present study highlights at least two symbiont acquisition events among pseudoscorpion species. Phylogenomic analysis indicates that the Wolbachia from Atemnus politus (wApol), forms a separate supergroup ("S") with the Wolbachia from Cordylochernes scorpioides (wCsco). Interestingly, the biotin operon, present in wApol, appears to have been horizontally transferred multiple times along Wolbachia evolutionary history.
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http://dx.doi.org/10.1186/s12866-020-01863-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325362PMC
June 2020

Genetic homogeneity of Anopheles maculatus in Indonesia and origin of a novel species present in Central Java.

Parasit Vectors 2019 Jul 15;12(1):351. Epub 2019 Jul 15.

University of Montpellier, Montpellier, France.

Background: Anopheles maculatus (s.s.) is an important vector of malaria in Indonesia. Previously it was considered the only member of the Maculatus Group present in Indonesia. A novel species was recently identified in the Kulon Progo District in Central Java. Until recently, few investigations have been conducted looking at An. maculatus genetic diversity in Indonesia, including allopatric island populations.

Methods: Indonesian An. maculatus (s.l.) samples were collected in several locations in Java, Lesser Sunda Island group, Sumatra and in Kulon Progo (Yogyakarta, central Java) where a novel species has been identified. Samples from a 30-year-old colony of the Kulon Progo population were also included in the analysis. Maximum-likelihood analysis established the phylogenies of the ITS2 (nuclear) and cox1 (mitochondrial) markers. Putative times of separation were based on cox1 genetic distances.

Results: Two species of the Maculatus Group are present in Indonesia. The novel sibling species is more closely related to Anopheles dispar than to An. maculatus (s.s.). Anopheles maculatus (s.s.) samples are homogeneous based on the ITS2 sequences. Indonesian samples and An. dispar belong to the same cox1 maternal lineage and differ from all other known members of the Maculatus Group. Divergence time between the different populations found in Java was estimated using an established cox1 mutation rate.

Conclusions: A novel species within the Maculatus Group, most closely related to An. dispar, is confirmed present in the Kulon Progo area of Central Java. The divergence of this species from An. maculatus (s.s.) is explained by the stable refugia in the Kulon Progo area during the quaternary period of intense volcanic activity throughout most of Java. This novel species awaits detailed morphological description before applying a formal species name. For the interim, it is proposed that the Kulon Progo population be designated An. maculatus var. menoreh to distinguish it from An. maculatus (s.s.).
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http://dx.doi.org/10.1186/s13071-019-3598-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6631912PMC
July 2019

Incidence of dengue and chikungunya viruses in mosquitoes and human patients in border provinces of Vietnam.

Parasit Vectors 2017 Nov 9;10(1):556. Epub 2017 Nov 9.

Cirad, Intertryp, UMR 17, TA-A17/G, Campus International de Baillarguet, 34398 Cedex 5, Montpellier, France.

Background: Dengue virus remains a major threat in Vietnam, while chikungunya virus is expected to become one. Surveillance was conducted from 2012 to 2014 in Vietnam to assess the presence of dengue and chikungunya viruses in patients hospitalized with acute fever in five Vietnam provinces neighboring Lao PDR and Cambodia. Surveillance was extended to mosquitoes present in the vicinity of the patients' households.

Results: A total 558 human serum samples were collected along with 1104 adult mosquitoes and 12,041 larvae from 2250 households. Dengue virus was found in 17 (3%) human serum samples and in 9 (0.8%) adult mosquitoes. Chikungunya virus was detected in 2 adult mosquitoes (0.18%) while no chikungunya virus was detected in humans. Differing densities of mosquito populations were found, with the highest in the Long An Province border with Cambodia. Long An Province also displayed the lowest rate of infection, despite a very high Breteau Index, high human population density and presence of the main cross border road system. The highest incidence was found in Dac Nong Province, where the Breteau and Container indices were the second lowest. Dengue virus was detected in five Aedes albopictus, three Aedes aegypti and one Culex vishnui. Chikungunya virus was detected in two Ae. aegypti. All infected mosquitoes belonged to haplotypes described in other parts of the world and a number of novel haplotypes were found among uninfected mosquitoes.

Conclusions: Dengue is considered to be regularly introduced to Vietnam from Cambodia, mostly through human movement. The data reported here provides a complementary picture. Due to intensive international trade, long-distance transportation of mosquito populations may play a role in the regular importation of dengue in Vietnam through Ho Chi Minh City. It is important to decipher the movement of mosquitoes in Vietnam, not only at the Lao PDR and Cambodia borders but also through international trade routes. Mosquito surveillance programs should address and follow mosquito populations instead of mosquito species.
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http://dx.doi.org/10.1186/s13071-017-2422-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5680899PMC
November 2017

Valine/isoleucine variants drive selective pressure in the VP1 sequence of EV-A71 enteroviruses.

BMC Infect Dis 2017 05 8;17(1):333. Epub 2017 May 8.

Cirad, UMR 17, Intertryp, TA-A17/G, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France.

Background: In 2011-2012, Northern Vietnam experienced its first large scale hand foot and mouth disease (HFMD) epidemic. In 2011, a major HFMD epidemic was also reported in South Vietnam with fatal cases. This 2011-2012 outbreak was the first one to occur in North Vietnam providing grounds to study the etiology, origin and dynamic of the disease. We report here the analysis of the VP1 gene of strains isolated throughout North Vietnam during the 2011-2012 outbreak and before.

Methods: The VP1 gene of 106 EV-A71 isolates from North Vietnam and 2 from Central Vietnam were sequenced. Sequence alignments were analyzed at the nucleic acid and protein level. Gene polymorphism was also analyzed. A Factorial Correspondence Analysis was performed to correlate amino acid mutations with clinical parameters.

Results: The sequences were distributed into four phylogenetic clusters. Three clusters corresponded to the subgenogroup C4 and the last one corresponded to the subgenogroup C5. Each cluster displayed different polymorphism characteristics. Proteins were highly conserved but three sites bearing only Isoleucine (I) or Valine (V) were characterized. The isoleucine/valine variability matched the clusters. Spatiotemporal analysis of the I/V variants showed that all variants which emerged in 2011 and then in 2012 were not the same but were all present in the region prior to the 2011-2012 outbreak. Some correlation was found between certain I/V variants and ethnicity and severity.

Conclusions: The 2011-2012 outbreak was not caused by an exogenous strain coming from South Vietnam or elsewhere but by strains already present and circulating at low level in North Vietnam. However, what triggered the outbreak remains unclear. A selective pressure is applied on I/V variants which matches the genetic clusters. I/V variants were shown on other viruses to correlate with pathogenicity. This should be investigated in EV-A71. I/V variants are an easy and efficient way to survey and identify circulating EV-A71 strains.
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http://dx.doi.org/10.1186/s12879-017-2427-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422960PMC
May 2017

Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts.

PeerJ 2016 28;4:e1840. Epub 2016 Mar 28.

UMR5554 ISEM, Université de Montpellier II , Montpellier , France.

Wolbachia is an alpha-proteobacterial symbiont widely distributed in arthropods. Since the identification of Wolbachia in certain animal-parasitic nematodes (the Onchocercidae or filariae), the relationship between arthropod and nematode Wolbachia has attracted great interest. The obligate symbiosis in filariae, which renders infected species susceptible to antibiotic chemotherapy, was held to be distinct from the Wolbachia-arthropod relationship, typified by reproductive parasitism. While co-evolutionary signatures in Wolbachia-arthropod symbioses are generally weak, reflecting horizontal transmission events, strict co-evolution between filariae and Wolbachia has been reported previously. However, the absence of close outgroups for phylogenetic studies prevented the determination of which host group originally acquired Wolbachia. Here, we present the largest co-phylogenetic analysis of Wolbachia in filariae performed to date including: (i) a screening and an updated phylogeny of Wolbachia; (ii) a co-phylogenetic analysis; and (iii) a hypothesis on the acquisition of Wolbachia infection. First, our results show a general overestimation of Wolbachia occurrence and support the hypothesis of an ancestral absence of infection in the nematode phylum. The accuracy of supergroup J is also underlined. Second, although a global pattern of coevolution remains, the signal is derived predominantly from filarial clades associated with Wolbachia in supergroups C and J. In other filarial clades, harbouring Wolbachia supergroups D and F, horizontal acquisitions and secondary losses are common. Finally, our results suggest that supergroup C is the basal Wolbachia clade within the Ecdysozoa. This hypothesis on the origin of Wolbachia would change drastically our understanding of Wolbachia evolution.
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http://dx.doi.org/10.7717/peerj.1840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824920PMC
April 2016

Surveillance of dengue and chikungunya infection in Dong Thap, Vietnam: A 13-month study.

Asian Pac J Trop Med 2016 Jan 19;9(1):39-43. Epub 2015 Dec 19.

National Institute of Hygiene and Epidemiology, 1 Yersin Street, 10000 Hanoi, Viet Nam. Electronic address:

Objective: To establish a surveillance in Dong Thap, at the border with Cambodia by assessing the presence of DENV serotypes and CHIKV among patients hospitalized at Dong Thap general hospital.

Methods: Cross-sectional descriptive analysis was conducted on a cohort of 131 patients hospitalized with acute fever and symptoms compatible with dengue or chikungunya. The study was conducted from January 2012 to February 2013. The full clinical picture was established as well as serological and molecular detection. Serological analysis was sequentially performed on blood samples collected on admission and an average of seven days after admission. The detection of IgM antibody to DENV was performed by IgM capture ELISA and the detection of DENV and CHIKV RNA was done by reverse-transcription multiplex PCR.

Results: 101 patients out of 131 (77%) were confirmed with dengue. All four dengue serotypes were detected with a predominance of DENV2 and DENV4. No chikungunya infection was detected although reported in neighboring Cambodia. A differential efficiency of serological dengue detection was observed. Efficiency was 29% upon admission and 53% after seven days on the same patients. 30 patients out of 131 (23%) were negative with both DENV and CHIKV.

Conclusions: Dengue is at risk of being underestimated and chikungunya is not systematically detected. Changes in detection and surveillance procedures are therefore discussed to increase efficiency of dengue detection and continue the monitoring the emergence of CHIKV in Dong Thap province and in Vietnam.
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http://dx.doi.org/10.1016/j.apjtm.2015.12.008DOI Listing
January 2016

Shaking the Tree: Multi-locus Sequence Typing Usurps Current Onchocercid (Filarial Nematode) Phylogeny.

PLoS Negl Trop Dis 2015 Nov 20;9(11):e0004233. Epub 2015 Nov 20.

Unité Molécules de Communication et Adaptation des Microorganismes, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France.

During the past twenty years, a number of molecular analyses have been performed to determine the evolutionary relationships of Onchocercidae, a family of filarial nematodes encompassing several species of medical or veterinary importance. However, opportunities for broad taxonomic sampling have been scarce, and analyses were based mainly on 12S rDNA and coxI gene sequences. While being suitable for species differentiation, these mitochondrial genes cannot be used to infer phylogenetic hypotheses at higher taxonomic levels. In the present study, 48 species, representing seven of eight subfamilies within the Onchocercidae, were sampled and sequences of seven gene loci (nuclear and mitochondrial) analysed, resulting in the hitherto largest molecular phylogenetic investigation into this family. Although our data support the current hypothesis that the Oswaldofilariinae, Waltonellinae and Icosiellinae subfamilies separated early from the remaining onchocercids, Setariinae was recovered as a well separated clade. Dirofilaria, Loxodontofilaria and Onchocerca constituted a strongly supported clade despite belonging to different subfamilies (Onchocercinae and Dirofilariinae). Finally, the separation between Splendidofilariinae, Dirofilariinae and Onchocercinae will have to be reconsidered.
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http://dx.doi.org/10.1371/journal.pntd.0004233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654488PMC
November 2015

Role of Aedes aegypti and Aedes albopictus during the 2011 dengue fever epidemics in Hanoi, Vietnam.

Asian Pac J Trop Med 2015 Jul 9;8(7):543-8. Epub 2015 Jul 9.

National Institute of Hygiene and Epidemiology, 1 Yersin Street, 10000 Hanoi, Viet Nam.

Objective: To record the human cases of dengue fever (DF) and investigate the Aedes mosquito species circulating during the Hanoi 2011 DF epidemics.

Methods: 24 different outbreak points were recorded in 8 districts between August and December 2011.

Results: 140 patients were hospitalized following dengue diagnostic with a predominance of males (59.3%) and the 15-34 age class. Only DENV-1 (11.27%) and DENV-2 (88.73%) serotypes were detected in human samples. Mosquito sampling performed in and around patients households revealed the predominance of Aedes aegypti (A. aegypti) (95.15%) versus Aedes albopictus (4.85%).

Conclusions: There is a positive correlation between the population density of A. aegypti and the number of human cases and duration of outbreaks. This was not observed for Aedes albopictus. Three pools of A. aegypti were positive with dengue virus, two with DENV-1 and one with DENV-2.
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http://dx.doi.org/10.1016/j.apjtm.2015.06.009DOI Listing
July 2015

Orientia tsutsugamushi, agent of scrub typhus, displays a single metapopulation with maintenance of ancestral haplotypes throughout continental South East Asia.

Infect Genet Evol 2015 Apr 8;31:1-8. Epub 2015 Jan 8.

UM2, CPBS, UMR 5236, CNRS-UM1-UM2, 1919 route de Mende, 34293 Montpellier Cedex 5, France; Cirad, UMR 17, Cirad-Ird, TA-A17/G, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France. Electronic address:

Orientia tsutsugamushi is the causative agent of scrub typhus, a major cause of febrile illness in rural area of Asia-Pacific region. A multi-locus sequence typing (MLST) analysis was performed on strains isolated from human patients from 3 countries in Southeast Asia: Cambodia, Vietnam and Thailand. The phylogeny of the 56-kDa protein encoding gene was analyzed on the same strains and showed a structured topology with genetically distinct clusters. MLST analysis did not lead to the same conclusion. DNA polymorphism and phylogeny of individual gene loci indicated a significant level of recombination and genetic diversity whereas the ST distribution indicated the presence of isolated patches. No correlation was found with the geographic origin. This work suggests that weak divergence in core genome and ancestral haplotypes are maintained by permanent recombination in mites while the 56-kDa protein gene is diverging in higher speed due to selection by the mammalian immune system.
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http://dx.doi.org/10.1016/j.meegid.2015.01.005DOI Listing
April 2015

Fitness cost of Litomosoides sigmodontis filarial infection in mite vectors; implications of infected haematophagous arthropod excretory products in host-vector interactions.

Biomed Res Int 2013 9;2013:584105. Epub 2013 Sep 9.

UMR 7245 MCAM MNHN CNRS, Muséum National d'Histoire Naturelle, 61 rue Buffon, CP52, 75231 Paris Cedex 05, France ; UMR 5554 ISEM CNRS, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier, France.

Filariae are a leading cause of infections which are responsible for serious dermatological, ocular, and vascular lesions. Infective third stage larvae (L3) are transmitted through the bite of a haematophagous vector. Litomosoides sigmodontis is a well-established model of filariasis in the mouse, with the vector being the mite Ornithonyssus bacoti. The aim of the study was to analyse the filarial infection in mites to determine the consequences of filarial infection in the blood-feeding and the reproduction of mites as well as in the regulation of vector-induced inflammation in the mouse skin. Firstly, L3 are unevenly distributed throughout the host population and the majority of the population harbours a moderate infection (1 to 6 L3). Filarial infection does not significantly affect the probing delay for blood feeding. The number of released protonymphs is lower in infected mites but is not correlated with the L3 burden. Finally, induced excreted proteins from infected mites but not from uninfected mites stimulate TNF- α and the neutrophil-chemoattractant KC production by antigen-presenting cells (APCs). Altogether, these results describe the modification of the mite behavior under filarial infection and suggest that the immunomodulatory capacity of the mite may be modified by the presence of the parasite, hindering its defensive ability towards the vertebrate host.
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http://dx.doi.org/10.1155/2013/584105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781844PMC
June 2014

A new type F Wolbachia from Splendidofilariinae (Onchocercidae) supports the recent emergence of this supergroup.

Int J Parasitol 2012 Oct 4;42(11):1025-36. Epub 2012 Oct 4.

Muséum National d'Histoire Naturelle, 61 Rue Buffon, Paris Cedex 05, France.

Wolbachia are vertically transmitted endosymbiotic bacteria of arthropods and onchocercid nematodes. It is commonly accepted that they co-evolved with their filarial hosts, and have secondarily been lost in some species. However, most of the data on the Wolbachia/Onchocercidae relationship have been derived from studies on two subfamilies, the Dirofilariinae and the Onchocercinae, which harbour parasites of humans and domestic animals. Within the last few years, analyses of more diverse material have suggested that some groups of Onchocercidae do not have Wolbachia, such as recently studied Splendidofilariinae from birds. This study takes advantage of the analysis of additional Splendidofilariinae, Rumenfilaria andersoni from a Finnish reindeer and Madathamugadia hiepei from a South African gecko, using PCR, immunohistochemical staining and whole-mount fluorescent analysis to detect Wolbachia and describe its strains. A DNA barcoding approach and phylogenetic analyses were used to investigate the symbiosis between Wolbachia and the Onchocercidae. A new supergroup F Wolbachia was demonstrated in M. hiepei, representing the first filarial nematode harbouring Wolbachia described in a non-mammalian host. In the adult, Wolbachia infects the female germline but not the hypodermis, and intestinal cells are also infected. The phylogenetic analyses confirmed a recent emergence of supergroup F. They also suggested several events of horizontal transmission between nematodes and arthropods in this supergroup, and the existence of different metabolic interactions between the filarial nematodes and their symbionts.
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http://dx.doi.org/10.1016/j.ijpara.2012.09.004DOI Listing
October 2012

Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade.

Infect Genet Evol 2013 Apr 7;15:87-94. Epub 2012 Jun 7.

Virology Unit/National Influenza Centre, Institut Pasteur in Cambodia, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia.

In Cambodia, the first detection of HPAI H5N1 virus in birds occurred in January 2004 and since then there have been 33 outbreaks in poultry while 21 human cases were reported. The origin and dynamics of these epizootics in Cambodia remain unclear. In this work we used a range of bioinformatics methods to analyze the Cambodian virus sequences together with those from neighboring countries. Six HA lineages belonging to clades 1 and 1.1 were identified since 2004. Lineage 1 shares an ancestor with viruses from Thailand and disappeared after 2005, to be replaced by lineage 2 originating from Vietnam and then by lineage 3. The highly adapted lineage 4 was seen only in Cambodia. Lineage 5 is circulating both in Vietnam and Cambodia since 2008 and was probably introduced in Cambodia through unregistered transboundary poultry trade. Lineage 6 is endemic to Cambodia since 2010 and could be classified as a new clade according to WHO/OIE/FAO criteria for H5N1 virus nomenclature. We propose to name it clade 1.1A. There is a direct filiation of lineages 2 to 6 with a temporal evolution and geographic differentiation for lineages 4 and 6. By the end of 2011, two lineages, i.e. lineages 5 and 6, with different transmission paths cocirculate in Cambodia. The presence of lineage 6 only in Cambodia suggests the existence of a transmission specific to this country whereas the presence of lineage 5 in both Cambodia and Vietnam indicates a distinct way of circulation of infected poultry.
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http://dx.doi.org/10.1016/j.meegid.2012.05.013DOI Listing
April 2013

Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters.

Infect Genet Evol 2013 Apr 5;15:77-86. Epub 2012 Jun 5.

Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, 5 Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia.

The Dengue National Control Program was established in Cambodia in 2000 and has reported between 10,000 and 40,000 dengue cases per year with a case fatality rate ranging from 0.7 to 1.7. In this study 39 DENV-2 and 57 DENV-3 viruses isolated from patients between 2000 and 2008 were fully sequenced. Five DENV2 and four DENV3 distinct lineages with different dynamics were identified. Each lineage was characterized by the presence of specific mutations with no evidence of recombination. In both DENV-2 and DENV-3 the lineages present prior to 2003 were replaced after that date by unrelated lineages. After 2003, DENV-2 lineages D2-3 and D2-4 cocirculated until 2007 when they were almost completely replaced by a lineage D2-5 which emerged from D2-3 Conversely, all DENV-3 lineages remained, diversified and cocirculated with novel lineages emerging. Years 2006 and 2007 were marked by a high prevalence of DENV-3 and 2007 with a large dengue outbreak and a high proportion of patients with severe disease. Selective sweeps in DENV-1 and DENV-2 were linked to immunological escape to a predominately DENV-3-driven immunological response. The complex dynamic of dengue in Cambodia in the last ten years has been associated with a combination of stochastic climatic events, cocirculation, coevolution, adaptation to different vector populations, and with the human population immunological landscape.
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http://dx.doi.org/10.1016/j.meegid.2012.05.012DOI Listing
April 2013

The chemokine CXCL12 is essential for the clearance of the filaria Litomosoides sigmodontis in resistant mice.

PLoS One 2012 12;7(4):e34971. Epub 2012 Apr 12.

UMR 7245 MCAM MNHN CNRS & UMR 7205 OSEB MNHN CNRS, Muséum National d'Histoire Naturelle, Paris, France.

Litomosoides sigmodontis is a cause of filarial infection in rodents. Once infective larvae overcome the skin barrier, they enter the lymphatic system and then settle in the pleural cavity, causing soft tissue infection. The outcome of infection depends on the parasite's modulatory ability and also on the immune response of the infected host, which is influenced by its genetic background. The goal of this study was to determine whether host factors such as the chemokine axis CXCL12/CXCR4, which notably participates in the control of immune surveillance, can influence the outcome of the infection. We therefore set up comparative analyses of subcutaneous infection by L. sigmodontis in two inbred mouse strains with different outcomes: one susceptible strain (BALB/c) and one resistant strain (C57BL/6). We showed that rapid parasite clearance was associated with a L. sigmodontis-specific CXCL12-dependent cell response in C57BL/6 mice. CXCL12 was produced mainly by pleural mesothelial cells during infection. Conversely, the delayed parasite clearance in BALB/c mice was neither associated with an increase in CXCL12 levels nor with cell influx into the pleural cavity. Remarkably, interfering with the CXCL12/CXCR4 axis in both strains of mice delayed filarial development, as evidenced by the postponement of the fourth molting process. Furthermore, the in vitro growth of stage 4 filariae was favored by the addition of low amounts of CXCL12. The CXCL12/CXCR4 axis thus appears to have a dual effect on the L. sigmodontis life cycle: by acting as a host-cell restriction factor for infection, and as a growth factor for worms.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034971PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325259PMC
December 2012

Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia.

Infect Genet Evol 2013 Apr 2;15:59-68. Epub 2011 Jul 2.

Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, 5 Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia.

In Cambodia, dengue virus (DENV) was first isolated in 1963 and has become endemic with peak epidemic during raining season. Since 2000, the Dengue National Control Program has reported from 10,000 to 40,000 cases per year with fatality rates ranging from 0.7 to 1.7. All four dengue serotypes are found circulating in Cambodia with alternative predominance of serotypes DENV-2 and DENV-3. The DENV-1 represents from 5% to 20% of all circulating viruses, depending upon the year. In this work, 79 clinical strains of DENV-1 were isolated between 2000 and 2009 and their genome fully sequenced. Four distinct lineages with different dynamics were identified. The main evolutionary drive was negative selective pressure but each lineage was characterized by the presence of specific mutations acquired through evolution. Coexistence, extinction and replacement of lineages occurred over the 10-year period. Lineages 1, 2 and 3 were all detected since 2000-2002 and disappeared in 2003, 2004-2005 and 2007, respectively. Lineages 1 and 2 displayed different dynamics. Lineage 1 was very diverse whereas lineage 2 was very homogeneous. Lineage 4 which derived from lineage 3 in 2003 remained the only one at the end of the sampling period in 2008-2009 owing to a selective sweep. The lineages dynamic of DENV-1 viruses and consequences for molecular epidemiology are discussed.
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http://dx.doi.org/10.1016/j.meegid.2011.06.019DOI Listing
April 2013

Diversity of Orientia tsutsugamushi clinical isolates in Cambodia reveals active selection and recombination process.

Infect Genet Evol 2013 Apr 18;15:25-34. Epub 2010 Sep 18.

Virology Unit, Institut Pasteur in Cambodia, 5 Monivong blvd, PO Box 983, Phnom Penh, Cambodia.

Orientia tsutsugamushi, the causative agent of scrub typhus in South East Asia and Pacific, is an obligate intracellular bacterium closely related to the Rickettsia. The pathogen is transmitted to humans through the bites of infected larvae of trombiculid mites of the genus Leptotrombidium in which is maintained trough vertical transmission mechanism. The infection in rodents has been described in over 20 species. Scrub typhus is commonly confused with other tropical fevers and late diagnosis and treatment can lead to severe organ failures and a strain-dependent mortality rate of up to 50%. A MLST scheme associating seven core function genes: adk, lepB, lipA, lipB, secY, sodB and sucA was developed and validated on seven Cambodian strains detected in patients and two complete reference genomes from Korea and Japan. Sequence data were analyzed both with respect to sequence type (ST) diversity and DNA polymorphism. Differing trends were revealed. DNA polymorphism and phylogeny of individual gene loci indicated a significant level of recombination and genetic diversity. However, the ST distribution is clearly clonal and the clinical situation can be summarized by the formula: one patient, one strain, one ST. This contradiction is only apparent and is most likely the consequence of the unique life cycle of O. tsutsugamushi. The quasi exclusive vertical transmission mode in mites generates repeated bottlenecks and small-size populations and strongly limits genetic diversity. O. tsutsugamushi has developed specific mechanisms for generating genetic diversity which include recombination, duplication and conjugation. Recombination and other mechanisms for increasing genetic diversity are likely to occur in rodents which can act as maintenance hosts, although occurrence in mites cannot be excluded. Consequences for the epidemiology of scrub typhus are discussed.
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http://dx.doi.org/10.1016/j.meegid.2010.08.015DOI Listing
April 2013

Costs and benefits of Wolbachia infection in immature Aedes albopictus depend upon sex and competition level.

J Invertebr Pathol 2010 Nov 31;105(3):341-6. Epub 2010 Aug 31.

Department of Entomology, University of Kentucky, Lexington, KY 40546-0091, USA.

Bacterial endosymbionts induce various effects on hosts and can dramatically impact host fitness and development. An example is provided by obligate, maternally-inherited Wolbachia, which infect a broad range of invertebrates. Wolbachia are capable of altering host reproduction, thereby promoting infection spread. Wolbachia also pose direct physiological costs and benefits to hosts, complicating their categorization as parasites or mutualists. This study examines for an effect of Wolbachia infection in intra-specific larval competition by Aedes albopictus mosquitoes, with the goal of examining for an impact of Wolbachia infection in mixed populations. Similar to prior work examining for an influence of Wolbachia infection on the fitness of A. albopictus in adults, the results presented here support the hypothesized impact of Wolbachia across all life stages, including immatures. The differential competitiveness of infected larvae detected in our experiments indicates that Wolbachia infected A. albopictus females are less competitive relative to uninfected females when competing under highly competitive conditions. In contrast, under low competitive pressures, infected females experience higher survivorship. Thus, Wolbachia infection shifts from parasitism to mutualism as a function of developmental conditions. Results are discussed in relation to the invasion and persistence of Wolbachia in A. albopictus populations. The results are important to the evolution of stable Wolbachia symbioses, including Wolbachia invasion of an uninfected population. The resulting infection dynamics that occur in an infected population are discussed.
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http://dx.doi.org/10.1016/j.jip.2010.08.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3401884PMC
November 2010

Artificial triple Wolbachia infection in Aedes albopictus yields a new pattern of unidirectional cytoplasmic incompatibility.

Appl Environ Microbiol 2010 Sep 2;76(17):5887-91. Epub 2010 Jul 2.

Department of Entomology, University of Kentucky, Lexington, KY 40546, USA.

Obligately intracellular Wolbachia bacteria infect numerous invertebrates and often manipulate host reproduction to facilitate the spread of infection. An example of reproductive manipulation is Wolbachia-induced cytoplasmic incompatibility (CI), which occurs commonly in insects. This CI has been the focus both of basic scientific studies of naturally occurring invasion events and of applied investigations on the use of Wolbachia as a vehicle to drive desired genotypes into insect populations ("gene drive" or "population replacement" strategies). The latter application requires an ability to generate artificial infections that cause a pattern of unidirectional incompatibility with the targeted host population. A suggested target of population replacement strategies is the mosquito Aedes albopictus (Asian tiger mosquito), an important invasive pest and disease vector. Aedes albopictus individuals are naturally "superinfected" with two Wolbachia types: wAlbA and wAlbB. Thus, generating a strain that is unidirectionally incompatible with field populations requires the introduction of an additional infection into the preexisting superinfection. Although prior reports demonstrate an ability to transfer Wolbachia infections to A. albopictus artificially, including both intra- and interspecific Wolbachia transfers, previous efforts have not generated a strain capable of invading natural populations. Here we describe the generation of a stable triple infection by introducing Wolbachia wRi from Drosophila simulans into a naturally superinfected A. albopictus strain. The triple-infected strain displays a pattern of unidirectional incompatibility with the naturally infected strain. This unidirectional CI, combined with a high fidelity of maternal inheritance and low fecundity effects, suggests that the artificial cytotype could serve as an appropriate vehicle for gene drive.
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http://dx.doi.org/10.1128/AEM.00218-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935066PMC
September 2010

Clonal origin of emerging populations of Ehrlichia ruminantium in Burkina Faso.

Infect Genet Evol 2010 Oct 27;10(7):903-12. Epub 2010 May 27.

CIRDES Laboratoire de Biotechnologie (URBIO), 559, 3-51 Avenue du Gouverneur Louveau, B.P. 454, Bobo-Dioulasso, Burkina Faso, France.

Cowdriosis or heartwater is a major tick-borne disease on ruminants in Africa and the Caribbean. The causative agent is Ehrlichia ruminantium, an intracellular bacterium. Development of vaccines against heartwater has been hampered the limited efficiency of vaccine in the field, thought to be a consequence of the high genetic diversity of strains circulating in a same area. A sampling scheme was set to collect ticks over 2 years in a delimited area and well identified flock. Prevalence was low at about 3%. A set of 37 strains was considered for MLST analysis along with two reference strains, i.e. ERGA and ERWO, for which full-length genome was available, using a previously described scheme based on the genes gltA, groEL, lepA, lipA, lipB, secY, sodB and sucA. Two populations were identified both with limited genetic variability but with differing evolutionary patterns. Population 1 is in genomic stasis, in agreement with the paradigm for intracellular bacteria. The two reference strains, one from the Caribbean separated from West African strains three centuries ago and another one isolated in South Africa, belong to Population 1. Population 2 is on expansion following a recent clonal emergence from Population 1. The founder strain was identified as strain 395. Strain 623 displays a particularly high rate of mutations in groEL. Owing to the chaperone function of GroEL, this might indicate another clonal emergence under way. This work brings further insight in the genomic plasticity of E. ruminantium and its impact on vaccine strategy.
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http://dx.doi.org/10.1016/j.meegid.2010.05.011DOI Listing
October 2010

Wolbachia infection and resource competition effects on immature Aedes albopictus (Diptera: Culicidae).

J Med Entomol 2009 May;46(3):451-9

Department of Entomology, University of Kentucky, S-225 Agricultural Science Center, Building North, Lexington, KY 40546-0091, USA.

Wolbachia pipientis Hertig and Wolbach (Rickettsiales: Rickettsiaceae) are intracellular alpha-proteobacteria that occur naturally in Aedes albopictus (Skuse) (Diptera: Culicidae) and numerous other invertebrates. These endosymbionts can invade host populations by manipulating host reproduction. Wolbachia infections have been shown to impart both costs and benefits to hosts in terms of development, survival, and fecundity. Here, we monitor intraspecific competition among independent cohorts of infected or uninfected larvae. Levels of competition are manipulated by varying initial larval densities and food levels. Although larval density is observed to have major impacts on immature survivorship, sex ratio of eclosing adults, and developmental rates, the Wolbachia infection status had minimal impact on male immatures and no effect on immature females under these experimental conditions. Female and male immatures were observed to respond differently to competitive pressure, with the functional relationships of females and males consistent with scramble and contest competition, respectively. The results are discussed in relation to the evolution of naturally occurring Wolbachia infections in Ae. albopictus (i.e., natural population replacement events) and public health strategies that propose the manipulation of Wolbachia infections in Ae. albopictus populations.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2719795PMC
http://dx.doi.org/10.1603/033.046.0306DOI Listing
May 2009

Genome-wide analysis of the interaction between the endosymbiotic bacterium Wolbachia and its Drosophila host.

BMC Genomics 2008 Jan 2;9. Epub 2008 Jan 2.

Department of Entomology; University of Kentucky; Lexington, KY 40546, USA.

Background: Intracellular Wolbachia bacteria are obligate, maternally-inherited, endosymbionts found frequently in insects and other invertebrates. The success of Wolbachia can be attributed in part to an ability to alter host reproduction via mechanisms including cytoplasmic incompatibility (CI), parthenogenesis, feminization and male killing. Despite substantial scientific effort, the molecular mechanisms underlying the Wolbachia/host interaction are unknown.

Results: Here, an in vitro Wolbachia infection was generated in the Drosophila S2 cell line, and transcription profiles of infected and uninfected cells were compared by microarray. Differentially-expressed patterns related to reproduction, immune response and heat stress response are observed, including multiple genes that have been previously reported to be involved in the Wolbachia/host interaction. Subsequent in vivo characterization of differentially-expressed products in gonads demonstrates that Angiotensin Converting Enzyme (Ance) varies between Wolbachia infected and uninfected flies and that the variation occurs in a sex-specific manner. Consistent with expectations for the conserved CI mechanism, the observed Ance expression pattern is repeatable in different Drosophila species and with different Wolbachia types. To examine Ance involvement in the CI phenotype, compatible and incompatible crosses of Ance mutant flies were conducted. Significant differences are observed in the egg hatch rate resulting from incompatible crosses, providing support for additional experiments examining for an interaction of Ance with the CI mechanism.

Conclusion: Wolbachia infection is shown to affect the expression of multiple host genes, including Ance. Evidence for potential Ance involvement in the CI mechanism is described, including the prior report of Ance in spermatid differentiation, Wolbachia-induced sex-specific effects on Ance expression and an Ance mutation effect on CI levels. The results support the use of Wolbachia infected cell cultures as an appropriate model for predicting in vivo host/Wolbachia interactions.
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http://dx.doi.org/10.1186/1471-2164-9-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253531PMC
January 2008

Absence of Wolbachia in nonfilariid worms parasitizing arthropods.

Curr Microbiol 2007 Sep 25;55(3):193-7. Epub 2007 Jul 25.

Equipe Génétique de l'Adaptation, Institut des Sciences de l'Evolution, Université de Montpellier II, C.C. 065, F-34095 Montpellier, cedex 05, France.

Wolbachia are strictly intracellular maternally inherited alpha-proteobacteria, largely widespread among arthropods and filariids (i.e., filarial nematodes). Wolbachia capacities to infect new host species have been greatly evidenced and the transfer of Wolbachia between arthropods and filariids has probably occurred more than once. Interestingly, among nematode species, Wolbachia infection was found in filariids but not in closely related lineages. Their occurrence in filariids has been supposed a consequence of the parasitic lifestyle of worms within Wolbachia-infected arthropods, implying that nonfilariid worms parasitizing arthropods are also likely to be infected by some Wolbachia acquired from their hosts. To further investigate this hypothesis, we have examined seven species of nonfilariid worms of Nematoda and Nematomorpha phyla, all interacting intimately with arthropods. Wolbachia infection in nonfilariid parasitic worms was never detected by polymerase chain reaction assays of the 16S rDNA and wsp genes. By contrast, some arthropod hosts are well infected by Wolbachia of the B supergroup. Then the intimate contact with infected arthropods is not a sufficient condition to explain the Wolbachia occurrence in filariids and could underline a physiological singularity or a particular evolutionary event to acquire and maintain Wolbachia infection.
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http://dx.doi.org/10.1007/s00284-006-0578-4DOI Listing
September 2007

A Survey of the bacteriophage WO in the endosymbiotic bacteria Wolbachia.

Mol Biol Evol 2007 Feb 9;24(2):427-35. Epub 2006 Nov 9.

Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS, IFR 41, University Lyon 1, Villeurbanne, France.

Bacteriophages are common viruses infecting prokaryotes. In addition to their deadly effect, phages are also involved in several evolutionary processes of bacteria, such as coding functional proteins potentially beneficial to them, or favoring horizontal gene transfer through transduction. The particular lifestyle of obligatory intracellular bacteria usually protects them from phage infection. However, Wolbachia, an intracellular alpha-proteobacterium, infecting diverse arthropod and nematode species and best known for the reproductive alterations it induces, harbors a phage named WO, which has recently been proven to be lytic. Here, phage infection was checked in 31 Wolbachia strains, which induce 5 different effects in their hosts and infect 25 insect species and 3 nematodes. Only the Wolbachia infecting nematodes and Trichogramma were found devoid of phage infection. All the 25 detected phages were characterized by the DNA sequence of a minor capsid protein gene. Based on all data currently available, phylogenetic analyses show a lack of congruency between Wolbachia or insect and phage WO phylogenies, indicating numerous horizontal transfers of phage among the different Wolbachia strains. The absence of relation between phage phylogeny and the effects induced by Wolbachia suggests that WO is not directly involved in these effects. Implications on phage WO evolution are discussed.
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http://dx.doi.org/10.1093/molbev/msl171DOI Listing
February 2007