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Novel highly divergent reassortant bat rotaviruses in Cameroon, without evidence of zoonosis

View Article: PubMed Central - PubMed

ABSTRACT

Bats are an important reservoir for zoonotic viruses. To date, only three RVA strains have been reported in bats in Kenya and China. In the current study we investigated the genetic diversity of RVAs in fecal samples from 87 straw-colored fruit bats living in close contact with humans in Cameroon using viral metagenomics. Five (near) complete RVA genomes were obtained. A single RVA strain showed a partial relationship with the Kenyan bat RVA strain, whereas the other strains were completely novel. Only the VP7 and VP4 genes showed significant variability, indicating the occurrence of frequent reassortment events. Comparing these bat RVA strains with currently used human RVA screening primers indicated that most of the novel VP7 and VP4 segments would not be detected in routine epidemiological screening studies. Therefore, novel consensus screening primers were developed and used to screen samples from infants with gastroenteritis living in close proximity with the studied bat population. Although RVA infections were identified in 36% of the infants, there was no evidence of zoonosis. This study identified multiple novel bat RVA strains, but further epidemiological studies in humans will have to assess if these viruses have the potential to cause gastroenteritis in humans.

No MeSH data available.


Phylogenetic trees of full-length ORF nucleotide sequences of the RVA NSP1 and NSP4 gene segments.Filled triangle: Cameroonian strains; open triangles: previously described bat RVA strains. Bootstrap values (500 replicates) above 70 are shown.
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f5: Phylogenetic trees of full-length ORF nucleotide sequences of the RVA NSP1 and NSP4 gene segments.Filled triangle: Cameroonian strains; open triangles: previously described bat RVA strains. Bootstrap values (500 replicates) above 70 are shown.

Mentions: The VP7 gene of BatLy03 was 96% identical (on the nucleotide (nt) level, supplementary data S1) to the Kenyan bat RVA strain KE4852 counterpart, which had been previously classified as a G25 genotype (Fig. 2). BatLi10 and BatLi09 were 100% identical and also clustered closely with strain BatLy17 (92% similar). This cluster was only distantly related to all other known VP7 RVA sequences as well as to strain BatLi08, which also formed a unique long branch in the phylogenetic tree. Both clusters only show similarities below 74% with established genotypes (Fig. 2). The VP7 of these 4 strains (BatLi10, BatLi09, BatLy17 and BatLi08) did not belong to any of the established RVA G-genotypes, according to the established criteria6, and were assigned genotypes G30 (BatLi09, BatLi10 and BatLy17) and G31 (BatLi08) by the RCWG. For VP4, VP1 and VP3, all five Cameroonian bat RVAs strains were distantly related to other known RVA strains, including the Kenyan and Chinese RVA strains and were therefore assigned to novel genotypes according to the RCWG classification criteria (Fig. 3). The VP4 gene of strains BatLi08, BatLi09 and BatLi10 (representatives of the novel genotype P[42]) were almost 99–100% identical to each other and only 56–75% identical to any other P-genotype. That of strains BatLy03 and BatLy17 had 29% nt dissimilarity to each other and their nt identity ranged from 60–76% with other P-genotypes and therefore were assigned the genotypes P[43] and P[47], respectively. The VP1 and VP3 genes of BatLi08, BatLi09, BatLi10 and BatLy17 were nearly identical (nt identity range 99–100%) and clustered together but distinct from other established R and M-genotypes, thereby representing the new genotypes R15 and M14, respectively (Fig. 3). The VP1 and VP3 genes of BatLy03 were only distantly related to the other four Cameroonian bat RVAs (68–77% nt identity) and are the sole member of the newly assigned genotypes R16 and M15, respectively (Fig. 3). The VP6, VP2, NSP2, NSP3 and NSP5 gene segments of 4 of our strains (BatLi08, BatLi09, BatLi10 and BatLy17) were distantly related to their counterparts of other mammalian and avian RVAs (Fig. 4). For all the 4 strains, these gene segments clustered together and were 99–100% identical to each other and consequently they constitute new genotypes for the different gene segments (I22, C15 N15, T17 and H17, respectively). The VP6, VP2, NSP2, NSP3 and NSP5 gene segments of BatLy03 phylogenetically clustered together with the Kenyan bat RVA strain KE4852 in the previously established I15, C8, N8, T11 and H10 genotypes, respectively (Fig. 4). For NSP1, the Cameroonian bat strains BatLi08, BatLi09, BatLi10 and BatLy17 clustered closely together (98–100% nucleotide sequence identity) in the novel genotype A25, and showed only 67% nucleotide similarity to strain BatLy03 (A26). These 5 new NSP1 gene segments were only 42–45% identical to that of the most closely related established NSP1 genotype A13 and A14 (from cow) (Fig. 5). The NSP4 gene segments of all the 5 RVAs discovered in this study were quite divergent to those of other known bat rotaviruses (at most 69% nucleotide sequence identity) and other RVAs (approximately 45–68% nucleotide similarity) forming two distinct clusters. The NSP4 gene segments of strains BatLi08, BatLi09, BatLi10 and BatLy03 (genotype E22) were 100% identical but all were 37–38% divergent from that of BatLy03 (E23, Fig. 5).


Novel highly divergent reassortant bat rotaviruses in Cameroon, without evidence of zoonosis
Phylogenetic trees of full-length ORF nucleotide sequences of the RVA NSP1 and NSP4 gene segments.Filled triangle: Cameroonian strains; open triangles: previously described bat RVA strains. Bootstrap values (500 replicates) above 70 are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
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f5: Phylogenetic trees of full-length ORF nucleotide sequences of the RVA NSP1 and NSP4 gene segments.Filled triangle: Cameroonian strains; open triangles: previously described bat RVA strains. Bootstrap values (500 replicates) above 70 are shown.
Mentions: The VP7 gene of BatLy03 was 96% identical (on the nucleotide (nt) level, supplementary data S1) to the Kenyan bat RVA strain KE4852 counterpart, which had been previously classified as a G25 genotype (Fig. 2). BatLi10 and BatLi09 were 100% identical and also clustered closely with strain BatLy17 (92% similar). This cluster was only distantly related to all other known VP7 RVA sequences as well as to strain BatLi08, which also formed a unique long branch in the phylogenetic tree. Both clusters only show similarities below 74% with established genotypes (Fig. 2). The VP7 of these 4 strains (BatLi10, BatLi09, BatLy17 and BatLi08) did not belong to any of the established RVA G-genotypes, according to the established criteria6, and were assigned genotypes G30 (BatLi09, BatLi10 and BatLy17) and G31 (BatLi08) by the RCWG. For VP4, VP1 and VP3, all five Cameroonian bat RVAs strains were distantly related to other known RVA strains, including the Kenyan and Chinese RVA strains and were therefore assigned to novel genotypes according to the RCWG classification criteria (Fig. 3). The VP4 gene of strains BatLi08, BatLi09 and BatLi10 (representatives of the novel genotype P[42]) were almost 99–100% identical to each other and only 56–75% identical to any other P-genotype. That of strains BatLy03 and BatLy17 had 29% nt dissimilarity to each other and their nt identity ranged from 60–76% with other P-genotypes and therefore were assigned the genotypes P[43] and P[47], respectively. The VP1 and VP3 genes of BatLi08, BatLi09, BatLi10 and BatLy17 were nearly identical (nt identity range 99–100%) and clustered together but distinct from other established R and M-genotypes, thereby representing the new genotypes R15 and M14, respectively (Fig. 3). The VP1 and VP3 genes of BatLy03 were only distantly related to the other four Cameroonian bat RVAs (68–77% nt identity) and are the sole member of the newly assigned genotypes R16 and M15, respectively (Fig. 3). The VP6, VP2, NSP2, NSP3 and NSP5 gene segments of 4 of our strains (BatLi08, BatLi09, BatLi10 and BatLy17) were distantly related to their counterparts of other mammalian and avian RVAs (Fig. 4). For all the 4 strains, these gene segments clustered together and were 99–100% identical to each other and consequently they constitute new genotypes for the different gene segments (I22, C15 N15, T17 and H17, respectively). The VP6, VP2, NSP2, NSP3 and NSP5 gene segments of BatLy03 phylogenetically clustered together with the Kenyan bat RVA strain KE4852 in the previously established I15, C8, N8, T11 and H10 genotypes, respectively (Fig. 4). For NSP1, the Cameroonian bat strains BatLi08, BatLi09, BatLi10 and BatLy17 clustered closely together (98–100% nucleotide sequence identity) in the novel genotype A25, and showed only 67% nucleotide similarity to strain BatLy03 (A26). These 5 new NSP1 gene segments were only 42–45% identical to that of the most closely related established NSP1 genotype A13 and A14 (from cow) (Fig. 5). The NSP4 gene segments of all the 5 RVAs discovered in this study were quite divergent to those of other known bat rotaviruses (at most 69% nucleotide sequence identity) and other RVAs (approximately 45–68% nucleotide similarity) forming two distinct clusters. The NSP4 gene segments of strains BatLi08, BatLi09, BatLi10 and BatLy03 (genotype E22) were 100% identical but all were 37–38% divergent from that of BatLy03 (E23, Fig. 5).

View Article: PubMed Central - PubMed

ABSTRACT

Bats are an important reservoir for zoonotic viruses. To date, only three RVA strains have been reported in bats in Kenya and China. In the current study we investigated the genetic diversity of RVAs in fecal samples from 87 straw-colored fruit bats living in close contact with humans in Cameroon using viral metagenomics. Five (near) complete RVA genomes were obtained. A single RVA strain showed a partial relationship with the Kenyan bat RVA strain, whereas the other strains were completely novel. Only the VP7 and VP4 genes showed significant variability, indicating the occurrence of frequent reassortment events. Comparing these bat RVA strains with currently used human RVA screening primers indicated that most of the novel VP7 and VP4 segments would not be detected in routine epidemiological screening studies. Therefore, novel consensus screening primers were developed and used to screen samples from infants with gastroenteritis living in close proximity with the studied bat population. Although RVA infections were identified in 36% of the infants, there was no evidence of zoonosis. This study identified multiple novel bat RVA strains, but further epidemiological studies in humans will have to assess if these viruses have the potential to cause gastroenteritis in humans.

No MeSH data available.