Phylogenetic Analyses of Rotavirus A from Cattle in Uruguay Reveal the Circulation of Common and Uncommon Genotypes and Suggest Interspecies Transmission

Abstract

Uruguay is one of the main exporters of beef and dairy products, and cattle production is one of the main economic sectors in this country. Rotavirus A (RVA) is the main pathogen associated with neonatal calf diarrhea (NCD), a syndrome that leads to significant economic losses to the livestock industry. The aims of this study are to determine the frequency of RVA infections, and to analyze the genetic diversity of RVA strains in calves in Uruguay. A total of 833 samples from dairy and beef calves were analyzed through RT-qPCR and sequencing. RVA was detected in 57.0% of the samples. The frequency of detection was significantly higher in dairy (59.5%) than beef (28.4%) calves (p < 0.001), while it did not differ significantly among calves born in herds that were vaccinated (64.0%) or not vaccinated (66.7%) against NCD. The frequency of RVA detection and the viral load were significantly higher in samples from diarrheic (72.1%, 7.99 log₁₀ genome copies/mL of feces) than non-diarrheic (59.9%, 7.35 log₁₀ genome copies/mL of feces) calves (p < 0.005 and p = 0.007, respectively). The observed G-types (VP7) were G6 (77.6%), G10 (20.7%), and G24 (1.7%), while the P-types were P[5] (28.4%), P[11] (70.7%), and P[33] (0.9%). The G-type and P-type combinations were G6P[11] (40.4%), G6P[5] (38.6%), G10P[11] (19.3%), and the uncommon genotype G24P[33] (1.8%). VP6 and NSP1-5 genotyping were performed to better characterize some strains. The phylogenetic analyses suggested interspecies transmission, including transmission between animals and humans.

Keywords: bovine; diarrhea; genotypes; interspecies transmission; rotavirus.

Figure 1

Frequency of Rotavirus A (RVA) detection in calves. (a) Frequency of RVA detection in dairy vs. beef calves; (b) frequency of RVA detection in live vs. deceased calves; (c) frequency of RVA detection in calves from vaccinated ^a vs. unvaccinated dairy herds; (d) frequency of RVA detection in diarrheic vs. non diarrheic dairy calves. Comparisons with statistically significant differences are indicated. ^a Most of the vaccines against neonatal calf diarrhea available in Uruguay include two RVA strains.

Figure 2

Maximum likelihood tree of the G6 genotype of the VP7 gene. The best nucleotide substitution model (TIM2 + I + G) and the maximum likelihood tree were obtained with W-IQ-TREE. Uruguayan strains are shown in red. Shimodaira–Hasegawa-approximate likelihood-ratio test (SH-aLRT) values ≥ 80 are shown.

Figure 3

Maximum likelihood tree of the G10 genotype of the VP7 gene. The best nucleotide substitution model (TPM3 + G) and the maximum likelihood tree were obtained with W-IQ-TREE. Uruguayan strains are shown in red. SH-aLRT values ≥ 80 are shown.

Figure 4

Maximum likelihood tree of the P[5] genotype of the VP4 gene. The best nucleotide substitution model (TIM + G) and the maximum likelihood tree were obtained with W-IQ-TREE. Uruguayan strains are shown in red. SH-aLRT values ≥ 80 are shown.

Figure 5

Maximum likelihood tree of the P[11] genotype of the VP4 gene. The best nucleotide substitution model (TPM3u + G) and the maximum likelihood tree were obtained with W-IQ-TREE. Uruguayan strains are shown in red. SH-aLRT values ≥ 80 are shown.

Figure 6

Map of Uruguay, the regions from which samples were collected shown in grey.