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Hakim MS, Gazali FM, Widyaningsih SA, Parvez MK. Driving forces of continuing evolution of rotaviruses. World J Virol 2024; 13:93774. [DOI: 10.5501/wjv.v13.i2.93774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 06/24/2024] Open
Abstract
Rotaviruses are non-enveloped double-stranded RNA virus that causes acute diarrheal diseases in children (< 5 years). More than 90% of the global rotavirus infection in humans was caused by Rotavirus group A. Rotavirus infection has caused more than 200000 deaths annually and predominantly occurs in the low-income countries. Rotavirus evolution is indicated by the strain dynamics or the emergence of the unprecedented strain. The major factors that drive the rotavirus evolution include the genetic shift that is caused by the reassortment mechanism, either in the intra- or the inter-genogroup. However, other factors are also known to have an impact on rotavirus evolution. This review discusses the structure and types, epidemiology, and evolution of rotaviruses. This article also reviews other supplemental factors of rotavirus evolution, such as genetic reassortment, mutation rate, glycan specificity, vaccine introduction, the host immune responses, and antiviral drugs.
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Affiliation(s)
- Mohamad Saifudin Hakim
- Postgraduate School of Molecular Medicine, Erasmus MC-University Medical Center, Rotterdam 3015GD, Netherlands
- Viral Infection Working Group, International Society of Antimicrobial Chemotherapy, London EC4R 9AN, United Kingdom
| | - Faris Muhammad Gazali
- Master Program in Biotechnology, Postgraduate School, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Suci Ardini Widyaningsih
- Master of Medical Sciences in Clinical Investigation, Harvard Medical School, Boston, MA 02115, United States
| | - Mohammad Khalid Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
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A shift in circulating rotaviral genotypes among hospitalized neonates. Sci Rep 2022; 12:2842. [PMID: 35181717 PMCID: PMC8857175 DOI: 10.1038/s41598-022-06506-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/27/2022] [Indexed: 11/19/2022] Open
Abstract
In neonates, rotavirus (RV) infection is generally nosocomial. The control of rotaviral infection within hospital settings is challenging due to prolonged shedding of the virus and contamination of the surrounding environment. There are few studies that have reported asymptomatic infection within neonates. In this study, neonates were screened for RV infection and possible clinical manifestations that may play a role in RV acquisition were analysed. Stool samples were collected from 523 hospitalized neonates admitted for > 48 h in a low-cost and higher-cost tertiary centre. RV antigen was screened using ELISA and the samples which tested positive were confirmed by semi-nested RT-PCR. RV was detected in 34% of participants and genotypes identified included G12P[11] (44.4%), G10 P[11] (42.6%), G10G12P[11] (10.1%) and G3P[8] (2.9%). ICU admissions were associated with higher viral shedding (p < 0.05). Hospitalization in the low-cost facility ICU was associated with higher RV acquisition risk (p < 0.05). RV was detected in higher rates (36.9%) among neonates with gastrointestinal manifestations. G10P[11] was the predominant genotype for several years (1988–2016) among neonates within India. The preponderance of an emerging G12P[11] genotype and heterotypic distribution was documented. RV surveillance is important to identify emerging strains and establish the road ahead in managing RV infection.
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Ranshing S, Ganorkar N, Ramji S, Gopalkrishna V. Complete genomic analysis of uncommon G12P[11] rotavirus causing a nosocomial outbreak of acute diarrhea in the newborns in New Delhi, India. J Med Virol 2021; 94:2613-2623. [PMID: 34811775 DOI: 10.1002/jmv.27468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/19/2021] [Indexed: 11/06/2022]
Abstract
Rotaviruses (RVs) are the major causative agents of acute gastroenteritis in children, but in neonates, RV infections are generally nosocomial in origin and mostly asymptomatic. However, there have been infrequent reports of nosocomial outbreaks of clinical disease in this population. In this study, we describe uncommon RV genotype; G12P[11] associated with an outbreak of acute gastroenteritis in the neonatal ward and neonatal intensive care unit (NICU) in New Delhi, North India. Full-genome analyses of the pathogenic G12P[11] strain was carried out to map the genotype constellation and further to explore the variations in the antigenic epitopes on the immunodominant VP7 and VP4 proteins, the amino acid sequences were compared with neonatal strains; ROTAVAC® (G9P[11]) and asymptomatic G12P[11] and also other G/P-type matched strains. The study revealed G12-P[11]-I1-R1-C1-M1-A1-N1-T1-E1-H1 human Wa-like genotype constellation and highlights evidence of gene reassortment. No significant differences were observed in the sequences of structural (except VP3) and nonstructural encoding genes of G12P[11] strains recovered from symptomatic and asymptomatic neonates. Presence of additional N-linked glycosylation site was noted in the G12 strains, as a consequence of a change from Asp→Asn at amino acid position 238. Interestingly, only two and four amino acids substitution within the 7-1a and 8-1 antigenic epitope were observed, respectively, compared with asymptomatic G12P[11] strain. The study emphasizes the importance of close monitoring of RV outbreaks in neonates for early alarming of novel strain.
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Affiliation(s)
- Sujata Ranshing
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Nital Ganorkar
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Siddarth Ramji
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
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Babji S, Sindhu KN, Selvarajan S, Ramani S, Venugopal S, Khakha SA, Hemavathy P, Ganesan SK, Giri S, Reju S, Gopalakrishnan K, Ninan B, Iturriza-Gomara M, Srikanth P, Kang G. Persistence of G10P[11] neonatal rotavirus infections in southern India. J Clin Virol 2021; 144:104989. [PMID: 34607240 PMCID: PMC8556361 DOI: 10.1016/j.jcv.2021.104989] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/06/2021] [Accepted: 09/23/2021] [Indexed: 12/16/2022]
Abstract
Background: Neonatal rotavirus infections are predominantly caused by distinct genotypes restricted to this age-group and are mostly asymptomatic. Method: Stool samples from neonates admitted for >48 h in neonatal intensive care units (NICUs) in Vellore (2014–2015) and Chennai (2015–2016) in southern India, and from neonates born at hospitals in Vellore but not admitted to NICUs (2015–2016) were tested for rotavirus by ELISA and genotyped by hemi-nested RT-PCR. Results: Of 791 neonates, 150 and 336 were recruited from Vellore and Chennai NICUs, and 305 were born in five hospitals in Vellore. Positivity rates in the three settings were 49.3% (74/150), 29.5% (99/336) and 54% (164/305), respectively. G10P[11] was the commonly identified genotype in 87.8% (65/74), 94.9% (94/99) and 98.2% (161/164) of the neonates in Vellore and Chennai NICUs, and those born at Vellore hospitals, respectively. Neonates delivered by lower segment cesarian section (LSCS) at Vellore hospitals, not admitted to NICUs, had a significantly higher odds of acquiring rotavirus infection compared to those delivered vaginally [p = 0.002, OR = 2.4 (1.4–4.3)]. Conclusions: This report demonstrates the persistence of G10P[11] strain in Vellore and Chennai, indicating widespread neonatal G10P[11] strain in southern India and their persistence over two decades, leading to interesting questions about strain stability.
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Affiliation(s)
- Sudhir Babji
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | - Sribal Selvarajan
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Chennai, India
| | - Sasirekha Ramani
- Baylor College of Medicine, Houston, TX, United States of America
| | - Srinivasan Venugopal
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Shainey Alokit Khakha
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Priya Hemavathy
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Santhosh Kumar Ganesan
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Sidhartha Giri
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Sudhabharathi Reju
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Chennai, India
| | - Krithika Gopalakrishnan
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Chennai, India
| | - Binu Ninan
- Department of Neonatology, Sri Ramachandra Medical College and Research Institute, Chennai, India
| | - Miren Iturriza-Gomara
- NIHR Health Protection Research Unit in Gastrointestinal Infections at University of Liverpool, Liverpool, United Kingdom of Great Britain
| | - Padma Srikanth
- Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Chennai, India
| | - Gagandeep Kang
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India.
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Genetic characterisation of novel G29P[14] and G10P[11] rotavirus strains from African buffalo. INFECTION GENETICS AND EVOLUTION 2020; 85:104463. [PMID: 32693063 DOI: 10.1016/j.meegid.2020.104463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 11/22/2022]
Abstract
We report the first description of rotavirus A strains in African buffalo (Syncerus caffer). Following RNA extraction from stool samples, cDNA was prepared, followed either by sequence-independent amplification and 454 pyrosequencing or direct sequencing on an Illumina MiSeq platform. RVA/Buffalo-wt/ZAF/4426/2002/G29P[14] exhibited a novel G29P[14] combination and an artiodactyl backbone: I2-R2-C2-M2-A11-N2-T6-E2-H3. RVA/Buffalo-wt/ZAF/1442/2007/G10P[11] also exhibited an artiodactyl backbone: I2-R2-C2-M2-A13-N2-T6-E2-H3. Characterisation of these genome constellations indicate that the two buffalo strains are moderately diverse from each other and related to South African bovine RVA strains. The detection of RVA in buffalo contribute to our understanding of the host range of rotavirus in animals.
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Ranshing SS, Cherian SS, Agarwal MS, Jagtap AS, Patil CM, Gopalkrishna V. Full genome based sequence and structural characterization of an unusual group A rotavirus G12P[11] isolated from neonates in Pune, western India. Vaccine 2020; 38:2275-2291. [DOI: 10.1016/j.vaccine.2020.01.081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 11/27/2022]
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Timurkan MÖ, Alkan F. Identification of rotavirus A strains in small ruminants: first detection of G8P[1] genotypes in sheep in Turkey. Arch Virol 2019; 165:425-431. [PMID: 31828508 DOI: 10.1007/s00705-019-04476-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022]
Abstract
Although members of rotavirus group A (RVA) are major enteric pathogens of humans and animals of many species, their impact on the health of small ruminants is not well documented. In this study, we conducted a molecular analysis of VP4, VP7, VP6 and NSP4 genes of RVAs detected using a commercial antigen ELISA in small ruminants with or without diarrhea in Turkey. Of the RVAs detected in sheep, one strain (Kutahya) was characterized as genotype G8P[1]-I2-E2. Two others (Ankara-1 and Ankara-2) were identified as NSP4 E2 and VP6 I2 genotypes, although they were untyped for the VP4 and VP7 genes. The RVAs from two goats were characterized as genotype G6P [1]-I2-E2. This is the first detection of in goats RVA genotypes G6P [1], which had previously only been found in cattle in Turkey, and of RVA in sheep. The study extends our current knowledge about the circulation of two RVA G genotypes, G6 and G8, in goat herds, and the detection of the G8 genotype in sheep in Turkey. This provides further information about the molecular epidemiology of RVAs in different animal species and indicates that additional surveillance programs are needed to determine the epidemiology of RVA in small ruminants and other species.
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Affiliation(s)
- Mehmet Özkan Timurkan
- Department of Virology, Faculty of Veterinary Medicine, Atatürk University, Erzurum, Turkey.
| | - Feray Alkan
- Department of Virology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
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