High detection rates of picobirnaviruses in free roaming rats (Rattus spp.): Molecular characterization of complete gene segment-2

Detection and Molecular Characterization of Picobirnaviruses (PBVs) in the Mongoose: Identification of a Novel PBV Using an Alternative Genetic Code

“…The screening results were confirmed by sequencing the~201 bp PCR amplicons of gene segment-2 of the mongoose PBV GI strains. None of the PBV positive mongooses exhibited clinical signs of diarrhea, corroborating previous reports on asymptomatic PBV infection in wildlife [5,6,13,15]. The mongooses were trapped in both urban and wild habitats, and most likely came into contact with humans and various animal species (cats, dogs, livestock, rodents, and vervet monkeys), which may have increased their chances of exposure and PBV infection ( Figure 2).…”

“…A significant portion (~1200 bp, corresponding to nt 283-nt 1478 of gene segment-2 of prototype PBV GI strain PBV/Human/CHN/1-CHN-97/1997) of gene segment-2 of the mongoose PBV strains (strains PBV/Mongoose/KNA/M33/2017, PBV/Mongoose/KNA/M45/2017, PBV/Mongoose/KNA/ M46/2017, PBV/Mongoose/KNA/M58/2017, PBV/Mongoose/KNA/M67/2017 and PBV/Mongoose/ KNA/M72/2017) was amplified by two separate, overlapping RT-PCRs using published primers PBV 1.2FP and PicoB43, as well as primers PicoB25 and PBV 1.2RP (primer sequences are shown in supplementary material S1) [23,24]. The remaining 5 -portion of gene segment-2 of the 6 mongoose PBV strains, and the 3portion of gene segment-2 of a single mongoose PBV strain (strain M58) could be amplified using a modified non-specific primer-based amplification method with modifications as previously described (elaborated in supplementary material S2) [13,19]. A new reverse primer, designated as PBV-Con3 (5 -AAT GGT TTA CTG CAC CAT CTC-3 , nt 1665-nt 1644 of gene segment-2 of mongoose PBV strain M58), was designed from a short stretch of nt sequence that is conserved in the 3 -UTR of gene segment-2 of mongoose PBV strain M58 and PBV GI strains from other host species.…”

“…The complete/nearly complete gene segment-2 of the mongoose PBV GI strains was amplified by combining a modified non-specific primer-based amplification method with conventional RT-PCRs. Since the non-specific primer method is difficult, time consuming and requires large volumes of viral RNA as starting material [13][14][15][16]19], the inclusion of a newly designed reverse primer, PBV-Con3, greatly facilitated the amplification of the almost complete 3′-end region of the PBV strains by conventional RT-PCRs.…”

“…Until recently, most studies on genetic diversity of PBVs were limited to analyses of short nt sequences (~201 bp of gene segment-2) which may not be sufficient to obtain conclusive information on the putative RdRps, or genetic make-up of PBVs [5,6,12]. However, by applying a non-specific primer-based amplification method, or next-generation sequencing, it has been possible to obtain the whole genomes, or the complete/nearly complete gene segment-2 sequences of several PBV strains from various host species, providing important insights into the genetic diversity and evolution of PBVs [1,2,10,[13][14][15][16][17][18][19][20].…”

“…Although PBVs have been detected in a wide variety of host species including wildlife [5,6,10,13,15,20], there have been no reports on PBVs from the mongoose so far. In the present study, we report for the first time detection and molecular characterization of complete/nearly complete gene segment-2 (full length minus partial 3 -untranslated region (UTR)) of PBV strains from the small Indian mongoose (Urva auropunctata) on the Caribbean island of St. Kitts.…”