Genomic characterization of novel picobirnaviruses in camels

Abstract

Due to the recent emergency of Middle East Respiratory Coronavirus (MERS-CoV), the study of novel viruses in dromedaries has given rise to an enormous interest. In this study, the molecular epidemiology of picobirnaviruses (PBVs) in dromedary fecal samples and the complete genome sequencing of genogroup I and genogroup II PBVs were carried out. Camel fecal samples (n=229) were collected in Dubai for detection of PBVs using newly designed PCR primers targeting the RdRp gene in which 94 of 229 (41%) were confirmed for positive genogroup I PBVs while 50 of 229 (22%) were confirmed positive for genogroup II PBVs. Among these 121 positive samples, 23 (19%) were positive for both genogroup I and genogroup II PBVs, while 98 (81%) were positive for either genogroup I or genogroup II PBVs. Marked nucleotide polymorphisms were observed in most of the RdRp sequences of both genogroup I and genogroup II PBVs, suggesting the possible existence of multiple strains in the same specimen. Phylogenetic analysis based on 205-bp or 207-bp fragment in the RdRp gene revealed that high diversity of PBVs observed in dromedaries. In addition, 5 genogroup I and 3 genogroup II PBVs among the positive samples were selected for whole genome sequencing. In genogroup I, 2 complete and near-complete genomes of segment 1 and 3 complete and near-complete genomes of segment 2 were sequenced. In genogroup II, 2 partial genomes of segment 1 and 3 partial genomes of segment 2 were sequenced as well. During the process of genome sequencing, two different sequence types of segment 1 were found in one camel sample (103C) positive for genogroup I PBV, sharing only 43% amino acid identity. The genome organization of the PBVs camel samples were compared with PBV genome references in Genbank; genome characteristic including the sequence length, G+C content, the conserved motif in segment 1(ExxRxNxxxE) and three conserved motifs in segment 2 (DxT/SxxD, SFxxxT,GDD) are typical to existing PBVs genomes. Phylogenetic analysis was also performed based on the amino acid sequence of capsid and RdRp proteins respectively. Overall; the topology of the phylogenetic tree based on capsid sequence was concordant with that based on RdRp sequence. However, further confirmation requires to be studied by having more availability of capsid sequences. PBV probably evolves through mechanisms similar to other segmented RNA viruses, as it was observed that two different sequences types of segment 1 can be present in the same specimen which may provide a good opportunity for reassortment.