Alejandra Badaracco

Complete molecular genome analyses of equine rotavirus A strains from different continents reveal several novel genotypes and a largely conserved genotype constellation

In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P[18], RVA/Horse-wt/IRL/03V04954/2003/G3P[12] and RVA/Horse-wt/IRL/04V2024/2004/G14P[12] from Europe; RVA/Horse-wt/ARG/E30/1993/G3P[12], RVA/Horse-wt/ARG/E403/2006/G14P[12] and RVA/Horse-wt/ARG/E4040/2008/G14P[12] from Argentina; and RVA/Horse-wt/ZAF/EqRV-SA1/2006/G14P[12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), E14 (NSP4), and H7 and H11 (NSP5). The genotype constellation of L338 was unique: G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11. The six remaining equine RVA strains showed a largely conserved genotype constellation: G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2/E12-H7, which is highly divergent from other known non-equine RVA genotype constellations. Phylogenetic analyses revealed that the sequences of these equine RVA strains are related distantly to non-equine RVA strains, and that at least three lineages exist within equine RVA strains. A small number of reassortment events were observed. Interestingly, the three RVA strains from Argentina possessed the E12 genotype, whereas the three RVA strains from Ireland and South Africa possessed the E2 genotype. The unusual E12 genotype has until now only been described in Argentina among RVA strains collected from guanaco, cattle and horses, suggesting geographical isolation of this NSP4 genotype. This conserved genetic configuration of equine RVA strains could be useful for future vaccine development or improvement of currently used equine RVA vaccines.

Bovine rotavirus strains circulating in beef and dairy herds in Argentina from 2004 to 2010

Bovine Group A Rotavirus (RVA) is one of the main causes of neonatal calf diarrhea worldwide. The present study reports the genotyping of bovine RVA strains circulating in Argentinean cattle from 2004 to 2010. Additionally, a new set of typing primers was designed and tested to differentiate between G8 and G6 (lineage III and IV) RVA strains. Bovine RVA was detected in 30% (435/1462) of the tested samples, corresponding to 49% (207/423) of the studied outbreaks with a similar detection rates in beef (53%; 67/127) and dairy herds (52%; 65/126). The RVA strains circulating in Argentinean cattle belonged to the common bovine genotypes G6 (lineages III and IV), G8, G10, P[5] and P[11]. A different RVA G/P-genotype distribution was found between the exploitation types, with the combination G6(IV)P[5] being by fare the most prevalent RVA strain in beef herds (58%), whereas a more even distribution of G6(III)P[11] (15%), G10P[11] (17%), G6(IV)P[5] (14%), and G6(IV)P[11] (6%) RVA strains was detected in dairy herds. G8 RVA strains were found in two dairy farms in calves co-infected with G8+G6(III)P[11]. A high percentage of co-infections and co-circulation of RVA strains with different genotypes during the same outbreak were registered in both exploitation types (20% of the outbreaks from beef herds and 23% from dairy herds), indicating a potential environment for reassortment. This finding is significant because G10P[11] and G6(III)P[11] strains may possess zoonotic potential. Continuous surveillance of the RVA strains circulating in livestock provides valuable information for a better understanding of rotavirus ecology and epidemiology.

Discovery and molecular characterization of a group A rotavirus strain detected in an Argentinean vicuña (Vicugna vicugna)

The wild vicuña (Vicugna vicugna) is one of the four species of native South American camelids (SACs) in addition to the wild guanaco, and their domesticated counterparts, alpaca and llama, respectively. Serological data have indicated the presence of group A rotaviruses (RVA) specific antibodies in all 4 members of the SAC, and so far, RVA has been detected from alpacas, llamas and guanacos. A total of 59 fecal samples from healthy wild newborn and juvenile vicuñas, raised in captivity in Jujuy, Argentina were collected and analyzed by ELISA to detect RVA antigen. Two samples (3%) were found to contain G8 RVA strains and one strain (RVA/Vicuña-wt/ARG/C75/2010/G8P[14]) was selected for further genome analyses, revealing the G8-P[14]-I2-R2-C2-M2-Ax-N2-T6-E3-Hx genotype constellation. Unfortunately, no sequence data could be obtained for NSP1 and NSP5. Except for the E3 NSP4 genotype, this partial genotype constellation is reminiscent to bovine RVA strains and bovine-like RVA strains isolated from sheep, guanaco, antelope and humans. This relationship was confirmed phylogenetically, providing further evidence of the widespread presence of this genotype constellation in animals belonging to the artiodactyls. In particular, a close phylogenetic relationship was found between C75 and guanaco RVA strain RVA/Guanaco-wt/ARG/Chubut/1999/G8P[14] for at least 5 gene segments, suggesting a partial conservation of the genotype constellation of RVA strains infecting different species of SACs, even though nowadays their natural habitats are not overlapping. The further monitoring of the sanitary health of wild newborn and juvenile vicuñas is essential to improve the management practices applied in their sustainable exploitation.

Phylogenetic analyses of typical bovine rotavirus genotypes G6, G10, P(5) and P(11) circulating in Argentinean beef and dairy herds

Group A rotavirus (RVA) is one of the main causes of neonatal calf diarrhea worldwide. RVA strains affecting Argentinean cattle mainly possess combinations of the G6, G10, P[5] and P[11] genotypes. To determine RVA diversity among Argentinean cattle, representative bovine RVA strains detected in diarrheic calves were selected from a survey conducted during 1997-2009. The survey covered the main livestock regions of the country from dairy and beef herds. Different phylogenetic approaches were used to investigate the genetic evolution of RVA strains belonging to the prevalent genotypes. The nucleotide phylogenetic tree showed that all genotypes studied could be divided into several lineages. Argentinean bovine RVA strains were distributed across multiple lineages and most of them were distinct from the lineage containing the vaccine strains. Only the aminoacid phylogenetic tree of G6 RVA strains maintained the same lineages as observed at the nucleotide level, whereas a different clustering pattern was observed for the aminoacid phylogenetic trees of G10, P[5] and P[11] suggesting that the strains are more closely related at the aminoacid level than G6 strains. Association between P[5] and G6(IV), prevalent in beef herd, and between P[11] and G6(III) or G10 (VI and V), prevalent in dairy herds, were found. In addition, Argentinean G6(III), G10, P[5] and P[11] bovine RVA strains grouped together with human strains, highlighting their potential for zoonotic transmission. Phylogenetic studies of RVA circulating in animals raised for consumption and in close contact with humans, such as cattle, contribute to a better understanding of the epidemiology of the RVA infection and evolution.

The first caprine rotavirus detected in Argentina displays genomic features resembling virus strains infecting members of the Bovidae and Camelidae.

Rotavirus group A (RVA) is a major cause of diarrhea in humans and young animals including small ruminants. The purpose of this study was to identify RVA in dairy goat kids, and to characterize the complete genomic constellation and genetic relatedness with other RVA strains. Four out of twenty fecal samples from diarrheic and non-diarrheic goat kids were positive for RVA by ELISA. A representative sample was selected for further genome analyses. The RVA strain RVA/Goat-wt/ARG/0040/2011/G8P[1] displayed the following genomic constellation: G8-P[1]-I2-R5-C2-M2-A3-N2-T6-E12-H3, reminiscent to guanaco and other bovine-like RVA strains detected in Argentina. Phylogenetic analyses revealed that most of the genome segments had a rather close relatedness with RVA strains typically obtained from cattle, sheep, South American camelids and goats. Interestingly, strain 0040 possessed the R5 and E12 genotypes which have up to date only been found in different animal species from Argentina. Overall, these findings suggest that strain 0040 could represent a typical goat RVA genome constellation similar to those previously found in other animal species within the order Artiodactyla.

Molecular detection of bovine noroviruses in Argentinean dairy calves: Circulation of a tentative new genotype

Abstract Bovine noroviruses are enteric pathogens detected in fecal samples of both diarrheic and non-diarrheic calves from several countries worldwide. However, epidemiological information regarding bovine noroviruses is still lacking for many important cattle producing countries from South America. In this study, three bovine norovirus genogroup III sequences were determined by conventional RT-PCR and Sanger sequencing in feces from diarrheic dairy calves from Argentina (B4836, B4848, and B4881, all collected in 2012). Phylogenetic studies based on a partial coding region for the RNA-dependent RNA polymerase (RdRp, 503 nucleotides) of these three samples suggested that two of them (B4836 and B4881) belong to genotype 2 (GIII.2) while the third one (B4848) was more closely related to genotype 1 (GIII.1) strains. By deep sequencing, the capsid region from two of these strains could be determined. This confirmed the circulation of genotype 1 (B4848) together with the presence of another sequence (B4881) sharing its highest genetic relatedness with genotype 1, but sufficiently distant to constitute a new genotype. This latter strain was shown in silico to be a recombinant: phylogenetic divergence was detected between its RNA-dependent RNA polymerase coding sequence (genotype GIII.2) and its capsid protein coding sequence (genotype GIII.1 or a potential norovirus genotype). According to this data, this strain could be the second genotype GIII.2_GIII.1 bovine norovirus recombinant described in literature worldwide. Further analysis suggested that this strain could even be a potential norovirus GIII genotype, tentatively named GIII.4. The data provides important epidemiological and evolutionary information on bovine noroviruses circulating in South America.

Molecular and antigenic characterization of bovine Coronavirus circulating in Argentinean cattle during 1994-2010.

Abstract Bovine coronavirus (BCoV) is an important viral pathogen associated with neonatal calf diarrhea. Our aim was to investigate the incidence of BCoV in diarrhea outbreaks in beef and dairy herds from Argentina during 1994–2010. A total of 5.365 fecal samples from diarrheic calves were screened for BCoV diagnosis by ELISA. The virus was detected in 1.71% (92/5365) of the samples corresponding to 5.95% (63/1058) of the diarrhea cases in 239 beef and 324 dairy farms. The detection rate of BCoV was significantly higher in dairy than in beef herds: 12.13% (29/239) vs. 4.32% (14/324) respectively. Phylogenetic analysis of the hypervariable S1 region of seven representative samples (from different husbandry systems, farm locations and years of sampling) indicated that BCoV strains circulating in Argentinean beef and dairy herds formed a cluster distinct from other geographical regions. Interestingly, Argentinean strains are distantly related (at both the nucleotide and amino acid levels) with the Mebus historic reference BCoV strain included in the vaccines currently available in Argentina. However, Mebus-induced antibodies were capable of neutralizing the BCoV Arg95, a field strain adapted to grow in vitro, and vice versa, indicating that both strains belong to the same CoV serotype reported in cattle. This work represents the first large survey describing BCoV circulation in Argentinean cattle.