Whole genome analysis of selected human and animal rotaviruses identified in Uganda from 2012 to 2014 reveals complex genome reassortment events between human, bovine, caprine and porcine strains

Abstract

Rotaviruses of species A (RVA) are a common cause of diarrhoea in children and the young of various other mammals and birds worldwide. To investigate possible interspecies transmission of RVAs, whole genomes of 18 human and 6 domestic animal RVA strains identified in Uganda between 2012 and 2014 were sequenced using the Illumina HiSeq platform. The backbone of the human RVA strains had either a Wa- or a DS-1-like genetic constellation. One human strain was a Wa-like mono-reassortant containing a DS-1-like VP2 gene of possible animal origin. All eleven genes of one bovine RVA strain were closely related to those of human RVAs. One caprine strain had a mixed genotype backbone, suggesting that it emerged from multiple reassortment events involving different host species. The porcine RVA strains had mixed genotype backbones with possible multiple reassortant events with strains of human and bovine origin.Overall, whole genome characterisation of rotaviruses found in domestic animals in Uganda strongly suggested the presence of human-to animal RVA transmission, with concomitant circulation of multi-reassortant strains potentially derived from complex interspecies transmission events. However, whole genome data from the human RVA strains causing moderate and severe diarrhoea in under-fives in Uganda indicated that they were primarily transmitted from person-to-person.

Fig 1. The maps of Uganda, Kampala and Masaka districts showing the hospitals and households at which the study children and animals (rotavirus positives that were sequenced) were recruited respectively.

Fig 2. VP1 gene (segment 1).

Maximum Likelihood phylogenetic trees of nucleotide sequences of rotavirus genome segment 1 of humans and animal RVA strains circulating in Uganda, 2012–2014. Bootstrap values above 70 are shown for 1000 replicates. The Ugandan human strains are labelled with blue circles and the Ugandan animal strains with red triangles. The Pigeon strain RVA/Pigeon-tc/PN/PO-13/1983/G18P[17] served as the outgroup. The scale bar at the bottom of the tree calibrates the genetic distance expressed as nucleotide substitution per site.

Fig 3. VP6 gene (segment 6).

Maximum Likelihood phylogenetic trees of nucleotide sequences of rotavirus genome segment 6 of human and animal RVA strains circulating in Uganda, 2012–2014. Bootstrap values above 70 are shown for 1000 replicates. The Ugandan human strains are labelled with blue circles and the Ugandan animal strains with red triangles. Chicken strain RVA/Chicken-tc/GBR/Ch-2/1979/G3P[30] served as the outgroup. The scale bar at the bottom of the tree calibrates the genetic distance expressed as nucleotide substitution per site.

Fig 4. NSP2 gene (segment 8).

Maximum Likelihood phylogenetic trees of nucleotide sequences of genome segment 8 of human and animal RVA strains circulating in Uganda, 2012–2014. Bootstrap values above 70 are shown for 1000 replicates. The Ugandan human strains are labelled with blue circles and the Ugandan animal strains with red triangles. Pigeon strain RVA/Pigeon-tc/PN/PO-13/1983/G18P[17] served as the outgroup. The scale bar at the bottom of the tree calibrates the genetic distance expressed as nucleotide substitution per site.

Fig 5. NSP4 gene (segment 10).

Maximum Likelihood phylogenetic trees of nucleotide sequences of genome segment 10 gene of human and animal RVA strains circulating in Uganda, 2012–2014. Bootstrap values above 70 are shown for 1000 replicates. The Ugandan human strains are labelled with blue circles and the Ugandan animal strains with red triangles. Pigeon strain RVA/Pigeon-tc/PN/PO-13/1983/G18P[17] served as the outgroup. The scale bar at the bottom of the tree calibrates the genetic distance expressed as nucleotide substitution per site.

Fig 6. NSP5 gene (segment 11).

Maximum Likelihood phylogenetic trees of nucleotide sequences of genome segment 11 of human and animal RVA strains circulating in Uganda, 2012–2014. Bootstrap values above 70 are shown for 1000 replicates. The Ugandan human strains are labelled with blue circles and the Ugandan animal strains with red triangles. Pigeon strain RVA/Pigeon-tc/PN/PO-13/1983/G18P[17] served as the outgroup. The scale bar at the bottom of the tree calibrates the genetic distance expressed as nucleotide substitution per site.

Fig 7. VP4 gene (segment 4).

Maximum Likelihood phylogenetic trees of nucleotide sequences of rotavirus genome segment 4 of human and animal RVA strains circulating in Uganda, 2012–2014. Bootstrap values above 70 are shown for 1000 replicates. The Ugandan human strains are labelled with blue circles and the Ugandan animal strains with red triangles. Chicken strain, RVA/Chicken-tc/GBR/Ch-2/1979/G3P[30] served as the outgroup. The scale bar at the bottom of the tree calibrates the genetic distance expressed as nucleotide substitution per site.

Fig 8. VP7 gene (segment 9).

Maximum Likelihood phylogenetic trees of nucleotide sequences of rotavirus genome segment 9 of human and animal RVA strains circulating in Uganda, 2012–2014. Bootstrap values above 70 are shown for 1000 replicates. The Ugandan human strains are labelled with blue circles and the Ugandan animal strains with red triangles. Chicken strain RVA/Chicken-wt/KOR/ArRv-2/2011/G19P[30] served as the outgroup. The scale bar at the bottom of the tree calibrates the genetic distance expressed as nucleotide substitution per site.