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1.
Gene ; 835: 146641, 2022 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-35700806

RESUMO

The subgenus Sarbecovirus includes two human viruses, SARS-CoV and SARS-CoV-2, respectively responsible for the SARS epidemic and COVID-19 pandemic, as well as many bat viruses and two pangolin viruses. Here, the synonymous nucleotide composition (SNC) of Sarbecovirus genomes was analysed by examining third codon-positions, dinucleotides, and degenerate codons. The results show evidence for the eight following groups: (i) SARS-CoV related coronaviruses (SCoVrC including many bat viruses from China), (ii) SARS-CoV-2 related coronaviruses (SCoV2rC; including five bat viruses from Cambodia, Thailand and Yunnan), (iii) pangolin sarbecoviruses, (iv) three bat sarbecoviruses showing evidence of recombination between SCoVrC and SCoV2rC genomes, (v) two highly divergent bat sarbecoviruses from Yunnan, (vi) the bat sarbecovirus from Japan, (vii) the bat sarbecovirus from Bulgaria, and (viii) the bat sarbecovirus from Kenya. All these groups can be diagnosed by specific nucleotide compositional features except the one concerned by recombination between SCoVrC and SCoV2rC. In particular, SCoV2rC genomes have less cytosines and more uracils at third codon-positions than other sarbecoviruses, whereas the genomes of pangolin sarbecoviruses show more adenines at third codon-positions. I suggest that taxonomic differences in the imbalanced nucleotide pools available in host cells during viral replication can explain the eight groups of SNC here detected among Sarbecovirus genomes. A related effect due to hibernating bats and their latitudinal distribution is also discussed. I conclude that the two independent host switches from Rhinolophus bats to pangolins resulted in convergent mutational constraints and that SARS-CoV-2 emerged directly from a horseshoe bat sarbecovirus.


Assuntos
COVID-19 , Quirópteros , Vírus da SARS , Animais , China/epidemiologia , Quirópteros/genética , Genoma Viral , Humanos , Nucleotídeos/genética , Pandemias , Pangolins , Filogenia , SARS-CoV-2/genética
2.
Viruses ; 14(2)2022 02 21.
Artigo em Inglês | MEDLINE | ID: mdl-35216033

RESUMO

Recombination creates mosaic genomes containing regions with mixed ancestry, and the accumulation of such events over time can complicate greatly many aspects of evolutionary inference. Here, we developed a sliding window bootstrap (SWB) method to generate genomic bootstrap (GB) barcodes to highlight the regions supporting phylogenetic relationships. The method was applied to an alignment of 56 sarbecoviruses, including SARS-CoV and SARS-CoV-2, responsible for the SARS epidemic and COVID-19 pandemic, respectively. The SWB analyses were also used to construct a consensus tree showing the most reliable relationships and better interpret hidden phylogenetic signals. Our results revealed that most relationships were supported by just a few genomic regions and confirmed that three divergent lineages could be found in bats from Yunnan: SCoVrC, which groups SARS-CoV related coronaviruses from China; SCoV2rC, which includes SARS-CoV-2 related coronaviruses from Southeast Asia and Yunnan; and YunSar, which contains a few highly divergent viruses recently described in Yunnan. The GB barcodes showed evidence for ancient recombination between SCoV2rC and YunSar genomes, as well as more recent recombination events between SCoVrC and SCoV2rC genomes. The recombination and phylogeographic patterns suggest a strong host-dependent selection of the viral RNA-dependent RNA polymerase. In addition, SARS-CoV-2 appears as a mosaic genome composed of regions sharing recent ancestry with three bat SCoV2rCs from Yunnan (RmYN02, RpYN06, and RaTG13) or related to more ancient ancestors in bats from Yunnan and Southeast Asia. Finally, our results suggest that viral circular RNAs may be key molecules for the mechanism of recombination.


Assuntos
Código de Barras de DNA Taxonômico/métodos , Reservatórios de Doenças/veterinária , Evolução Molecular , Genômica/métodos , Recombinação Genética , Vírus da SARS/genética , SARS-CoV-2/genética , Animais , China , Quirópteros/virologia , Reservatórios de Doenças/virologia , Genoma Viral , Filogeografia
3.
Viruses ; 14(2)2022 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-35215769

RESUMO

Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extreme example is the insertion of the P10 gene from reoviruses in the bat CoV GCCDC1, first discovered in Rousettus leschenaultii bats in China. Here, we report the detection of GCCDC1 in four different bat species (Eonycteris spelaea, Cynopterus sphinx, Rhinolophus shameli and Rousettus sp.) in Cambodia. This finding demonstrates a much broader geographic and bat species range for this virus and indicates common cross-species transmission. Interestingly, one of the bat samples showed a co-infection with an Alpha CoV most closely related to RsYN14, a virus recently discovered in the same genus (Rhinolophus) of bat in Yunnan, China, 2020. Taken together, our latest findings highlight the need to conduct active surveillance in bats to assess the risk of emerging CoVs, especially in Southeast Asia.


Assuntos
Quirópteros/virologia , Infecções por Coronaviridae/veterinária , Coronaviridae/classificação , Coronaviridae/genética , Reservatórios de Doenças/veterinária , Reservatórios de Doenças/virologia , Filogeografia , Recombinação Genética , Animais , Camboja/epidemiologia , China/epidemiologia , Quirópteros/classificação , Coronaviridae/isolamento & purificação , Infecções por Coronaviridae/epidemiologia , Infecções por Coronaviridae/transmissão , Evolução Molecular , Genoma Viral , Filogenia
4.
Nat Commun ; 12(1): 6563, 2021 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-34753934

RESUMO

Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bats sampled in Cambodia in 2010. Metagenomic sequencing identifies nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a region of the spike, which is not compatible with human ACE2-mediated entry. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously reported, and suggests that Southeast Asia represents a key area to consider for future surveillance for coronaviruses.


Assuntos
COVID-19/virologia , Quirópteros/virologia , SARS-CoV-2/genética , Sequência de Aminoácidos , Animais , COVID-19/epidemiologia , COVID-19/metabolismo , Camboja/epidemiologia , Evolução Molecular , Genoma Viral , Filogenia , SARS-CoV-2/isolamento & purificação , SARS-CoV-2/metabolismo , Alinhamento de Sequência , Glicoproteína da Espícula de Coronavírus/genética , Glicoproteína da Espícula de Coronavírus/metabolismo
5.
Sci Rep ; 11(1): 14276, 2021 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-34253798

RESUMO

The Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the causal agent of the coronavirus disease 2019 (COVID-19) pandemic. To date, viruses closely related to SARS-CoV-2 have been reported in four bat species: Rhinolophus acuminatus, Rhinolophus affinis, Rhinolophus malayanus, and Rhinolophus shameli. Here, we analysed 343 sequences of the mitochondrial cytochrome c oxidase subunit 1 gene (CO1) from georeferenced bats of the four Rhinolophus species identified as reservoirs of viruses closely related to SARS-CoV-2. Haplotype networks were constructed in order to investigate patterns of genetic diversity among bat populations of Southeast Asia and China. No strong geographic structure was found for the four Rhinolophus species, suggesting high dispersal capacity. The ecological niche of bat viruses closely related to SARS-CoV-2 was predicted using the four localities in which bat viruses were recently discovered and the localities where bats showed the same CO1 haplotypes than virus-positive bats. The ecological niche of bat viruses related to SARS-CoV was deduced from the localities where bat viruses were previously detected. The results show that the ecological niche of bat viruses related to SARS-CoV2 includes several regions of mainland Southeast Asia whereas the ecological niche of bat viruses related to SARS-CoV is mainly restricted to China. In agreement with these results, human populations in Laos, Vietnam, Cambodia, and Thailand appear to be much less affected by the COVID-19 pandemic than other countries of Southeast Asia. In the climatic transitional zone between the two ecological niches (southern Yunnan, northern Laos, northern Vietnam), genomic recombination between highly divergent viruses is more likely to occur. Considering the limited data and the risk of recombinant bat-CoVs emergence as the source of new pandemics in humans, the bat populations in these regions should be under surveillance.


Assuntos
COVID-19/virologia , Quirópteros/virologia , Filogeografia , Vírus/genética , Animais , Ásia Sudeste/epidemiologia , COVID-19/epidemiologia , COVID-19/genética , COVID-19/transmissão , China/epidemiologia , SARS-CoV-2/genética , SARS-CoV-2/patogenicidade , Vírus/patogenicidade
6.
Sci Rep ; 11(1): 13085, 2021 06 22.
Artigo em Inglês | MEDLINE | ID: mdl-34158533

RESUMO

Monkeypox is an emerging infectious disease, which has a clinical presentation similar to smallpox. In the two past decades, Central Africa has seen an increase in the frequency of cases, with many monkeypox virus (MPXV) isolates detected in the Democratic Republic of Congo (DRC) and the Central African Republic (CAR). To date, no complete MPXV viral genome has been published from the human cases identified in the CAR. The objective of this study was to sequence the full genome of 10 MPXV isolates collected during the CAR epidemics between 2001 and 2018 in order to determine their phylogenetic relationships among MPXV lineages previously described in Central Africa and West Africa. Our phylogenetic results indicate that the 10 CAR isolates belong to three lineages closely related to those found in DRC. The phylogenetic pattern shows that all of them emerged in the rainforest block of the Congo Basin. Since most human index cases in CAR occurred at the northern edge of western and eastern rainforests, transmissions from wild animals living in the rainforest is the most probable hypothesis. In addition, molecular dating estimates suggest that periods of intense political instability resulting in population movements within the country often associated also with increased poverty may have led to more frequent contact with host wild animals. The CAR socio-economic situation, armed conflicts and ecological disturbances will likely incite populations to interact more and more with wild animals and thus increase the risk of zoonotic spillover.


Assuntos
Vírus da Varíola dos Macacos/genética , Varíola dos Macacos/genética , Animais , Evolução Biológica , República Centro-Africana/epidemiologia , Evolução Molecular , Genômica , Humanos , Varíola dos Macacos/epidemiologia , Vírus da Varíola dos Macacos/isolamento & purificação , Vírus da Varíola dos Macacos/patogenicidade , Filogenia , Zoonoses/genética
7.
Mol Phylogenet Evol ; 161: 107170, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-33798669

RESUMO

Two types of domestic water buffalo are currently recognized: the river buffalo from the Indian subcontinent and Mediterranean countries and the swamp buffalo from China and Southeast Asia. To test the hypothesis of two separate species of water buffalo, we sequenced the genome of the lowland anoa, Bubalus depressicornis, which is a dwarf wild buffalo endemic to Sulawesi, and two genomes of swamp buffalo, and made comparisons with 12 additional genomes. Three genomic data sets were constructed to infer phylogenetic relationships: the mitochondrial genome (15,468 bp; maternal transmission), two concatenated Y-chromosomal genes, AMELY and DDX3Y (20,036 bp; paternal transmission), and a selection of 30 nuclear genes representing all cattle chromosomes (364,887 bp; biparental transmission). The comparisons between our 30 nuclear gene sequences obtained by read mapping and those directly extracted from Bos taurus and Bubalus bubalis genome assemblies show that the mapping approach revealed higher levels of heterozygosity at both nucleotide sites and indels (insertions and deletions) (0.09-0.15%), as well as several sequence errors (0.07%). Our phylogenetic and molecular dating analyses provide strong evidence that the lowland anoa, river buffalo, and swamp buffalo are three distinct taxa which separated rapidly from each other during the Pleistocene epoch. We therefore conclude that two species of domestic water buffalo should be distinguished: Bubalus bubalis for the river buffalo and Bubalus kerabau for the swamp buffalo. The new classification can have deep implications for understanding the evolution and selection of domesticated forms and for the conservation and management of wild buffalo populations in South and Southeast Asia.


Assuntos
Búfalos/genética , Genoma , Filogenia , Rios , Áreas Alagadas , Animais , Búfalos/classificação , Bovinos , Feminino , Masculino , Análise de Sequência de DNA
9.
Mitochondrial DNA B Resour ; 6(1): 145-147, 2021 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-33537423

RESUMO

Here, we sequenced the complete mitochondrial genome of 29 Egyptian river buffaloes collected in two breeding stations of Egypt. The genome is 16,357-16,359 base pairs in length and contains the 37 genes found in a typical mammalian genome. The overall base composition is A: 33.1%, C: 26.6%, G: 13.9%, and T: 26.4%. Our analyses confirm that the mitochondrial genomes of swamp and river buffaloes are divergent (mean nucleotide distance = 2.3%), and show that Indian river buffalo haplotypes cluster into three haplogroups, named RB1, RB2, and RB3 (mean distance = 0.25-0.26%) and that the 24 Egyptian buffalo haplotypes fall into RB1 (with the Bangladeshi, Chinese and Italian buffalo haplotypes) and RB2.

10.
PLoS One ; 16(2): e0240770, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33591975

RESUMO

The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 21 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.


Assuntos
Carnívoros/classificação , Carnívoros/genética , Genoma Mitocondrial/genética , Animais , Evolução Biológica , DNA Mitocondrial/genética , Evolução Molecular , Fósseis , Variação Genética/genética , Filogenia , Análise de Sequência de DNA/métodos
11.
PLoS One ; 15(2): e0217956, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32053589

RESUMO

Molecular data are now commonly used in taxonomy for delimiting cryptic species. In the case of giraffes, which were treated as a single species (Giraffa camelopardalis) during half of a century, several molecular studies have suggested a splitting into four to seven species, but the criteria applied for taxonomic delimitation were not fully described. In this study, we have analysed all multi-locus DNA sequences available for giraffes using multispecies coalescent (MSC: *BEAST, BPP and STACEY), population genetic (STRUCTURE, allelic networks, haplotype network and bootstrapping, haplowebs and conspecificity matrix) and phylogenetic (MrBayes, PhyML, SuperTRI) methods to identify the number of species. Our results show that depending on the method chosen, different taxonomic hypotheses, recognizing from two to six species, can be considered for the genus Giraffa. Our results confirm that MSC methods can lead to taxonomic over-splitting, as they delimit geographic structure rather than species. The 3-species hypothesis, which recognizes G. camelopardalis sensu strico A, G. giraffa, and G. tippelskirchi, is highly supported by phylogenetic analyses and also corroborated by most population genetic and MSC analyses. The three species show high levels of nucleotide divergence in both nuclear (0.35-0.51%) and mitochondrial sequences (3-4%), and they are characterised by 7 to 12 exclusive synapomorphies (ES) detected in nine of the 21 nuclear introns analysed for this study. By contrast, other putative species, such as G. peralta, G. reticulata, G. thornicrofti or G. tippelskirchi sensu stricto, do not exhibit any ES in the nuclear genes. A robust mito-nuclear conflict was found for the position and monophyly of G. giraffa and G. tippelskirchi, which is interpreted as the result of a mitochondrial introgression from Masai to southeastern giraffe during the Pleistocene and nuclear gene flow mediated by male dispersal between southern populations (subspecies G. g. giraffa and G. g. angolensis).


Assuntos
Genética Populacional/métodos , Girafas/classificação , Tipagem de Sequências Multilocus , Distribuição Animal , Animais , Teorema de Bayes , DNA Mitocondrial/genética , Conjuntos de Dados como Assunto , Feminino , Fluxo Gênico , Variação Genética , Girafas/genética , Haplótipos , Masculino , Filogenia
12.
Mol Phylogenet Evol ; 129: 96-105, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30121341

RESUMO

The bushbuck is the most widespread bovid species in Africa. Previous mitochondrial studies have revealed a polyphyletic pattern suggesting the possible existence of two distinct species. To assess this issue, we have sequenced 16 nuclear genes and one mitochondrial fragment (cytochrome b gene + control region) for most species of the tribe Tragelaphini, including seven bushbuck individuals belonging to the two divergent mtDNA haplogroups, Scriptus and Sylvaticus. Our phylogenetic analyses show that the Scriptus lineage is a sister-group of Sylvaticus in the nuclear tree, whereas it is related to Tragelaphus angasii in the mitochondrial tree. This mito-nuclear discordance indicates that the mitochondrial genome of Scriptus was acquired by introgression after one or several past events of hybridization between bushbuck and an extinct species closely related to T. angasii. The division into two bushbuck species is supported by the analyses of nuclear markers and by the karyotype here described for T. scriptus (2n = 57 M/58F), which is strikingly distinct from the one previously found for T. sylvaticus (2n = 33 M/34F). Molecular dating estimates suggest that the two species separated during the Early Pleistocene after an event of interspecific hybridization, which may have mediated massive chromosomal rearrangements in the common ancestor of T. scriptus.


Assuntos
Antílopes/genética , Bovinos/classificação , Cromossomos de Mamíferos/genética , Loci Gênicos , Especiação Genética , Hibridização Genética , Filogenia , Animais , Sequência de Bases , Teorema de Bayes , Núcleo Celular/genética , Citocromos b/genética , DNA Mitocondrial/genética , Feminino , Haplótipos/genética , Cariótipo , Masculino , Especificidade da Espécie , Fatores de Tempo
13.
Mol Phylogenet Evol ; 118: 108-121, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-28966123

RESUMO

The nearly cosmopolitan tribe Desmodieae (Fabaceae) includes many important genera for medicine and forage. However, the phylogenetic relationships among the infratribal groups circumscribed using morphological traits are still poorly known. In this study, we used chloroplast (rbcL, psbA-trnH) and nuclear (ITS-1) DNA sequences to investigate the molecular phylogeny and historical biogeography of Desmodieae, and infer ancestral states for several vegetative and reproductive traits. Three groups, corresponding to the Desmodium, Lespedeza, and Phyllodium groups sensu Ohashi were retrieved in the phylogenetic analyses. Conflicts in the topologies inferred from the chloroplast and nuclear datasets were detected. For instance, the Lespedeza clade was sister to the groups Phyllodium+Desmodium based on chloroplast DNA, but nested within the Desmodium group based on ITS-1. Moreover, the New Caledonian endemic genera Arthroclianthus and Nephrodesmus were not monophyletic but together formed a clade, which also included Hanslia and Ohwia based on chloroplast DNA. The hypothetical common ancestor of Desmodieae was dated to the Middle Oligocene (ca. 28.3Ma) and was likely an Asian shrub or tree producing indehiscent loments. Several colonization events towards Oceania, America, and Africa occurred (all less than ca. 17.5Ma), most probably through long distance dispersal. The fruits of Desmodieae repeatedly evolved from indehiscence to dehiscence. We also showed that indehiscent loments allow for more variability in the number of seeds per fruit than indehiscent legumes. Modularity seems here to allow variability in the number of ovules produced in a single ovary.


Assuntos
Fabaceae/classificação , Filogenia , Filogeografia , Teorema de Bayes , DNA de Cloroplastos/genética , Ecossistema , Fabaceae/genética , Frutas/anatomia & histologia , Nova Caledônia , Fenótipo , Sementes/anatomia & histologia , Especificidade da Espécie , Fatores de Tempo
14.
Zootaxa ; 4236(2): zootaxa.4236.2.10, 2017 Feb 22.
Artigo em Inglês | MEDLINE | ID: mdl-28264332

RESUMO

The taxonomy of sub-Saharan small insectivore bats of the family Vespertilionidae is unresolved and currently five named species of the genus Neoromicia are recognized from southern Africa, with N. melckorum considered a synonym of N. capensis. Since several years, the name "N. cf. melckorum" has been used in the literature to designate an apparently undescribed and moderately large bodied vespertilionid bat known from different localities in southern and southeastern Africa. Using new data from molecular genetics, bacular morphology, and cranio-dental characters, we conclude that N. melckorum sensu stricto is indeed nested within N. capensis and obtain the needed evidence to formally describe "N. cf. melckorum", named herein as N. stanleyi sp. nov. On the basis of molecular and bacular evidence, N. stanleyi is found in Botswana, Zimbabwe, and Zambia, and using a combination of other characters is presumed to occur in northern South Africa and Malawi. Bayesian and maximum likelihood analyses based on 12S rRNA sequences indicate that it belongs to a clade containing four species of Neoromicia (N. capensis, N. malagasyensis, N. matroka, and N. robertsi) and Laephotis. Neoromicia stanleyi shows at least 3.2% nucleotide divergence from its closest relatives. It is larger in cranial characters than other members of the capensis group occurring in the southern portion of Africa, and a number of bacular characters distinguish N. stanleyi from N. capensis.


Assuntos
Quirópteros , África do Norte , África Austral , Animais , Teorema de Bayes , Malaui , Filogenia , África do Sul , Zâmbia , Zimbábue
15.
Infect Genet Evol ; 48: 10-18, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-27932284

RESUMO

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 (ßCoV), respectively. The ßCoVs 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 ßCoVs of lineage D, whereas one coronavirus from Pipistrellus coromandra fell in the lineage C of ßCoVs 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.


Assuntos
Quirópteros/virologia , Coronavirus/genética , Animais , Sequência de Bases , Camboja , Reservatórios de Doenças , Evolução Molecular , Genes Virais , Variação Genética , Laos , Filogenia , Filogeografia , RNA Polimerase Dependente de RNA/genética , Análise de Sequência de DNA , Proteínas Virais/genética
16.
Infect Genet Evol ; 47: 41-50, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27871796

RESUMO

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.


Assuntos
Infecções por Astroviridae/veterinária , Infecções por Astroviridae/virologia , Astroviridae/genética , Quirópteros/virologia , Variação Genética/genética , Animais , Astroviridae/classificação , Camboja , Fezes/virologia , Laos , Pulmão/virologia , Boca/virologia , Filogenia , Reto/virologia
17.
C R Biol ; 339(11-12): 517-528, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27746072

RESUMO

Both Ebolavirus and Marburgvirus were detected in several fruit bat species of the family Pteropodidae, suggesting that this taxon plays a key role in the life cycle of filoviruses. After four decades of Zaire Ebolavirus (ZEBOV) outbreaks in Central Africa, the virus was detected for the first time in West Africa in 2014. To better understand the role of fruit bats as potential reservoirs and circulating hosts between Central and West Africa, we examine here the phylogeny and comparative phylogeography of Pteropodidae. Our phylogenetic results confirm the existence of four independent lineages of African fruit bats: the genera Eidolon and Rousettus, and the tribes Epomophorini and Scotonycterini, and indicate that the three species suspected to represent ZEBOV reservoir hosts (Epomops franqueti, Hypsignathus monstrosus, and Myonycteris torquata) belong to an African clade that diversified rapidly around 8-7 Mya. To test for phylogeographic structure and for recent gene flow from Central to West Africa, we analysed the nucleotide variation of 675 cytochrome b gene (Cytb) sequences, representing eight fruit bat species collected in 48 geographic localities. Within Epomophorina, our mitochondrial data do not support the monophyly of two genera (Epomops and Epomophorus) and four species (Epomophorus gambianus, Epomops franqueti, Epomops buettikoferi, and Micropteropus pusillus). In Epomops, however, we found two geographic haplogroups corresponding to the Congo Basin and Upper Guinea forests, respectively. By contrast, we found no genetic differentiation between Central and West African populations for all species known to make seasonal movements, Eidolon helvum, E. gambianus, H. monstrosus, M. pusillus, Nanonycteris veldkampii, and Rousettus aegyptiacus. Our results suggest that only three fruit bat species were able to disperse directly ZEBOV from the Congo Basin to Upper Guinea: E. helvum, H. monstrosus, and R. aegyptiacus.


Assuntos
Quirópteros/fisiologia , Surtos de Doenças/estatística & dados numéricos , Doença pelo Vírus Ebola/epidemiologia , África Ocidental/epidemiologia , Animais , Quirópteros/classificação , Quirópteros/genética , DNA/genética , Reservatórios de Doenças , Fluxo Gênico , Marcadores Genéticos , Geografia , Filogenia , Filogeografia , Especificidade da Espécie
18.
Proc Natl Acad Sci U S A ; 113(35): 9834-9, 2016 08 30.
Artigo em Inglês | MEDLINE | ID: mdl-27528689

RESUMO

Haemosporidia parasites have mostly and abundantly been described using mitochondrial genes, and in particular cytochrome b (cytb). Failure to amplify the mitochondrial cytb gene of Nycteria parasites isolated from Nycteridae bats has been recently reported. Bats are hosts to a diverse and profuse array of Haemosporidia parasites that remain largely unstudied. There is a need to obtain more molecular data from chiropteran parasites. Such data would help to better understand the evolutionary history of Haemosporidia, which notably include the Plasmodium parasites, malaria's agents. We use next-generation sequencing to obtain the complete mitochondrial genome of Nycteria parasites from African Nycteris grandis (Nycteridae) and Rhinolophus alcyone (Rhinolophidae) and Asian Megaderma spasma (Megadermatidae). We report four complete mitochondrial genomes, including two rearranged mitochondrial genomes within Haemosporidia. Our results open outlooks into potentially undiscovered Haemosporidian diversity.


Assuntos
Quirópteros/parasitologia , Genoma Mitocondrial , Genoma de Protozoário , Haemosporida/genética , Proteínas Mitocondriais/genética , Proteínas de Protozoários/genética , Animais , Camboja , República Democrática do Congo , Haemosporida/classificação , Sequenciamento de Nucleotídeos em Larga Escala , Mitocôndrias/genética , Filogenia
19.
Artigo em Inglês | MEDLINE | ID: mdl-24937569

RESUMO

Here I report the complete mitochondrial genome of the African palm civet, (Nandinia binotata) as sequenced from overlapping PCR products. The genome is 17,103 bp in length and contains the 37 genes found in a typical mammalian genome: 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The control region of N. binotata includes both RS2 and RS3 tandem repeats. The overall base composition on the L-strand is A: 33.6%, C: 27.3%, G: 13.0%, and T: 26.1%.


Assuntos
DNA Mitocondrial/genética , Genoma Mitocondrial/genética , Mitocôndrias/genética , Nandiniidae/genética , Análise de Sequência de DNA/veterinária , África , Animais , Composição de Bases/genética , Sequência de Bases , Tamanho do Genoma , Dados de Sequência Molecular , Reação em Cadeia da Polimerase/veterinária , RNA Ribossômico/genética , RNA de Transferência/genética , Sequências de Repetição em Tandem/genética
20.
Artigo em Inglês | MEDLINE | ID: mdl-24937571

RESUMO

Here I report the complete mitochondrial genome of the Servaline Genet, Genetta servalina, as sequenced from overlapping PCR products. The genome is 16,938 base pairs in length and contains the 37 genes found in a typical mammalian genome: 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The control region of G. servalina includes both RS2 and RS3 tandem repeats. The overall base composition on the L-strand is A: 32.8%, C: 25.5%, G: 13.5%, and T: 28.2%.


Assuntos
DNA Mitocondrial/genética , Genoma Mitocondrial/genética , Mitocôndrias/genética , Análise de Sequência de DNA/veterinária , Viverridae/genética , África , Animais , Composição de Bases/genética , Sequência de Bases , Tamanho do Genoma , Masculino , Dados de Sequência Molecular , RNA Ribossômico/genética , RNA de Transferência/genética , Sequências de Repetição em Tandem/genética
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