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Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar.

Razanajatovo NH, Nomenjanahary LA, Wilkinson DA, Razafimanahaka JH, Goodman SM, Jenkins RK, Jones JP, Heraud JM - Virol. J. (2015)

Bottom Line: Certain Malagasy bats can be frequently found in close contact with humans and frugivorous bats feed in the same trees where people collect and consume fruits and are hunted and consumed as bush meat.Our findings suggest that CoVs circulate in frugivorous bats of Madagascar, demonstrating the needs to evaluate spillover risk to human populations especially for individuals that hunt and consume infected bats.Possible dispersal mechanisms as to how coronaviruses arrived on Madagascar are discussed.

View Article: PubMed Central - PubMed

Affiliation: Virology Unit, Institut Pasteur of Madagascar, Ambatofotsikely, BP 1274, Antananarivo, Madagascar, Dummy_Only. norosoa@pasteur.mg.

ABSTRACT

Background: Bats are amongst the natural reservoirs of many coronaviruses (CoVs) of which some can lead to severe infection in human. African bats are known to harbor a range of pathogens (e.g., Ebola and Marburg viruses) that can infect humans and cause disease outbreaks. A recent study in South Africa isolated a genetic variant closely related to MERS-CoV from an insectivorous bat. Though Madagascar is home to 44 bat species (41 insectivorous and 3 frugivorous) of which 34 are endemic, no data exists concerning the circulation of CoVs in the island's chiropteran fauna. Certain Malagasy bats can be frequently found in close contact with humans and frugivorous bats feed in the same trees where people collect and consume fruits and are hunted and consumed as bush meat. The purpose of our study is to detect and identify CoVs from frugivorous bats in Madagascar to evaluate the risk of human infection from infected bats.

Methods: Frugivorous bats belonging to three species were captured in four different regions of Madagascar. We analyzed fecal and throat swabs to detect the presence of virus through amplification of the RNA-dependent RNA polymerase (RdRp) gene, which is highly conserved in all known coronaviruses. Phylogenetic analyses were performed from positive specimens.

Results: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Phylogenetic analysis revealed that the Malagasy strains belong to the genus Betacoronavirus but form three distinct clusters, which seem to represent previously undescribed genetic lineages.

Conclusions: Our findings suggest that CoVs circulate in frugivorous bats of Madagascar, demonstrating the needs to evaluate spillover risk to human populations especially for individuals that hunt and consume infected bats. Possible dispersal mechanisms as to how coronaviruses arrived on Madagascar are discussed.

No MeSH data available.


Related in: MedlinePlus

Bayesian phylogenetic tree generated using 993 nucleotides of the RdRp gene sequences of Malagasy bat CoVs and reference strains of CoVs group. Major viral genera are shown. Strains detected in this study are marked with an*. Posterior probabilities superior to 0.9 are indicated by a dot, other posterior probabilities are indicated in decimal form to the right of each node, and some have been left off for clarity. The scale bar is expressed in years. The inset figure shows the partial phylogeny of the highlighted region of the Betacoronavirus subgroup, including additional reference sequences and with a total alignment length of 329 nucleotides. Techniques used for generating each phylogenetic representation were identical, as detailed in the materials and methods section.
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Fig2: Bayesian phylogenetic tree generated using 993 nucleotides of the RdRp gene sequences of Malagasy bat CoVs and reference strains of CoVs group. Major viral genera are shown. Strains detected in this study are marked with an*. Posterior probabilities superior to 0.9 are indicated by a dot, other posterior probabilities are indicated in decimal form to the right of each node, and some have been left off for clarity. The scale bar is expressed in years. The inset figure shows the partial phylogeny of the highlighted region of the Betacoronavirus subgroup, including additional reference sequences and with a total alignment length of 329 nucleotides. Techniques used for generating each phylogenetic representation were identical, as detailed in the materials and methods section.

Mentions: All amplicon sequences were aligned in-frame with a compilation of reference sequences from GenBank for which collection-date data was available [28], giving final alignments containing 51 different sequences of 993 bp in length and 64 different sequences of 329 bp in length. GTR + I + G was identified as the optimal substitution model using jModeltest v2.1.2 [29]. Multiple phylogenies were generated in BEAST using different combinations of model parameters, and the best models were selected using the Tracer [30]. Bayes factor analysis employing marginal likelihoods, as detailed in [12]. All parameter combinations produced identical, strongly supported tree topologies (data not shown). As has elsewhere been determined by Lau et al. [12], Bayesian skyline using a relaxed, exponentially distributed clock model was found to be the best fitting model for RdRp dated-tip phylogenies. The final phylogenetic analyses (Figure 2) revealed that strains from Madagascar are members of the Betacoronavirus genus, rooting with Hong Kong strain BtCoV-HKU9 (HM211100) and Kenyan strain KY77 (GU065421), with posterior probabilities of 1. These lineages could be described as SARS-like, and were uniquely affiliated with frugivorous bat hosts of the family Pteripodidae. Malagasy strains were sub-divided into three distinct clusters: two of which were closely related (clusters 1 and 2) and originating from P. rufus, and one more distantly related (cluster 3) containing a strain detected from E. dupreanum and sequences previously detected from E. helvum in Kenya [21].Figure 2


Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar.

Razanajatovo NH, Nomenjanahary LA, Wilkinson DA, Razafimanahaka JH, Goodman SM, Jenkins RK, Jones JP, Heraud JM - Virol. J. (2015)

Bayesian phylogenetic tree generated using 993 nucleotides of the RdRp gene sequences of Malagasy bat CoVs and reference strains of CoVs group. Major viral genera are shown. Strains detected in this study are marked with an*. Posterior probabilities superior to 0.9 are indicated by a dot, other posterior probabilities are indicated in decimal form to the right of each node, and some have been left off for clarity. The scale bar is expressed in years. The inset figure shows the partial phylogeny of the highlighted region of the Betacoronavirus subgroup, including additional reference sequences and with a total alignment length of 329 nucleotides. Techniques used for generating each phylogenetic representation were identical, as detailed in the materials and methods section.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4404003&req=5

Fig2: Bayesian phylogenetic tree generated using 993 nucleotides of the RdRp gene sequences of Malagasy bat CoVs and reference strains of CoVs group. Major viral genera are shown. Strains detected in this study are marked with an*. Posterior probabilities superior to 0.9 are indicated by a dot, other posterior probabilities are indicated in decimal form to the right of each node, and some have been left off for clarity. The scale bar is expressed in years. The inset figure shows the partial phylogeny of the highlighted region of the Betacoronavirus subgroup, including additional reference sequences and with a total alignment length of 329 nucleotides. Techniques used for generating each phylogenetic representation were identical, as detailed in the materials and methods section.
Mentions: All amplicon sequences were aligned in-frame with a compilation of reference sequences from GenBank for which collection-date data was available [28], giving final alignments containing 51 different sequences of 993 bp in length and 64 different sequences of 329 bp in length. GTR + I + G was identified as the optimal substitution model using jModeltest v2.1.2 [29]. Multiple phylogenies were generated in BEAST using different combinations of model parameters, and the best models were selected using the Tracer [30]. Bayes factor analysis employing marginal likelihoods, as detailed in [12]. All parameter combinations produced identical, strongly supported tree topologies (data not shown). As has elsewhere been determined by Lau et al. [12], Bayesian skyline using a relaxed, exponentially distributed clock model was found to be the best fitting model for RdRp dated-tip phylogenies. The final phylogenetic analyses (Figure 2) revealed that strains from Madagascar are members of the Betacoronavirus genus, rooting with Hong Kong strain BtCoV-HKU9 (HM211100) and Kenyan strain KY77 (GU065421), with posterior probabilities of 1. These lineages could be described as SARS-like, and were uniquely affiliated with frugivorous bat hosts of the family Pteripodidae. Malagasy strains were sub-divided into three distinct clusters: two of which were closely related (clusters 1 and 2) and originating from P. rufus, and one more distantly related (cluster 3) containing a strain detected from E. dupreanum and sequences previously detected from E. helvum in Kenya [21].Figure 2

Bottom Line: Certain Malagasy bats can be frequently found in close contact with humans and frugivorous bats feed in the same trees where people collect and consume fruits and are hunted and consumed as bush meat.Our findings suggest that CoVs circulate in frugivorous bats of Madagascar, demonstrating the needs to evaluate spillover risk to human populations especially for individuals that hunt and consume infected bats.Possible dispersal mechanisms as to how coronaviruses arrived on Madagascar are discussed.

View Article: PubMed Central - PubMed

Affiliation: Virology Unit, Institut Pasteur of Madagascar, Ambatofotsikely, BP 1274, Antananarivo, Madagascar, Dummy_Only. norosoa@pasteur.mg.

ABSTRACT

Background: Bats are amongst the natural reservoirs of many coronaviruses (CoVs) of which some can lead to severe infection in human. African bats are known to harbor a range of pathogens (e.g., Ebola and Marburg viruses) that can infect humans and cause disease outbreaks. A recent study in South Africa isolated a genetic variant closely related to MERS-CoV from an insectivorous bat. Though Madagascar is home to 44 bat species (41 insectivorous and 3 frugivorous) of which 34 are endemic, no data exists concerning the circulation of CoVs in the island's chiropteran fauna. Certain Malagasy bats can be frequently found in close contact with humans and frugivorous bats feed in the same trees where people collect and consume fruits and are hunted and consumed as bush meat. The purpose of our study is to detect and identify CoVs from frugivorous bats in Madagascar to evaluate the risk of human infection from infected bats.

Methods: Frugivorous bats belonging to three species were captured in four different regions of Madagascar. We analyzed fecal and throat swabs to detect the presence of virus through amplification of the RNA-dependent RNA polymerase (RdRp) gene, which is highly conserved in all known coronaviruses. Phylogenetic analyses were performed from positive specimens.

Results: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Phylogenetic analysis revealed that the Malagasy strains belong to the genus Betacoronavirus but form three distinct clusters, which seem to represent previously undescribed genetic lineages.

Conclusions: Our findings suggest that CoVs circulate in frugivorous bats of Madagascar, demonstrating the needs to evaluate spillover risk to human populations especially for individuals that hunt and consume infected bats. Possible dispersal mechanisms as to how coronaviruses arrived on Madagascar are discussed.

No MeSH data available.


Related in: MedlinePlus