Contributors:Liina Kinkar, Teivi Laurimäe, Urmas Saarma
Fasta file with 303 aligned E. granulosus s. s. mtDNA sequences. The alignment contains gaps: the strings of NNN-s represent gaps of estimated length based on the reference sequence (AB786664 in GenBank).
South-East Asia is a hot spot for emerging zoonotic diseases, and bats have been recognized as hosts for a large number of zoonotic viruses such as Severe Acute Respiratory Syndrome (SARS), responsible for acute respiratory syndrome outbreaks. Thus, it is important to expand our knowledge of the presence of viruses in bats which could represent a risk to humans. Coronaviruses (CoVs) have been reported in bat species from Thailand, China, Indonesia, Taiwan and the Philippines. However no such work was conducted in Cambodia or Lao PDR. Between 2010 and 2013, 1965 bats were therefore sampled at interfaces with human populations in these two countries. They were tested for the presence of coronavirus by consensus reverse transcription-PCR assay. A total of 93 samples (4.7%) from 17 genera of bats tested positive. Sequence analysis revealed the presence of potentially 37 and 56 coronavirus belonging to alpha-coronavirus (αCoV) and beta-CoV (βCoV), respectively. The βCoVs group is known to include some coronaviruses highly pathogenic to human, such as SARS-CoV and MERS-CoV. All coronavirus sequences generated from frugivorous bats (family Pteropodidae) (n=55) clustered with other bat βCoVs of lineage D, whereas one coronavirus from Pipistrellus coromandra fell in the lineage C of βCoVs which also includes the MERS-CoV. αCoVs were all detected in various genera of insectivorous bats and clustered with diverse bat αCoV sequences previously published. A closely related strain of PEDV, responsible for severe diarrhea in pigs (PEDV-CoV), was detected in 2 Myotis bats. We highlighted the presence and the high diversity of coronaviruses circulating in bats from Cambodia and Lao PDR. Three new bat genera and species were newly identified as host of coronaviruses, namely Macroglossus sp., Megaerops niphanae and Myotis horsfieldii.,P1 Cambodia bats Coronavirus data_2019Aug16_1658Data associated with bats sampled in Cambodia and tested for CoronavirusesP1 Laos bats Coronavirus Data_2019Aug16_1656Data associated with bats sampled in Lao PDR and tested for Coronaviruses,
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.,P1 Cambodia bats Astrovirus data_2019Aug16_1658Data pertaining to bats sampled in Cambodia for which Astrovirus family testing was performedP1 Laos bats Astrovirus Data_2019Aug16_1656Data pertaining to bats sampled in Lao PDR for which Astrovirus family testing was performed,
Contributors:Acevedo-Whitehouse, Karina, Gulland, Frances M. D., Bowen, Lizabeth
We examined the associations between California sea lion MHC class II DRB (Zaca-DRB) configuration and diversity, and leptospirosis. As Zaca-DRB gene sequences are involved with antigen presentation of bacteria and other extracellular pathogens, we predicted that they would play a role in determining responses to these pathogenic spirochaetes. Specifically, we investigated whether Zaca-DRB diversity (number of genes) and configuration (presence of specific genes) explained differences in disease severity, and whether higher levels of Zaca-DRB diversity predicted the number of specific Leptospira interrogans serovars that a sea lion's serum would react against. We found that serum from diseased sea lions with more Zaca-DRB loci reacted against a wider array of serovars. Specific Zaca-DRB loci were linked to reactions with particular serovars. Interestingly, sea lions with clinical manifestation of leptospirosis that had higher numbers of Zaca-DRB loci were less likely to recover from disease than those with lower diversity, and those that harboured Zaca-DRB.C or –G were 4.5 to 5.3 times more likely to die from leptospirosis, regardless of the infective serovars. We propose that for leptospirosis, a disadvantage of having a wider range of antigen presentation might be increased disease severity due to immunopathology. Ours is the first study to examine the importance of Zaca-DRB diversity for antigen detection and disease severity following natural exposure to infective leptospires.,ZacaDRB_Lepto_File1_DryadData file contains information on ZacaDRB genotyping, HL and leptospirosis status.,
Development and implementation of methods for the analysis of nucleic acid sequences is a priority task for the molecular biology. An integrated technology based on the use of low-density microarrays (biochips) comprised of hydrogel elements was developed and patented at the Engelhardt Institute of Molecular Biology (Moscow, Russia). The structure of the hydrogel can be adapted for immobilization of virtually any biological molecules in natural hydrophilic environment. The discrimination between matching and mismatching duplexes of nucleic acids in these conditions is more reliable than on conventional flat surfaces, minimizing the number of elements necessary to detect specific sequences. A highly sensitive procedure for multiplex amplification and fluorescence labelling of genome segments was proposed. A rotary-based platform with multiple disposable microfluidic modules for simultaneous automatic nucleic acid isolation was developed. The procedure is performed inside insulated individual disposable modules, which minimizes both the risk of infection of personnel and laboratory cross-contamination. The hydrogel biochips were successfully applied for laboratory diagnostics in a broad variety of clinical conditions involving identification of bacterial and viral pathogens, and also detection of plant-derived genetically modified organisms in food and feed products
Contributors:Fouet, Caroline, Kamdem, Colince, Gamez, Stephanie, White, Bradley J.
Malaria vectors are exposed to intense selective pressures due to large-scale intervention programs that are underway in most African countries. One of the current priorities is therefore to clearly assess the adaptive potential of Anopheline populations, which is critical to understand and anticipate the response mosquitoes can elicit against such adaptive challenges. The development of genomic resources that will empower robust examinations of evolutionary changes in all vectors including currently understudied species is an inevitable step toward this goal. Here we constructed double-digest Restriction Associated DNA (ddRAD) libraries and generated 6461 Single Nucleotide Polymorphisms (SNPs) that we used to explore the population structure and demographic history of wild-caught Anopheles moucheti from Cameroon. The genome-wide distribution of allelic frequencies among samples best fitted that of an old population at equilibrium, characterized by a weak genetic structure and extensive genetic diversity, presumably due to a large long term effective population size. Estimates of FST and Linkage Disequilibrium (LD) across SNPs reveal a very low genetic differentiation throughout the genome and the absence of segregating LD blocks among populations, suggesting an overall lack of local adaptation. Our study provides the first investigation of the genetic structure and diversity in An. moucheti at the genomic scale. We conclude that, despite a weak genetic structure, this species has the potential to challenge current vector control measures and other rapid anthropogenic and environmental changes thanks to its great genetic diversity.,Anopheles moucheti_part1Fastq files for Anopheles moucheti individuals from Cameroon - part 1moucheti_part1.tar.gzAnopheles moucheti_part2Fastq files for Anopheles moucheti individuals from Cameroon - part 2moucheti_part2.tar.gzAnopheles moucheti_part3Fastq files for Anopheles moucheti individuals from Cameroon - part 3moucheti_part3.tar.gzAnopheles moucheti_part4Fastq files for Anopheles moucheti individuals from Cameroon - part 4moucheti_part4.tar.gzAnopheles moucheti_part5Fastq files for Anopheles moucheti individuals from Cameroon - part 5moucheti_part5.tar.gzAnopheles moucheti data fileInformation on Anopheles moucheti samples sequenced from CameroonAn.moucheti_datafile.xlsx,
Contributors:Haynes, Benjamin T., Marcus, Alan D., Higgins, Damien P., Gongora, Jaime, Gray, Rachael, Slapeta, Jan
The high natal site fidelity of endangered Australian sea lions (Neophoca cinerea) along the southern Australian coast suggests that their maternally transmitted parasitic species, such as hookworms, will have restricted potential for dispersal. If this is the case, we would expect to find a hookworm haplotype structure corresponding to that of the host mtDNA haplotype structure; that is, restricted among geographically separated colonies. In this study, we used a fragment of the cytochrome c oxidase I mitochondrial DNA (mtDNA) gene to investigate the diversity of hookworms (Uncinaria sanguinis) in N. cinerea to assess the importance of host distribution and ecology on the evolutionary history of the parasite. High haplotype (h = 0.986) and nucleotide diversity (π = 0.013) were seen, with 45 unique hookworm mtDNA haplotypes across N. cinerea colonies; with most of the variation (78%) arising from variability within hookworms from individual colonies. This is supported by the low genetic differentiation co-efficient (GST = 0.007) and a high gene flow (Nm = 35.25) indicating a high migration rate between the populations of hookworms. The haplotype network demonstrated no clear distribution and delineation of haplotypes according to geographical location. Our data rejects the vicariance hypothesis; that female host natal site fidelity and the transmammary route of infection restrict hookworm gene flow between N. cinerea populations and highlights the value of studies of parasite diversity and dispersal to challenge our understanding of parasite and host ecology.,Unexpected absence of genetic separation of a highly diverse population of hookworms from geographically isolated hostsDRYAD.zip,