Genomic diversity among group A rotaviruses from diarrheic children, piglets, buffalo and cow calves of Madhya Pradesh

Seasonal pattern in occurrence of rotavirus infection (RV) in diarrheic children, calves and piglets from Bareilly, India

Rapid and reliable diagnosis for diarrhoeal disease is critically important for the differentiation of etiological agents and subsequent suitable treatment modalities. The objective of the study is to reveal the seasonal pattern in the occurrence of rotavirus in diarrheic children, calves and piglets from Bareilly, Uttar Pradesh, India. A total of 115 diarrhoeal samples were collected, out of which 51 were collected during post-monsoon/autumn (September 2018-November 2018) and 64 during the winter season (December 2018-February 2019). The samples were collected from children <5 years (n = 50), piglets <3 months (n = 35) and calves <6 months of age (n = 30). These samples were screened by ribonucleic acid-polyacrylamide gel electrophoresis (RNA-PAGE) and reverse transcriptase-polymerase chain reaction (RT-PCR) by targeting the VP6 gene of rotavirus A (RVA) and the two were compared. In RNA-PAGE 29.4% (5/17), 6.3% (1/16) and 0% (0/18) samples collected from children, calves and piglets, respectively were rotavirus positive during the autumn season while 45.5% (15/33), 21.4% (3/14) and 17.7% (3/17) samples in the winter season. In RT-PCR, 41.2% (7/17), 12.5% (2/16) and 0% (0/18) samples were rotavirus positive in the autumn season while 51.5% (17/33), 28.6% (4/14) and 29.4% (5/17) samples in winter season collected from children, calves and piglets, respectively. On statistical analysis, no significant difference between the season and number of positives in children and calves (p > 0.05) was observed, however in piglets significantly higher number of RVA positives were detected in the winter season than autumn (p < 0.01). The diagnostic test comparison of RNA-PAGE and RT-PCR showed no statistically significant difference in detecting the RVA positives (p > 0.05). Overall the percent positivity showed a seasonal pattern with higher positivity in winter as compared to autumn season.

Molecular characterization of porcine group A rotavirus to contain piglet diarrhea for productivity enhancement in North East India

Gastrointestinal tract infections with acute diarrhea are indeed a serious cause of concern that held back the swine industry of North East India and among the various etiological agents causing the disease, group A rotavirus is the most common. In this regard, molecular characterization of the viral strains circulating in the region is of utmost importance for a strategic approach to control the disease. Thus, in the present study, diarrheic fecal samples from piglets of Tripura and Assam were evaluated for genotypic characterization of VP7 and VP4 gene of the virus. The samples positive for group A rotavirus were subjected to G and P type determination by nested- multiplex RT PCR as well as nucleotide sequencing of VP7 and VP4 gene. Nested- multiplex RT PCR revealed the presence of porcine group A rotavirus in the genotypic combination of G1P[6], G3P[6], G8P[6] and G4P[6] in the two states of North East India. Nucleotide sequencing of VP7 and VP4 genes however, revealed emergence of an unusual genotypic combination G26P[13]. VP7 and VP4 nucleotide and its deduced amino acid sequences when compared with global isolates, showed that the present strains shared closest similarity to the porcine rotavirus strain TJ4-1from Japan and hp140 from Eastern India. Identification of a novel genotype G26P[13] in the RVA infected pig population of Tripura and Assam, suggested presence of a greater diversity in rotavirus strains in the region. Thus, it evokes the need for continuous monitoring to assess and consider the strain variability in the design of a suitable vaccine candidate against the virus.

Supplementary Information

The online version of this article (10.1007/s13337-021-00659-6) contains supplementary material, which is available to authorized users.

Molecular characterization of porcine rotavirus A from India revealing zooanthroponotic transmission

Rotaviruses A (RVA) are leading causes of diarrhea and dehydration in piglets and imply great economic loss to the pig farming community. In this study, the porcine RVA genotypes circulating in western and northern parts of India were determined by screening 214 fecal samples from diarrheic (n = 144) and non-diarrheic (n = 70) pigs. Subsequently, the structural (VP4 and VP7) and nonstructural (NSP3, and NSP4) genes were amplified, sequenced, and genetically characterized. The RVA positivity percentage was 7.94% (17/214) by RNA-PAGE and 10.28% (22/214) by RT-PCR. Higher RVA positivity was observed in samples from Uttar Pradesh (24.07%) followed by Maharashtra (6.77%) and Goa (2.38%). The sequence and automated genotyping software analysis confirmed the circulation of G4P[6] and G9P[13] RVA strains in porcine population. To note, the sequence similarity of the VP7 gene of Porcine/INDIA/RVA/PK-13 IVRI/Maharashtra/G4 and Porcine/INDIA/RVA/P-8/IVRI/U.P./G9 strain showed a relationship of 96.83 and 98.89% at the nucleotide level with human RVA strains indicating inter-species transmission. Additionally, the NSP3 (T1) and NSP4 (E1) genes (genotypes) also showed genetic relatedness with human RVA strains. Overall, the nucleotide sequences of VP7, NSP3, and NSP4 genes of porcine RVA indicate zooanthroponotic transmission. Further, we report the detection of G9P[13] RVA strain in porcine for the first time from India.HIGHLIGHTSRVA positivity was 7.94% (17/214) by RNA-PAGE and 10.28% (22/214) by RT-PCRThe RVA strain G9P[13] reported for the first time in Indian pigletsVP7, NSP3 and NSP4 genes analysis of porcine RVA showed genetic relatedness with human strains indicating evidence of zooanthroponotic transmission.

Cross-sectional study on rotavirus A (RVA) infection and assessment of risk factors in pre- and post-weaning piglets in India

Rotavirus A (RVA) infections are known to retard the piglets' growth and minimize the profit to the pig farming community. Between August 2014 and July 2017, in a cross-sectional study, we surveyed 13 organized pig farms located in the eight states of India representing northern, north-eastern and southern regions, to identify the risk factors associated with RVA infection in pre- and post-weaning piglets. Faecal samples (n = 411) comprising of non-diarrhoeic (n = 320) and diarrhoeic (n = 91) were collected and screened for RVA infection using VP6 gene-based RT-PCR. RVA positivity of 52.5% (168/320) in non-diarrhoeic and 59.3% (54/91) in diarrhoeic piglets was noticed. Further, 53.3% (120/225) and 54.8% (102/186) of the samples from pre- and post-weaned samples were positive for RVA, respectively. To note, no statistically significant association was noticed between RVA infection, health and weaning status. Additionally, a questionnaire-based survey was conducted to identify the risk factors for RVA infections in piglets. The analysis revealed that good ventilation (OR 0.2, 95% CI 0.15-0.39), use of deep well water (OR 0.2, 95% CI 0.13-0.43) and feeding of commercial feed (OR 0.3, 95% CI 0.18-0.41) were associated with reduced risk of RVA infection compared with poor ventilation, use of shallow well water and feeding of own milled feed, respectively. Contrarily, mixed farms (OR 2.1, 95% CI 1.26-3.37), use of heater or cooler (OR 5.9, 95% CI 3.74-9.30), sheds in different elevation (OR 2.5, 95% CI 1.20-5.01) and weekly and occasional use of disinfectant for surface cleaning (OR 1.8, 95% CI 1.12-2.96) were associated with higher RVA infection. Mitigating the risk factors might help in better health management of piglets and increase the economic return to pig farming community in the country.

Species C Rotaviruses in Children with Diarrhea in India, 2010-2013: A Potentially Neglected Cause of Acute Gastroenteritis

All over the world, children and adults are severely affected by acute gastroenteritis, caused by one of the emerging enteric pathogens, rotavirus C (RVC). At present, no extensive surveillance program is running for RVC in India, and its prevalence is largely unknown except cases of local outbreaks. Here, we intended to detect the presence of RVC in diarrheic children visiting or admitted to hospitals in Haldwani (state of Uttarakhand, India), a city located in the foothills of the Himalayas. During 2010-2013, we screened 119 samples for RVC by an RVC VP6 gene-specific RT-PCR. Of these, 38 (31.93%) were found positive, which is higher than the incidence rates reported so far from India. The phylogenetic analysis of the derived nucleotide sequences from one of the human RVC (HuRVC) isolates, designated as HuRVC/H28/2013/India, showed that the study isolate belongs to genotype I2, P2 and E2 for RVC structural genes 6 and 4 (VP6, and VP4) and non-structural gene 4 (NSP4), respectively. Furthermore, the VP6 gene of HuRVC/H28/2013/India shows the highest similarity to a recently-reported human-like porcine RVC (PoRVC/ASM140/2013/India, KT932963) from India suggesting zoonotic transmission. We also report a full-length NSP4 gene sequence of human RVC from India. Under the One-health platforms there is a need to launch combined human and animal RVC surveillance programs for a better understanding of the epidemiology of RVC infections and for implementing control strategies.Reoviridae, possess 11 double-stranded segments of RNA that encode six structural viral proteins (VP1, VP2, VP3, VP4, VP6, VP7) and five/six non-structural proteins (NSP1-NSP5/6) [7]. Based on the antigenic properties of the major inner capsid protein (VP6), RVs are subdivided into eight well-characterized species (A-H) and two putative species viz. I and J [8-10]. Humans and other mammalian species are affected by species A, B, C and H rotaviruses and birds by species D, F and G, and species E has been reported exclusively in pigs [7,8,11-17]. The newly-proposed species I is reported in dogs [18] and cats [19], whereas species J is found in bats [10].

Porcine Rotaviruses: Epidemiology, Immune Responses and Control Strategies

Rotaviruses (RVs) are a major cause of acute viral gastroenteritis in young animals and children worldwide. Immunocompetent adults of different species become resistant to clinical disease due to post-infection immunity, immune system maturation and gut physiological changes. Of the 9 RV genogroups (A–I), RV A, B, and C (RVA, RVB, and RVC, respectively) are associated with diarrhea in piglets. Although discovered decades ago, porcine genogroup E RVs (RVE) are uncommon and their pathogenesis is not studied well. The presence of porcine RV H (RVH), a newly defined distinct genogroup, was recently confirmed in diarrheic pigs in Japan, Brazil, and the US. The complex epidemiology, pathogenicity and high genetic diversity of porcine RVAs are widely recognized and well-studied. More recent data show a significant genetic diversity based on the VP7 gene analysis of RVB and C strains in pigs. In this review, we will summarize previous and recent research to provide insights on historic and current prevalence and genetic diversity of porcine RVs in different geographic regions and production systems. We will also provide a brief overview of immune responses to porcine RVs, available control strategies and zoonotic potential of different RV genotypes. An improved understanding of the above parameters may lead to the development of more optimal strategies to manage RV diarrheal disease in swine and humans.

Avian rotavirus enteritis - an updated review

Rotaviruses (RVs) are among the leading causes of enteritis and diarrhea in a number of mammalian and avian species, and impose colossal loss to livestock and poultry industry globally. Subsequent to detection of rotavirus in mammalian hosts in 1973, avian rotavirus (AvRV) was first reported in turkey poults in USA during 1977 and since then RVs of group A (RVA), D (RVD), F (RVF) and G (RVG) have been identified around the globe. Besides RVA, other AvRV groups (RVD, RVF and RVG) may also contribute to disease. However, their significance has yet to be unraveled. Under field conditions, co-infection of AvRVs occurs with other infectious agents such as astroviruses, enteroviruses, reoviruses, paramyxovirus, adenovirus, Salmonella, Escherichia coli, cryptosporidium and Eimeria species prospering severity of disease outcome. Birds surviving to RV disease predominantly succumb to secondary bacterial infections, mostly E. coli and Salmonella spp. Recent developments in molecular tools including state-of-the-art diagnostics and vaccine development have led to advances in our understanding towards AvRVs. Development of new generation vaccines using immunogenic antigens of AvRV has to be explored and given due importance. Till now, no effective vaccines are available. Although specific as well as sensitive approaches are available to identify and characterize AvRVs, there is still need to have point-of-care detection assays to review disease burden, contemplate new directions for adopting vaccination and follow improvements in public health measures. This review discusses AvRVs, their epidemiology, pathology and pathogenesis, immunity, recent trends in diagnostics, vaccines, therapeutics as well as appropriate prevention and control strategies.

Complete genome analysis of a rare group A rotavirus, G11P[25], isolated from a child in Mumbai, India, reveals interspecies transmission and reassortment with human rotavirus strains

Hospital-based rotavirus surveillance was carried out in Mumbai during 2005-2009. An isolate (B08299) with a rare genotype combination (G11P[25]) was detected. The present study was undertaken to characterize the complete genome of the isolate. B08299 exhibited a G11-P[25]-I12-R1-C1-M1-A1-N1-T1-E1-H1 genotype constellation. Phylogenetic analysis of the 11 gene segments of B08299 revealed that the VP2 and NSP5 genes of B08299 had a human origin, while the VP6 gene represented an I12 genotype of obscure origin. The remaining six genes formed a lineage distinct from human and porcine rotaviruses within genotype 1. Analysis of the structural and non-structural genes suggested that B08299 has evolved by gene reassortment. Our findings provide further evidence that interspecies transmission is an important mechanism involved in the evolution and genetic diversity of human rotaviruses in nature.

Detection and genetic diversity of porcine group A rotaviruses in historic (2004) and recent (2011 and 2012) swine fecal samples in Ohio: predominance of the G9P[13] genotype in nursing piglets

Epidemiological surveillance of porcine group A rotavirus (RVA) strains was conducted in five swine herds in Ohio using historical (2004) and recent (2011 to 2012) fecal samples. Of the 371 samples examined, 9.4% (35/371) were positive for RVA. The RVA detection rates increased from 5.9% in 2004 and 8.5% in 2011 to 13.8% in 2012. A total of 23 positive samples were analyzed for RVA G and P genotypes. The dominant G-P combination was G9P[13] found in 60.9% of positive samples. The other combinations were G9P[7] (8.7%), G4P[13] (8.7%), G11P[13] (4.3%), and G11P[7] (4.3%). Sequence analysis of partial VP7 genes of selected strains revealed that the G4 strains were closely related to one another (95%) and, to a lesser extent, to human (82 to 84%) and porcine (84 to 86%) G4 strains. The G11 strains detected shared identical VP7 gene sequences (100%) and were closely related to human (85 to 86%) and other porcine (83%) G11 strains. The G9 strains identified were closely related to one another and to human and other porcine strains (96 to 97%, 89 to 91%, and 89 to 91% nucleotide identities, respectively). The VP4 gene analysis revealed that P[7] strains were closely related to each other and to P[7] strains isolated from porcine, bovine, and panda samples (91 to 99%, 92 to 99% and 92 to 99%, respectively). The P[13] strains showed a higher diversity among themselves and with other porcine P[13] strains, ranging from 83% to 99% and from 82 to 97%, respectively. Our results demonstrate broad genetic heterogeneity of the RVA strains and suggest the possibility of genetic reassortment between different RVA genotypes within these farms.

Picobirnavirus detection in bovine and buffalo calves from foothills of Himalaya and Central India

The present study describes detection of picobirnavirus (PBV) in faecal samples from bovine and buffalo calves employing the polyacrylamide gel electrophoresis (PAGE). A total of 136 faecal samples from buffalo (n = 122) and cow calves (n = 14) exhibiting clinical signs of diarrhoea and from healthy calves were collected during 2007–2010 from subtropical (central India) and tarai area of western temperate Himalayan foothills (Uttarakhand). The dsRNA nature of the virus was confirmed by nuclease treatment (RNase A, RNaseT1 and DNase 1). PAGE results confirmed 3.67% (5/136) positivity for PBV, showing a typical genomic migration pattern with two discrete bands with size of approximately 2.4 and 1.7 kbps for the larger and smaller segments, respectively. Among the five PBV samples identified, three were from buffalo calves and one from cow calf exhibiting clinical signs of acute diarrhoea, while one sample from non-diarrhoeic buffalo calf also showed the presence of PBV. None of the samples showed dual infection of rotavirus and PBV. The preliminary findings indicate sporadic incidences of PBV in bovine calves and emphasize the need for the development of better diagnostics for early detection and genetic characterization of these emerging isolates of farm animals of economic significance.