Genotypic diversity of human and porcine group A rotaviruses in Uttar Pradesh, India

Abstract

Diarrheal diseases, particularly those caused by rotaviruses, pose a significant health threat, especially among children, and cause huge economic losses to the pig industry in the form of high morbidity, mortality, and stunted growth. Rotavirus A (RVA) remains the predominant viral agent for severe diarrheal episodes, contributing to high hospitalization and mortality rates in India. RVA’s high genetic diversity is attributed to frequent reassortment and mutations. This study aims to characterize the VP4, VP6, VP7, and NSP4 genes of RVA in stool samples collected from children and piglets in and around Bareilly, Uttar Pradesh, India. A total of 300 samples, including 100 from children and 200 from piglets, were screened for the detection of double-stranded RNA of RVA using ribonucleic acid-polyacrylamide gel electrophoresis (RNA-PAGE) and reverse transcription polymerase chain reaction (RT-PCR). Results revealed the RVA incidence, particularly in winter (end of November to beginning of February), aligning with observed seasonal trends. Among the 32 Rotavirus (RV)-positive samples from children, 21 (65.63%) were detected by RNA-PAGE, whereas 28 (87.5%) were identified by RT-PCR. Whereas, of the 80 RT-PCR positive samples from piglets, only 51 (63.75%) were detected by RNA-PAGE, indicating the superiority of RT-PCR. Molecular analysis identified the prevalent genotypes in human strains as G1, G2, G3, and P[8], whereas G9P[13]-I5-E1 dominated among piglets in a single farm outbreak. The findings underscore the critical need for continuous surveillance to monitor evolving RV genotypes from both humans and piglets, enabling the identification of new strains of RVA and subsequent modification of vaccination strategies to reduce RVA’s impact in India.

Keywords

Diarrheal diseases / Epidemiology / Genotypic diversity / India / RNA-PAGE / Rotavirus A / Reverse transcription polymerase chain reaction

Funding

The work was supported by grants (Project ID 10058006, File No. SERB/F/459/2016-17 dated 18.05.2016) from the Science and Engineering Research Board, DST, India, to Z.B.D.

Conflict of interest

The authors declare that they have no competing or conflict of interests.

References

[1] World Health Organization. World Health Statistics 2017: Monitoring Health for the SDGs, Sustainable Development Goals. Geneva: World Health Organization; 2017.

[2] Tate RL, Perdices M, Rosenkoetter U, et al. The single-case reporting guideline in behavioural interventions (SCRIBE) 2016 statement. Phys Ther. 2016; 96(7):e1-e10. doi: 10.2522/ptj.2016.96.7.e1

[3] Matthijnssens J, Ciarlet M, Rahman M, et al. Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments. Arch Virol. 2008; 153(8):1621-1629. doi: 10.1007/s00705-008-0155-1

[4] Matthijnssens J, Ciarlet M, McDonald SM, et al. Uniformity of Rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch Virol. 2011; 156(8):1397-1413. doi: 10.1007/s00705-011-1006-z

[5] Matthijnssens J, Ciarlet M, Heiman E, et al. Full genome-based classification of rotaviruses reveals a common origin between human Wa-Like and porcine Rotavirus strains and human DS-1-like and bovine Rotavirus strains. J Virol. 2008; 82(7):3204-3219. doi: 10.1128/JVI.02257-07

[6] Okitsu S, Khamrin P, Thongprachum A, et al. Whole-genomic analysis of G3P[23], G9P[23] and G3P[13] Rotavirus strains isolated from piglets with diarrhea in Thailand, 2006-2008. Infect Genet Evol. 2013; 18:74-86. doi: 10.1016/j.meegid.2013.05.005

[7] Khakha SA, Varghese T, Giri S, et al. Whole-genome characterization of common Rotavirus strains circulating in Vellore, India from 2002 to 2017: Emergence of non-classical genomic constellations. Gut Pathog. 2023; 15(1):44. doi: 10.1186/s13099-023-00569-6

[8] Gleason A, Kumar CK, Klein E, Laxminarayan R, Nandi A. Effect of Rotavirus vaccination on the burden of Rotavirus disease and associated antibiotic use in India: A dynamic agent-based simulation analysis. Vaccine. 2024; 42(22):126211. doi: 10.1016/j.vaccine.2024.126211

[9] Abass G, Dubal ZB, Rajak KK, et al. Molecular characterization of porcine Rotavirus A from India revealing zooanthroponotic transmission. Anim Biotechnol. 2020;33:1073-1085. doi: 10.1080/10495398.2020.1868486

[10] Herring AJ, Inglis NF, Ojeh CK, Snodgrass DR, Menzies JD. Rapid diagnosis of Rotavirus infection by direct detection of viral nucleic acid in silver-stained polyacrylamide gels. J Clin Microbiol. 1982; 16(3):473-477. doi: 10.1128/jcm.16.3.473-477.1982

[11] Svensson L, Uhnoo I, Grandien M, Wadell G. Molecular epidemiology of Rotavirus infections in Uppsala, Sweden, 1981: Disappearance of a predominant electropherotype. J Med Virol. 1986; 18(2):101-111. doi: 10.1002/jmv.1890180202

[12] Djikeng A, Halpin R, Kuzmickas R, et al. Viral genome sequencing by random priming methods. BMC Genomics. 2008;9:5. doi: 10.1186/1471-2164-9-5

[13] Maes P, Matthijnssens J, Rahman M,Van Ranst M. RotaC: A web-based tool for the complete genome classification of group A rotaviruses. BMC Microbiol. 2009;9:238. doi: 10.1186/1471-2180-9-238

[14] Chitambar SD, Arora R, Chhabra P. Molecular characterization of a rare G1P[19] Rotavirus strain from India: Evidence of reassortment between human and porcine Rotavirus strains. J Med Microbiol. 2009; 58(Pt 12):1611-1615. doi: 10.1099/jmm.0.012856-0

[15] Ghosh S, Kobayashi N. Whole-genomic analysis of Rotavirus strains: Current status and future prospects. Future Microbiol. 2011; 6(9):1049-1065.doi: 10.2217/fmb.11.90

[16] Jain V, Das BK, Bhan MK, Glass RI, Gentsch JR, Indian Strain Surveillance Collaborating Laboratories. Great diversity of group A Rotavirus strains and high prevalence of mixed Rotavirus infections in India. J Clin Microbiol. 2001; 39(10):3524-3529. doi: 10.1128/JCM.39.10.3524-3529.2001

[17] Broor S, Husain M, Chatterjee B, Chakraborty A, Seth P. Temporal variation in the distribution of Rotavirus electropherotypes in Delhi, India. J Diarrhoeal Dis Res. 1993; 11(1):14-18.

[18] Kelkar SD, Ayachit VL. Circulation of group A Rotavirus subgroups and serotypes in Pune,India, 1990-1997. J Health Popul Nutr. 2000; 18(3):163-170.

[19] Pol SS, Dedwal AK, Ranshing SS, Chitambar SD, Pednekar SN, Bharadwaj RS. Prevalence and characterization of rotaviruses in children hospitalized for diarrheal disease in a tertiary care hospital, Pune. Indian J Med Microbiol. 2017; 35(1):33-36. doi: 10.4103/ijmm.IJMM_16_94

[20] Giri S, Nair NP, Mathew A, et al. Rotavirus gastroenteritis in Indian children < 5 years hospitalized for diarrhoea, 2012 to 2016. BMC Public Health. 2019; 19(1):69. doi: 10.1186/s12889-019-6406-0

[21] Dhalaria P, Kapur S, Singh AK, Verma A, Priyadarshini P, Taneja G.Potential impact of Rotavirus vaccination on reduction of childhood diarrheal disease in India: An analysis of National Family Health Survey-5. Vaccine X. 2023;14:100319. doi: 10.1016/j.jvacx.2023.100319

[22] Haque W, Haque J, Barai D, et al. Distribution of Rotavirus genotypes in Dhaka, Bangladesh, 2012-2016: Re-emergence of G3P[8] after over a decade of interval. Vaccine. 2018; 36(43):6393-6400. doi: 10.1016/j.vaccine.2018.08.081

[23] Shrestha S, Thakali O, Raya S, Shrestha L, Parajuli K, Sherchand JB. Acute gastroenteritis associated with Rotavirus A among children less than 5 years of age in Nepal. BMC Infect Dis. 2019; 19(1):456. doi: 10.1186/s12879-019-4092-2

[24] Sadiq A, Bostan N, Bokhari H, et al. Molecular characterization of human group A Rotavirus genotypes circulating in Rawalpindi, Islamabad, Pakistan during 2015-2016. PLoS One. 2019; 14(7):e0220387. doi: 10.1371/journal.pone.0220387

[25] Troeger, CE Khalil IA, Blacker BF, et al. Quantifying risks and interventions that have affected the burden of diarrhoea among children younger than 5 years: An analysis of the Global Burden of Disease Study 2017. Lancet Infect Dis. 2019; 20(1):37-59. doi: 10.1016/S1473-3099(19)30401-3

[26] VinodhKumar OR, Sircar S, Pruthvishree BS, et al. Cross-sectional study on Rotavirus A (RVA) infection and assessment of risk factors in pre- and post-weaning piglets in India. Trop Anim Health Prod. 2020; 52(1):445-452. doi: 10.1007/s11250-019-01999-8

[27] Li Q, Wang Z, Jiang J, et al. Outbreak of piglet diarrhea associated with a new reassortant porcine Rotavirus B. Vet Microbiol. 2024;288:109947. doi: 10.1016/j.vetmic.2023.109947

[28] Kusumakar AL, Savita, Malik YS, Minakshi, Prasad G. Genomic diversity among group A rotaviruses from diarrheic children, piglets, buffalo and cow calves of Madhya Pradesh. Indian J Microbiol. 2010; 50(1):83-88. doi: 10.1007/s12088-010-0016-y

[29] Dubal ZB, Bhilegaonkar KN, Barbuddhe SB, et al. Prevalence and genotypic (G and P) determination of porcine group A rotaviruses from different regions of India. Trop Anim Health Prod. 2013; 45(2):609-615. doi: 10.1007/s11250-012-0267-1

[30] Kylla H, Dutta TK, Roychoudhury P, Mandakini R, Subudhi PK. Detection and characterization of Genogroup 5 Rotavirus associated with piglet diarrhoea in the North East Region of India. Vet Arhiv. 2018; 88(4):453-466. doi: 10.24099/vet.arhiv.170613a

[31] Das S, Varghese V, Chaudhuri S, et al. Genetic variability of human Rotavirus strains isolated from Eastern and Northern India. J Med Virol. 2004; 72(1):156-161. doi: 10.1002/jmv.10542

[32] Pradhan GN, Chitambar SD. Genetic analysis of Rotavirus G2P[4] strains in Pune, Western India: Circulation of a novel reassortant bearing E6 NSP4 genotype Arch Virol. 2018; 163(5):1391-1394. doi: 10.1007/s00705-018-3710-4

[33] Kang CI, Kim SH, Park WB, et al. Bloodstream infections caused by antibiotic-resistant gram-negative bacilli: Risk factors for mortality and impact of inappropriate initial antimicrobial therapy on outcome. Antimicrob Agents Chemother. 2005; 49(2):760-766. doi: 10.1128/AAC.49.2.760-766.2005

[34] George J, Lim JS, Jang SJ, et al. Comprehensive genomic profiles of small cell lung cancer. Nature. 2015; 524(7563):47-53. doi: 10.1038/nature14664

[35] Kumar A, Basu S, Vashishtha V, Choudhury P. Burden of Rotavirus diarrhea in under five Indian children. Indian Pediatr. 2016; 53(7):607-617. doi: 10.1007/s13312-016-0896-y

[36] Saluja S, Silverstein A, Mukhopadhyay S, et al. Using the consolidated framework for implementation research to implement and evaluate national surgical planning. BMJ Glob Health. 2017;2:e000269. doi: 10.1136/bmjgh-2016-000269

[37] Shrivastava AK, Reddy NS, Giri S, et al. Burden and molecular epidemiology of Rotavirus causing diarrhea among under-five children: A hospital-based study from Eastern India. J Glob Infect Dis. 2019; 11(4):147-152. doi: 10.4103/jgid.jgid_16_19

[38] Tate R, Kennedy M, Ponsford J, et al. INCOG recommendations for management of cognition following traumatic brain injury, part III: Executive function and self-awareness. J Head Trauma Rehabil. 2014; 29(4):338-352. doi: 10.1097/HTR.0000000000000068

[39] Shao L, Takeda K, Kato S, Mori S, Kodama T. Communication between lymphatic and venous systems in mice. J Immunol Methods. 2015; 424:100-105. doi: 10.1016/j.jim.2015.05.007

[40] Li Y, Wang F, Kan R, et al. Genetic and immunological characterization of G9 group A porcine rotaviruses in China. Zoonoses Public Health. 2022; 69(6):694-703. doi: 10.1111/zph.12958

[41] Gentsch JR, Glass RI, Woods P, et al. Identification of group A Rotavirus gene 4 types by polymerase chain reaction. J Clin Microbiol. 1992; 30(6):1365-1373. doi: 10.1128/jcm.30.6.1365-1373.1992

[42] Wang YH, Zhou X, Ghosh S, et al. Prevalence of human Rotavirus genotypes in Wuhan, China, during 2008-2011: Changing trend of predominant genotypes and emergence of strains with the P[8]b subtype of the VP4 gene Arch Virol. 2011; 156(12):2221-2231. doi: 10.1007/s00705-011-1122-9

[43] Das BK, Gentsch JR, Cicirello HG, et al. Characterization of Rotavirus strains from newborns in New Delhi, India. J Clin Microbiol. 1994; 32(7):1820-1822. doi: 10.1128/jcm.32.7.1820-1822.1994

[44] Abe M, Ito N, Morikawa S, et al. Molecular epidemiology of rotaviruses among healthy calves in Japan: Isolation of a novel bovine Rotavirus bearing new P and G genotypes. Virus Res. 2009; 144(1-2):250-257. doi: 10.1016/j.virusres.2009.05.005

[45] Taniguchi K, Wakasugi F, Pongsuwanna Y, et al. Identification of human and bovine Rotavirus serotypes by polymerase chain reaction. Epidemiol Infect. 1992; 109(2):303-312. doi: 10.1017/s0950268800050263

[46] Ghosh S, Alam MM, Ahmed MU, Talukdar RI, Paul SK, Kobayashi N. Complete genome constellation of a caprine group A Rotavirus strain reveals common evolution with ruminant and human Rotavirus strains. J Gen Virol. 2010; 91(Pt 9):2367-2373. doi: 10.1099/vir.0.022244-0