Publications by authors named "Roger Frutos"

69 Publications

Fast Expansion of the Asian-Pacific Genotype of the Chikungunya Virus in Indonesia.

Front Cell Infect Microbiol 2021 21;11:631508. Epub 2021 Apr 21.

Cirad, UMR 17, Intertryp, Montpellier, France.

Chikungunya is repeatedly affecting Indonesia through successive outbreaks. The Asian genotype has been present in Asia since the late 1950s while the ECSA-IOL (East/Central/South Africa - Indian Ocean Lineage) genotype invaded Asia in 2005. In order to determine the extension of the circulation of the chikungunya virus (CHIKV) in Indonesia, mosquitoes were collected in 28 different sites from 12 Indonesian provinces in 2016-2017. The E1 subunit of the CHIKV envelope gene was sequenced while mosquitoes were genotyped using the mitochondrial 1 (cytochrome C oxidase subunit 1) gene to determine whether a specific population was involved in the vectoring of CHIKV. A total of 37 CHIKV samples were found in 28 , 8 and 1 out of 15,362 samples collected and tested. These viruses, like all Indonesian CHIKV since 2000, belonged to a genotype we propose to call the Asian-Pacific genotype. It also comprises the Yap isolates and viruses having emerged in Polynesia, the Caribbean and South America. They differ from the CHIKV of the Asian genotype found earlier in Indonesia indicating a replacement. These results raise the question of the mechanisms behind this fast and massive replacement.
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http://dx.doi.org/10.3389/fcimb.2021.631508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8098665PMC
April 2021

Emergence of Bat-Related Betacoronaviruses: Hazard and Risks.

Front Microbiol 2021 15;12:591535. Epub 2021 Mar 15.

Aix Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.

The current Coronavirus Disease 2019 (COVID-19) pandemic, with more than 111 million reported cases and 2,500,000 deaths worldwide (mortality rate currently estimated at 2.2%), is a stark reminder that coronaviruses (CoV)-induced diseases remain a major threat to humanity. COVID-19 is only the latest case of betacoronavirus (β-CoV) epidemics/pandemics. In the last 20 years, two deadly CoV epidemics, Severe Acute Respiratory Syndrome (SARS; fatality rate 9.6%) and Middle East Respiratory Syndrome (MERS; fatality rate 34.7%), plus the emergence of HCoV-HKU1 which causes the winter common cold (fatality rate 0.5%), were already a source of public health concern. Betacoronaviruses can also be a threat for livestock, as evidenced by the Swine Acute Diarrhea Syndrome (SADS) epizootic in pigs. These repeated outbreaks of β-CoV-induced diseases raise the question of the dynamic of propagation of this group of viruses in wildlife and human ecosystems. SARS-CoV, SARS-CoV-2, and HCoV-HKU1 emerged in Asia, strongly suggesting the existence of a regional hot spot for emergence. However, there might be other regional hot spots, as seen with MERS-CoV, which emerged in the Arabian Peninsula. β-CoVs responsible for human respiratory infections are closely related to bat-borne viruses. Bats are present worldwide and their level of infection with CoVs is very high on all continents. However, there is as yet no evidence of direct bat-to-human coronavirus infection. Transmission of β-CoV to humans is considered to occur accidentally through contact with susceptible intermediate animal species. This zoonotic emergence is a complex process involving not only bats, wildlife and natural ecosystems, but also many anthropogenic and societal aspects. Here, we try to understand why only few hot spots of β-CoV emergence have been identified despite worldwide bats and bat-borne β-CoV distribution. In this work, we analyze and compare the natural and anthropogenic environments associated with the emergence of β-CoV and outline conserved features likely to create favorable conditions for a new epidemic. We suggest monitoring South and East Africa as well as South America as these regions bring together many of the conditions that could make them future hot spots.
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http://dx.doi.org/10.3389/fmicb.2021.591535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8005542PMC
March 2021

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

Meteorological Factors and the Transmissibility of Hand, Foot, and Mouth Disease in Xiamen City, China.

Front Med (Lausanne) 2020 22;7:597375. Epub 2021 Jan 22.

State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen City, China.

As an emerging infectious disease, the prevention and control of hand, foot, and mouth disease (HFMD) poses a significant challenge to the development of public health in China. In this study, we aimed to explore the mechanism of the seasonal transmission characteristics of HFMD and to reveal the correlation and potential path between key meteorological factors and the transmissibility of HFMD. Combined with daily meteorological data such as average temperature, average relative humidity, average wind velocity, amount of precipitation, average air pressure, evaporation capacity, and sunshine duration, a database of HFMD incidence and meteorological factors was established. Spearman rank correlation was used to calculate the correlation between the various meteorological factors and the incidence of HFMD. The effective reproduction number ( ) of HFMD was used as an intermediate variable to further quantify the dynamic relationship between the average temperature and . A total of 43,659 cases of HFMD were reported in Xiamen from 2014 to 2018. There was a significantly positive correlation between the average temperature and the incidence of HFMD ( = 0.596, < 0.001), and a significantly negative correlation between the average air pressure and the incidence of HFMD ( = -0.511, < 0.001). There was no correlation between the average wind velocity ( = 0.045, > 0.05) or amount of precipitation ( = 0.043, > 0.05) and incidence. There was a temperature threshold for HFMD's transmissibility. Owing to the seasonal transmission characteristics of HFMD in Xiamen, the temperature threshold of HFMD's transmissibility was 13.4-18.4°C and 14.5-29.3°C in spring and summer and in autumn and winter, respectively. HFMD's transmissibility may be affected by the average temperature; the temperature threshold range of transmissibility in autumn and winter is slightly wider than that in spring and summer. Based on our findings, we suggest that the relevant epidemic prevention departments should pay close attention to temperature changes in Xiamen to formulate timely prevention strategies before the arrival of the high-risk period.
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http://dx.doi.org/10.3389/fmed.2020.597375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7862718PMC
January 2021

Dengue fever transmission between a construction site and its surrounding communities in China.

Parasit Vectors 2021 Jan 6;14(1):22. Epub 2021 Jan 6.

Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, People's Republic of China.

Background: Due to an increase in mosquito habitats and the lack facilities to carry out basic mosquito control, construction sites in China are more likely to experience secondary dengue fever infection after importation of an initial infection, which may then increase the number of infections in the neighboring communities and the chance of community transmission. The aim of this study was to investigate how to effectively reduce the transmission of dengue fever at construction sites and the neighboring communities.

Methods: The Susceptible-Exposed-Infectious/Asymptomatic-Recovered (SEIAR) model of human and SEI model of mosquitoes were developed to estimate the transmission of dengue virus between humans and mosquitoes within the construction site and within a neighboring community, as well between each of these. With the calibrated model, we further estimated the effectiveness of different intervention scenarios targeting at reducing the transmissibility at different locations (i.e. construction sites and community) with the total attack rate (TAR) and the duration of the outbreak (DO).

Results: A total of 102 construction site-related and 131 community-related cases of dengue fever were reported in our area of study. Without intervention, the number of cases related to the construction site and the community rose to 156 (TAR: 31.25%) and 10,796 (TAR: 21.59%), respectively. When the transmission route from mosquitoes to humans in the community was cut off, the number of community cases decreased to a minimum of 33 compared with other simulated scenarios (TAR: 0.068%, DO: 60 days). If the transmission route from infectious mosquitoes in the community and that from the construction site to susceptible people on the site were cut off at the same time, the number of cases on the construction site dropped to a minimum of 74 (TAR: 14.88%, DO: 66 days).

Conclusions: To control the outbreak of dengue fever effectively on both the construction site and in the community, interventions needed to be made both within the community and from the community to the construction site. If interventions only took place within the construction site, the number of cases on the construction site would not be reduced. Also, interventions implemented only within the construction site or between the construction site and the community would not lead to a reduction in the number of cases in the community.
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http://dx.doi.org/10.1186/s13071-020-04463-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7787407PMC
January 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

COVID-19: Time to exonerate the pangolin from the transmission of SARS-CoV-2 to humans.

Infect Genet Evol 2020 10 5;84:104493. Epub 2020 Aug 5.

IHU-Méditerranée Infection and CNRS, Marseille, France.

The emergence of COVID-19 has triggered many works aiming at identifying the animal intermediate potentially involved in the transmission of SARS-CoV-2 to humans. The presence of SARS-CoV-2-related viruses in Malayan pangolins, in silico analysis of the ACE2 receptor polymorphism and sequence similarities between the Receptor Binding Domain (RBD) of the spike proteins of pangolin and human Sarbecoviruses led to the proposal of pangolin as intermediary. However, the binding affinity of the pangolin ACE2 receptor for SARS-CoV-2 RBD was later on reported to be low. Here, we provide evidence that the pangolin is not the intermediate animal at the origin of the human pandemic. Moreover, data available do not fit with the spillover model currently proposed for zoonotic emergence which is thus unlikely to account for this outbreak. We propose a different model to explain how SARS-CoV-2 related coronaviruses could have circulated in different species, including humans, before the emergence of COVID-19.
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http://dx.doi.org/10.1016/j.meegid.2020.104493DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7405773PMC
October 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

Imported malaria cases in former endemic and non-malaria endemic areas in China: are there differences in case profile and time to response?

Infect Dis Poverty 2019 Jul 5;8(1):61. Epub 2019 Jul 5.

National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research; Key Laboratory of Parasite and Vector Biology, Ministry of Health; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; WHO Collaborating Center for Tropical Diseases, Shanghai, China.

Background: China has achieved zero indigenous malaria case report in 2017. However, along with the increasing of international cooperation development, there is an increasing number of imported malaria cases from Chinese nationals returning from malaria-affected countries. Previous studies have focused on malaria endemic areas in China. There is thus limited information on non-endemic areas in China, especially on the performance of malaria surveillance and response in health facilities.

Methods: A comparative retrospective study was carried out based on routine malaria surveillance data collected from 2013 to 2017. All imported malaria cases reported within the mainland of China were included. Variables used in the comparative analysis between cases in former endemic and former non-endemic areas, included age, gender and occupation, destination of overseas travel, Plasmodium species and patient health outcome. Monthly aggregated data was used to compare seasonal and spatial characteristics. Geographical distribution and spatial-temporal aggregation analyses were conducted. Time to diagnosis and report, method of diagnosis, and level of reporting/diagnosing health facilities were used to assess performance of health facilities.

Results: A total of 16 733 malaria cases, out of which 90 were fatal, were recorded in 31 provinces. The majority of cases (96.2%) were reported from former malaria endemic areas while 3.8% were reported from former non-malaria endemic areas. Patients in the age class from 19 to 59 years and males made the highest proportion of cases in both areas. There were significant differences between occupational categories in the two areas (P <  0.001). In former endemic areas, the largest proportion of cases was among outdoor workers (80%). Two peaks (June, January) and three peaks (June, September and January) were found in former endemic and former non-endemic areas, respectively. Time between the onset of symptoms and diagnosis at clinics was significantly different between the two areas at different level of health facilities (P <  0.05).

Conclusions: All the former non-endemic areas are now reporting imported malaria cases. However, the largest proportion of imported cases is still reported from former endemic areas. Health facilities in former endemic areas outperformed those in former non-endemic areas. Information, treatment, and surveillance must be provided for expatriates while capacity building and continuous training must be implemented at health facilities in China.
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http://dx.doi.org/10.1186/s40249-019-0571-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6610923PMC
July 2019

First evidence of the presence of genotype-1 of Japanese encephalitis virus in Culex gelidus in Indonesia.

Parasit Vectors 2019 Jan 8;12(1):19. Epub 2019 Jan 8.

Université de Montpellier, Montpellier, France.

Background: Japanese encephalitis has become a public health threat in Indonesia. Three genotypes have been recorded in Indonesia, i.e. genotype II (GII), genotype III (GIII) and genotype IV (GIV). Genotype I (GI) and genotype V (GV) have never been reported in Indonesia.

Results: A Japanese encephalitis virus (JEV) belonging to the genotype I-a (GI-a) has been isolated for the first time from a Culex gelidus mosquito in the Province of Jambi, Indonesia. This virus is related to a 1983 isolate from Thailand whereas the infected Cx. gelidus mosquito belonged to a Chinese haplotype.

Conclusions: Surveillance of JEV and mosquito dissemination is recommended.
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http://dx.doi.org/10.1186/s13071-018-3285-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325860PMC
January 2019

Monitoring of malaria vectors at the China-Myanmar border while approaching malaria elimination.

Parasit Vectors 2018 Sep 15;11(1):511. Epub 2018 Sep 15.

Interdisciplinary Center for Mathematical and Computational Modelling, University of Warsaw, Tyniecka 15/17, 02-630, Warsaw, Poland.

Background: Tengchong County was one of the counties located at the China-Myanmar border with high malaria incidence in the previous decades. As the pilot county for malaria elimination at the border area, Tengchong County is aiming to be the first county to achieve malaria elimination goal. A cross-sectional entomological survey was carried out to evaluate the feasibility of elimination approach and assess the receptivity of malaria reintroduction.

Methods: Light traps associated with live baits were used to investigate the abundance of adult mosquitoes in nine villages in Tengchong County. Light traps were set to collect adult mosquitoes in both human houses and cowsheds from dusk till dawn in each site.

Results: A total of 4948 adult Anopheles mosquitoes were collected from May to December in two villages. Of the mosquitoes were captured, 24.2% were in human houses and 75.8% in cowsheds. The peak of abundance occurred in July for An. sinensis and in September-October for An. minimus (s.l.) Ten Anopheles species were collected, the most prevalent being An. sinensis (50.3%), An. peditaeniatus (31.6%) and An. minimus (s.l.) (15.8%), contributing to 97.6% of the sample. Potential breeding sites were also investigated and a total of 407 larvae were collected, with An. sinensis (50.1%) and An. minimus (s.l.) (46.2%) as predominant species. Ponds and rice fields were the two preferred breeding sites for Anopheles mosquitoes; however, the difference between the number of adults and larvae captured suggest other breeding sites might exist. Both An. sinensis and An. minimus (s.l.) were found zoophilic with human blood index as 0.21 and 0.26, respectively. No Plasmodium positive Anopheles specimens were found by PCR among 4,000 trapped mosquitoes.

Conclusions: Although no indigenous malaria cases have been reported in Tengchong County since 2013, there is still a risk from the presence of vectors in the context of human population movements from neighboring malaria endemic areas. The presence of An. sinensis, associated to rice fields, is particularly worrying. Sustained entomological surveillance is strongly suggested even after malaria elimination certification.
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http://dx.doi.org/10.1186/s13071-018-3073-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6139178PMC
September 2018

Japanese encephalitis in Indonesia: An update on epidemiology and transmission ecology.

Acta Trop 2018 Nov 15;187:240-247. Epub 2018 Aug 15.

National Institute of Health Research and Development, MoH, Indonesia.

The Japanese Encephalitis (JE) virus circulation in Indonesia was first documented in Lombok in 1960, and the virus was first isolated in 1972 from Culex tritaeniorhynchus in Bekasi, West Java and Kapuk, West Jakarta. Since then, Indonesia has been recognized as an endemic country for JE transmission. Up to now, JE cases have been found in at least 29 provinces, with Bali, West Kalimantan, East Nusa Tenggara, West Java and East Java, being the areas of highest incidence. However, routine surveillance on JE has not been established at the national level even though many surveys were conducted. JEV has been isolated from 10 mosquito species: Culex tritaeniorhynchus, Cx. gelidus, Cx. vishnui, Cx. fuscocephala, Cx. bitaeniorhynchus, Cx. quinquefasciatus, Anopheles vagus, An. kochi, An. annularis, and Armigeres subalbatus. Culex tritaeniorhynchus is the main JE vector in Indonesia. JE has been detected throughout the Indonesian archipelago from West to East. However, due to a lack of routine, systematic and standardized diagnostic approaches, the JE burden has still not been clearly established yet. Long term and systematic JE surveillance across Indonesia is a priority, the burden needs to be better assessed and appropriate control measures must be implemented.
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http://dx.doi.org/10.1016/j.actatropica.2018.08.017DOI Listing
November 2018

Bats, Coronaviruses, and Deforestation: Toward the Emergence of Novel Infectious Diseases?

Front Microbiol 2018 11;9:702. Epub 2018 Apr 11.

Aix Marseille Université, Centre National de la Recherche Scientifique, IRD, Institut National de la Santé et de la Recherche Médicale, AP-HM, URMITE, IHU-Méditerranée Infection, Marseille, France.

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http://dx.doi.org/10.3389/fmicb.2018.00702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5904276PMC
April 2018

Distribution of bat-borne viruses and environment patterns.

Infect Genet Evol 2018 03 23;58:181-191. Epub 2017 Dec 23.

CIRAD, UMR 17, CIRAD-IRD, Montpellier, France; Université de Montpellier, IES, UMR 5214, CNRS-UM, Montpellier, France.

Environmental modifications are leading to biodiversity changes, loss and habitat disturbance. This in turn increases contacts between wildlife and hence the risk of transmission and emergence of zoonotic diseases. We analyzed the environment and land use using remote spatial data around the sampling locations of bats positive for coronavirus (21 sites) and astrovirus (11 sites) collected in 43 sites. A clear association between viruses and hosts was observed. Viruses associated to synanthropic bat genera, such as Myotis or Scotophilus were associated to highly transformed habitats with human presence while viruses associated to fruit bat genera were correlated with natural environments with dense forest, grassland areas and regions of high elevation. In particular, group C betacoronavirus were associated with mosaic habitats found in anthropized environments.
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http://dx.doi.org/10.1016/j.meegid.2017.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106095PMC
March 2018

Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia.

Malar J 2017 Dec 19;16(1):493. Epub 2017 Dec 19.

Institut de Biologie Computationnelle (IBC), 34095, Montpellier, France.

Background: Plasmodium falciparum malaria is one of the most widespread parasitic infections in humans and remains a leading global health concern. Malaria elimination efforts are threatened by the emergence and spread of resistance to artemisinin-based combination therapy, the first-line treatment of malaria. Promising molecular markers and pathways associated with artemisinin drug resistance have been identified, but the underlying molecular mechanisms of resistance remains unknown. The genomic data from early period of emergence of artemisinin resistance (2008-2011) was evaluated, with aim to define k13 associated genetic background in Cambodia, the country identified as epicentre of anti-malarial drug resistance, through characterization of 167 parasite isolates using a panel of 21,257 SNPs.

Results: Eight subpopulations were identified suggesting a process of acquisition of artemisinin resistance consistent with an emergence-selection-diffusion model, supported by the shifting balance theory. Identification of population specific mutations facilitated the characterization of a core set of 57 background genes associated with artemisinin resistance and associated pathways. The analysis indicates that the background of artemisinin resistance was not acquired after drug pressure, rather is the result of fixation followed by selection on the daughter subpopulations derived from the ancestral population.

Conclusions: Functional analysis of artemisinin resistance subpopulations illustrates the strong interplay between ubiquitination and cell division or differentiation in artemisinin resistant parasites. The relationship of these pathways with the P. falciparum resistant subpopulation and presence of drug resistance markers in addition to k13, highlights the major role of admixed parasite population in the diffusion of artemisinin resistant background. The diffusion of resistant genes in the Cambodian admixed population after selection resulted from mating of gametocytes of sensitive and resistant parasite populations.
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http://dx.doi.org/10.1186/s12936-017-2140-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5735551PMC
December 2017

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

Anopheles Vectors in Mainland China While Approaching Malaria Elimination.

Trends Parasitol 2017 11 19;33(11):889-900. Epub 2017 Jul 19.

Institut de Recherche pour le Développement (IRD France), LIPMC, UMR-MD3, Faculté de Pharmacie, 34093 Montpellier, France.

China is approaching malaria elimination; however, well-documented information on malaria vectors is still missing, which could hinder the development of appropriate surveillance strategies and WHO certification. This review summarizes the nationwide distribution of malaria vectors, their bionomic characteristics, control measures, and related studies. After several years of effort, the area of distribution of the principal malaria vectors was reduced, in particular for Anopheles lesteri (synonym: An. anthropophagus) and Anopheles dirus s.l., which nearly disappeared from their former endemic regions. Anopheles sinensis is becoming the predominant species in southwestern China. The bionomic characteristics of these species have changed, and resistance to insecticides was reported. There is a need to update surveillance tools and investigate the role of secondary vectors in malaria transmission.
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http://dx.doi.org/10.1016/j.pt.2017.06.010DOI Listing
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

Genetic diversity of coronaviruses in bats in Lao PDR and Cambodia.

Infect Genet Evol 2017 03 6;48:10-18. Epub 2016 Dec 6.

Institut Pasteur du Cambodge, Virology Unit, Phnom Penh, Cambodia; GSK Vaccines R&D, 150 Beach road, # 22-00, 189720, Singapore. Electronic address:

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.
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http://dx.doi.org/10.1016/j.meegid.2016.11.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106194PMC
March 2017

Diversity of bat astroviruses in Lao PDR and Cambodia.

Infect Genet Evol 2017 01 15;47:41-50. Epub 2016 Nov 15.

Institut Pasteur du Cambodge, Virology Unit, Phnom Penh, Cambodia; GSK Vaccines R&D, 150 Beach road, # 22-00, 189720, Singapore. Electronic address:

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.
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http://dx.doi.org/10.1016/j.meegid.2016.11.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106329PMC
January 2017

Fate of insecticidal Bacillus thuringiensis Cry protein in soil: differences between purified toxin and biopesticide formulation.

Pest Manag Sci 2016 Dec 24;72(12):2247-2253. Epub 2016 Mar 24.

INRA, UMR Eco & Sols, INRA-IRD-Cirad-SupAgro, Montpellier, France.

Background: Bacillus thuringiensis produces insecticidal proteins known as Cry, and its efficiency and absence of side effects make it the most widely used biopesticide. There is little information on the role of soils in the fate of Cry proteins from commercial biopesticide formulations, unlike toxins from genetically modified crops, which have been intensively studied in recent years. The persistence of Cry in soil was followed under field and laboratory conditions.

Results: Sunlight accelerated loss of detectable Cry under laboratory conditions, but little effect of shade was observed under field conditions. The half-life of biopesticide proteins in soil under natural conditions was about 1 week. Strong temperature effects were observed, but they differed for biopesticide and purified protein, indicating different limiting steps.

Conclusion: For the biopesticide, the observed decline in detectable protein was due to biological factors, possibly including the germination of B. thuringiensis spores, and was favoured by higher temperature. In contrast, for purified proteins, the decline in detectable protein was slower at low temperature, probably because the conformational changes of the soil-adsorbed protein, which cause fixation and hence reduced extraction efficiency, are temperature dependent. © 2016 Society of Chemical Industry.
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http://dx.doi.org/10.1002/ps.4262DOI Listing
December 2016

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions.

Sci Rep 2016 10 18;6:35284. Epub 2016 Oct 18.

Antigen Discovery Inc., Irvine, CA, 92618 USA.

Babesia microti, a tick-transmitted, intraerythrocytic protozoan parasite circulating mainly among small mammals, is the primary cause of human babesiosis. While most cases are transmitted by Ixodes ticks, the disease may also be transmitted through blood transfusion and perinatally. A comprehensive analysis of genome composition, genetic diversity, and gene expression profiling of seven B. microti isolates revealed that genetic variation in isolates from the Northeast United States is almost exclusively associated with genes encoding the surface proteome and secretome of the parasite. Furthermore, we found that polymorphism is restricted to a small number of genes, which are highly expressed during infection. In order to identify pathogen-encoded factors involved in host-parasite interactions, we screened a proteome array comprised of 174 B. microti proteins, including several predicted members of the parasite secretome. Using this immuno-proteomic approach we identified several novel antigens that trigger strong host immune responses during the onset of infection. The genomic and immunological data presented herein provide the first insights into the determinants of B. microti interaction with its mammalian hosts and their relevance for understanding the selective pressures acting on parasite evolution.
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http://dx.doi.org/10.1038/srep35284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082761PMC
October 2016

Plasmodium falciparum parasite population structure and gene flow associated to anti-malarial drugs resistance in Cambodia.

Malar J 2016 06 14;15:319. Epub 2016 Jun 14.

Institut de Biologie Computationnelle (IBC), Montpellier, France.

Background: Western Cambodia is recognized as the epicentre of emergence of Plasmodium falciparum multi-drug resistance. The emergence of artemisinin resistance has been observed in this area since 2008-2009 and molecular signatures associated to artemisinin resistance have been characterized in k13 gene. At present, one of the major threats faced, is the possible spread of Asian artemisinin resistant parasites over the world threatening millions of people and jeopardizing malaria elimination programme efforts. To anticipate the diffusion of artemisinin resistance, the identification of the P. falciparum population structure and the gene flow among the parasite population in Cambodia are essential.

Methods: To this end, a mid-throughput PCR-LDR-FMA approach based on LUMINEX technology was developed to screen for genetic barcode in 533 blood samples collected in 2010-2011 from 16 health centres in malaria endemics areas in Cambodia.

Results: Based on successful typing of 282 samples, subpopulations were characterized along the borders of the country. Each 11-loci barcode provides evidence supporting allele distribution gradient related to subpopulations and gene flow. The 11-loci barcode successfully identifies recently emerging parasite subpopulations in western Cambodia that are associated with the C580Y dominant allele for artemisinin resistance in k13 gene. A subpopulation was identified in northern Cambodia that was associated to artemisinin (R539T resistant allele of k13 gene) and mefloquine resistance.

Conclusions: The gene flow between these subpopulations might have driven the spread of artemisinin resistance over Cambodia.
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http://dx.doi.org/10.1186/s12936-016-1370-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908689PMC
June 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

Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures.

BMC Genomics 2016 Jan 7;17:34. Epub 2016 Jan 7.

Institut de Recherche en Cancérologie de Montpellier, IRCM - INSERM U1194 & Université de Montpellier & ICM, Institut régional du Cancer Montpellier, Campus Val d'Aurelle, 34298, Montpellier cedex 5, France.

Background: The microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. Although each chromosome end is known to contain a single rDNA unit, the incomplete assembly of subtelomeric regions following sequencing of the genome identified only 3 of the 22 expected rDNA units. While chromosome end assembly remains a difficult process in most eukaryotic genomes, it is of significant importance for pathogens because these regions encode factors important for virulence and host evasion.

Results: Here we report the first complete assembly of E. cuniculi chromosome ends, and describe a novel mosaic structure of segmental duplications (EXT repeats) in these regions. EXT repeats range in size between 3.5 and 23.8 kbp and contain four multigene families encoding membrane associated proteins. Twenty-one recombination sites were identified in the sub-terminal region of E. cuniculi chromosomes. Our analysis suggests that these sites contribute to the diversity of chromosome ends organization through Double Strand Break repair mechanisms. The region containing EXT repeats at chromosome extremities can be differentiated based on gene composition, GC content, recombination sites density and chromosome landscape.

Conclusion: Together this study provides the complete structure of the chromosome ends of E. cuniculi GB-M1, and identifies important factors, which could play a major role in parasite diversity and host-parasite interactions. Comparison with other eukaryotic genomes suggests that terminal regions could be distinguished precisely based on gene content, genetic instability and base composition biais. The diversity of processes assciated with chromosome extremities and their biological consequences, as they are presented in the present study, emphasize the fact that great effort will be necessary in the future to characterize more carefully these regions during whole genome sequencing efforts.
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http://dx.doi.org/10.1186/s12864-015-1920-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704409PMC
January 2016

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

Genetic diversity of human rhinoviruses in Cambodia during a three-year period reveals novel genetic types.

Infect Genet Evol 2015 Oct 29;35:42-9. Epub 2015 Jul 29.

Institut Pasteur in Cambodia, Virology Unit, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia. Electronic address:

Acute respiratory viral infections are a major cause of morbidity during early childhood in developing countries. Human rhinoviruses are the most frequent cause of upper respiratory tract infections in humans, which can range in severity from asymptomatic to clinically severe disease. In this study we collected 4170 nasopharyngeal swabs from patients hospitalised with influenza-like illness in two Cambodian provincial hospitals between 2007 and 2010. Samples were screened for 18 respiratory viruses using 5 multiplex PCRs. A total of 11.2% of samples tested positive for human rhinoviruses (HRV). VP4/2 and VP1 regions were amplified and sequenced to study the distribution of rhinoviruses genotypes and species in Cambodia during this three-year period. Five novel genotypes, 2 species A, 2 species B and 1 species C were identified based on VP1 sequences. Co-infections with other viruses were demonstrated.
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http://dx.doi.org/10.1016/j.meegid.2015.07.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7105975PMC
October 2015

Gaps between research and public health priorities in low income countries: evidence from a systematic literature review focused on Cambodia.

Implement Sci 2015 Mar 11;10:32. Epub 2015 Mar 11.

Epidemiology and Public Health Unit, Institut Pasteur, Phnom Penh, Cambodia.

Background: Evidence-based public health requires that research provides policymakers with reliable and accessible information reflecting the disease threats. We described the scientific production of research in Cambodia and assessed to what extent it provides appropriate insights and implications for practice to guide health policymakers and managers and knowledge relevant for translation.

Methods: We conducted a systematic review of scientific articles published on biomedical research in Cambodia. Regression analysis assessed the trends over time and factors associated with actionable messages in the articles' abstracts.

Results: From 2000 to 2012, 628 articles were published in 237 journals with a significant increase over time (from 0.6/million population to 5.9/million population, slope coefficient 7.6, 95% CI 6.5-8.7, p < 0.001). Most publications on diseases addressed communicable diseases (n = 410, 65.3%). Non-communicable diseases (NCD) were under-addressed (7.7% of all publications) considering their burden (34.5% of the disease burden). Of all articles, 67.8% reported descriptive studies and 4.3% reported studies with a high level of evidence; 27.4% of studies were led by an institution based in Cambodia. Factors associated with an actionable message (n = 73, 26.6%) were maternal health (OR 3.08, 95% CI 1.55-6.13, p = 0.001), the first author's institution being Cambodian (OR 1.78, 95% CI 1.06-2.98, p = 0.02) and a free access to full article (OR 3.07, 95% CI 1.08-8.70, p = 0.03). Of all articles, 87% (n = 546) were accessible in full text from Cambodia.

Conclusions: Scientific publications do not fully match with health priorities. Gaps remain regarding NCD, implementation studies, and health system research. A health research agenda would help align research with health priorities. We recommend 1) that the health authorities create an online repository of research findings with abstracts in the local language; 2) that academics emphasize the importance of research in their university teaching; and 3) that the researcher teams involve local researchers and that they systematically provide a translation of their abstracts upon submission to a journal. We conclude that building the bridge between research and public health requires a willful, comprehensive strategy rather than relying solely only publications.
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http://dx.doi.org/10.1186/s13012-015-0217-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357145PMC
March 2015