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Sadiq A, Khan J, Basit A, Sardar N, Ajmal MN. Rotavirus genotype dynamics in Pakistan: G9 and G12 emerging as dominant strains in vaccinated children (2019). Acta Trop 2024; 257:107300. [PMID: 38909724 DOI: 10.1016/j.actatropica.2024.107300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/02/2024] [Accepted: 06/21/2024] [Indexed: 06/25/2024]
Abstract
Rotavirus A (RVA) is a leading cause of severe gastroenteritis in children worldwide, and vaccination has become a pivotal strategy to reduce the associated morbidity and mortality. This study presents a molecular characterization of RVA genotypes circulating among vaccinated children in Pakistan during the year 2019. A total of 510 stool samples were collected from children of up to five years of age presenting with acute gastroenteritis symptoms in Rawalpindi, Islamabad regions of Pakistan. The RVA antigen was detected using ELISA on these samples. RVA G/P genotyping was performed on ELISA positive samples using Multiplex semi-nested reverse transcriptase PCR. RVA was found in 130 fecal samples, with an overall prevalence of 25.4 %. G9P[8] (20 %) is the most prevalent genotype, followed by G12P[6] (17 %), G3P[8] (14 %), G1P[8] (12 %), G2P[4] (10 %), G12P[8] (7 %), G9P[6] (7 %), G3P[6] (6 %), G3P[4] (4 %) and G1P[6] (3 %) respectively. There is a statistically significant difference (p < 0.05) found in the group age (in months) of RVA gastroenteritis cases as detected by RT-PCR. The highest number of positive cases was found in the age range from 0 to 6 months, followed by 7-12 months, 13-24 months, and 25-60 months, respectively. Dehydration is statistically significantly associated (p˂ 0.05) in RVA gastroenteritis cases compared to those who tested negative. This study emphasizes the significance of maintaining a continuous surveillance system and conducting genomic analysis of RVA genotypes in children upto the age of 5 years. This is essential for tracking the circulation of RVA genotypes. The results from this research enhance our comprehension of how RVA genotypes are changing over time in Pakistan, underscoring the ongoing necessity for improving vaccine coverage and effectiveness. This, in turn, can help reduce the impact of RVA-related illnesses in children.
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Affiliation(s)
- Asma Sadiq
- Department of Microbiology, University of Jhang, Jhang, Pakistan.
| | - Jadoon Khan
- Department of Microbiology, Quaid-i-Azam Unievrsity, Islamabad, Pakistan; Madina Institute of Science and Technology (Affiliated), Khyber Medical University, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Basit
- Department of Microbiology, University of Jhang, Jhang, Pakistan
| | - Nageen Sardar
- Department of Microbiology, University of Jhang, Jhang, Pakistan
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Wandera EA, Kurokawa N, Mutua MM, Muriithi B, Nyangao J, Khamadi SA, Kathiiko C, Wachira M, Njuguna E, Mwaura B, Golicha RO, Njau J, Morita K, Kaneko S, Komoto S, Tsutsui N, Ichinose Y. Long-term impact of rotavirus vaccination on all-cause and rotavirus-specific gastroenteritis and strain distribution in Central Kenya: An 11-year interrupted time-series analysis. Vaccine 2024; 42:126210. [PMID: 39151233 DOI: 10.1016/j.vaccine.2024.126210] [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: 03/27/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 08/19/2024]
Abstract
BACKGROUND Kenya introduced a monovalent rotavirus vaccine administered orally at 6 and 10 weeks of age into her National Immunization Program in July 2014. The study evaluated the long-term impact of the vaccine on hospitalization for all-cause and rotavirus-specific acute gastroenteritis (AGE) and strain epidemiology in Kenya. METHODS Data on all-cause and rotavirus-specific AGE and strain distribution were derived from an eleven-year hospital-based surveillance of AGE among children aged <5 years at Kiambu County Teaching and Referral Hospital (KCTRH) in Central Kenya between 2009 and 2020. Fecal samples were screened for group A rotavirus using ELISA and genotyped using multiplex semi-nested RT-PCR. Trends in all-cause and rotavirus-related AGE and strain distribution were compared between the pre-vaccine (July 2009-June 2014), early post-vaccine (July 2014-June 2016) and late post-vaccine (February 2019-October 2020) periods. RESULTS Rotavirus-specific AGE was detected at 27.5% (429/1546, 95% CI: 25.5-30.1%) in the pre-vaccine period; 13.8% (91/658, 95% CI: 11.3-16.6%) in the early post-vaccine period (July 2014-June 2016); and 12.0% (229/1916, 95% CI: 10.6-13.5%) in the late post-vaccine period (February 2019-October 2020). This amounted to a decline of 49.8% (95% CI: 34.6%-63.7%) in rotavirus-specific AGE in the early post-vaccine period and 53.4% (95% CI: 41.5-70.3%) in the late post-vaccine period when compared to the pre-vaccine period. All-cause AGE hospitalizations declined by 40.2% (95% CI: 30.8%-50.2%) and 75.3% (95% CI: 65.9-83.1%) in the early post-vaccine and late post-vaccine periods, respectively, when compared to the pre-vaccine period. G3P [8] was the predominant strain in the late post-vaccine period, replacing G1P[8] which had predominated in the pre-vaccine and early post-vaccine periods. Additionally, we detected considerable proportions of uncommon strains G3P[6] (4.8%) and G12P[6] (3.5%) in the post-vaccine era. CONCLUSION Rotavirus vaccination has resulted in a significant decline in all-cause and rotavirus-specific AGE, and thus, provides strong evidence for public health policy makers in Kenya to support the sustained use of the rotavirus vaccine in routine immunization. However, the shift in strain dominance and age distribution of rotavirus AGE in the post-vaccine era underscores the need for continued surveillance to assess any possible vaccine-induced selective pressure that could diminish the vaccine effectiveness over time.
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Affiliation(s)
- Ernest Apondi Wandera
- Centre for Virus Research, Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya,; Institute of Tropical Medicine, Nagasaki University, P.O. Box 19993-00202, Nairobi, Kenya,.
| | - Natsuki Kurokawa
- Department of Project Planning and Management, Mitsubishi Tanabe Pharma Corporation, 1-1-1, Marunouchi Chiyoda-ku, Tokyo 100-8205, Japan
| | - Maurine Mumo Mutua
- Institute of Tropical Medicine, Nagasaki University, P.O. Box 19993-00202, Nairobi, Kenya
| | - Betty Muriithi
- Institute of Tropical Medicine, Nagasaki University, P.O. Box 19993-00202, Nairobi, Kenya
| | - James Nyangao
- Centre for Virus Research, Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya
| | - Samoel Ashimosi Khamadi
- Centre for Virus Research, Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya
| | - Cyrus Kathiiko
- Institute of Tropical Medicine, Nagasaki University, P.O. Box 19993-00202, Nairobi, Kenya
| | - Mary Wachira
- Institute of Tropical Medicine, Nagasaki University, P.O. Box 19993-00202, Nairobi, Kenya
| | - Eunice Njuguna
- Institute of Tropical Medicine, Nagasaki University, P.O. Box 19993-00202, Nairobi, Kenya
| | - Boniface Mwaura
- Institute of Tropical Medicine, Nagasaki University, P.O. Box 19993-00202, Nairobi, Kenya
| | - Rahma Ordofa Golicha
- Centre for Microbiology Research, Kenya Medical Research Institute, P.O. Box 54840-00200 Nairobi, Kenya
| | - Joseph Njau
- Department of Pediatrics, Kiambu County Teaching and Referral Hospital, P.O. Box 39-00900 Kiambu, Kenya
| | - Kouichi Morita
- Institute of Tropical Medicine, Nagasaki University, P.O. Box 19993-00202, Nairobi, Kenya
| | - Satoshi Kaneko
- Institute of Tropical Medicine, Nagasaki University, P.O. Box 19993-00202, Nairobi, Kenya
| | - Satoshi Komoto
- Department of Virology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho,Toyoake, Aichi 470-1192, Japan,; Division of One Health, Research Center for Global and Local Infectious Diseases, 1-1 Idaigaoka, Hasama-machi, Oita University, Yufu 879-5593, Oita, Japan
| | - Naohisa Tsutsui
- Department of Project Planning and Management, Mitsubishi Tanabe Pharma Corporation, 1-1-1, Marunouchi Chiyoda-ku, Tokyo 100-8205, Japan
| | - Yoshio Ichinose
- Institute of Tropical Medicine, Nagasaki University, P.O. Box 19993-00202, Nairobi, Kenya
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Morozova OV, Sashina TA, Epifanova NV, Velikzhanina EI, Novikova NA. Phylodynamic characteristics of reassortant DS-1-like G3P[8]-strains of rotavirus type A isolated in Nizhny Novgorod (Russia). Braz J Microbiol 2023; 54:2867-2877. [PMID: 37897627 PMCID: PMC10689624 DOI: 10.1007/s42770-023-01155-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Since 2013, there has been an increase in reports of the spread of a double intergroup reassortant strain of rotavirus type A (RVA) with the genotype G3P[8] and other genes belonging to the second genogroup I2-R2-C2-M2-A2-N2-T2-E2-H2. In our study, we provide a molecular genetic characterization of rotaviruses with genotype G3P[8]-I2 isolated in Nizhny Novgorod. In our study, we used RT-PCR, Sanger sequencing, RNA-PAGE methods. Phylogenetic and phylodynamic analysis were performed using the Bayesian approach. According to our study, there was a significant increase in the proportion of G3P[8] from 15% during the period of 2020-2021 to 53% during the period of 2021-2022 in Nizhny Novgorod, Russia. Phylogenetic analysis based on the VP4 gene revealed that DS-1-like RVAs isolated in Nizhny Novgorod belong to different clusters of the P[8]-3.1 lineage, with a level of variation ranging from 1.1% to 1.3%. Based on the VP6 gene, the equine-like RVAs identified by us carry genetic variants belonging to three distinct clusters of the lineage I2-V, with a variation level ranging from 2.0% to 4.5%. These data indicate the genotypic diversity of circulating DS-1-like G3 RVAs. Phylogenetic analysis of the VP7 gene allowed us to assign the isolates identified in our study to the G3-1 lineage. We estimated that the circulation of the most recent common ancestor of the spreading strains dates back to 2002. Additionally, we determined the typical level of mutations in the VP7 gene, which amounted to 2.14*10-3 substitutions/per site/per year.
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Affiliation(s)
- Olga V Morozova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia.
| | - T A Sashina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N V Epifanova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - E I Velikzhanina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N A Novikova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
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Tran H, Friendship R, Poljak Z. Classification of group A rotavirus VP7 and VP4 genotypes using random forest. Front Genet 2023; 14:1029185. [PMID: 37323680 PMCID: PMC10267748 DOI: 10.3389/fgene.2023.1029185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction: Group A rotaviruses are major pathogens in causing severe diarrhea in young children and neonates of many different species of animals worldwide and group A rotavirus sequence data are becoming increasingly available over time. Different methods exist that allow for rotavirus genotyping, but machine learning methods have yet to be explored. Usage of machine learning algorithms such as random forest alongside alignment-based methodology may allow for both efficient and accurate classification of circulating rotavirus genotypes through the dual classification system. Methods: Random forest models were trained on positional features obtained from pairwise and multiple sequence alignment and cross-validated using methods of repeated 10-fold cross-validation thrice and leave one- out cross validation. Models were then validated on unseen data from the testing datasets to observe real-world performance. Results: All models were found to perform strongly in classification of VP7 and VP4 genotypes with high overall accuracy and kappa values during model training (0.975-0.992, 0.970-0.989) and during model testing (0.972-0.996, 0.969-0.996), respectively. Models trained on multiple sequence alignment generally had slightly higher overall accuracy and kappa values than models trained on pairwise sequence alignment method. In contrast, pairwise sequence alignment models were found to be generally faster than multiple sequence alignment models in computational speed when models do not need to be retrained. Models that used repeated 10-fold cross-validation thrice were also found to be much faster in model computational speed than models that used leave-one-out cross validation, with no noticeable difference in overall accuracy and kappa values between the cross-validation methods. Discussion: Overall, random forest models showed strong performance in the classification of both group A rotavirus VP7 and VP4 genotypes. Application of these models as classifiers will allow for rapid and accurate classification of the increasing amounts of rotavirus sequence data that are becoming available.
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Makori TO, Bargul JL, Lambisia AW, Mwanga MJ, Murunga N, de Laurent ZR, Lewa CS, Mutunga M, Kellam P, Cotten M, Nokes DJ, Phan M, Agoti CN. Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012-8. Virus Evol 2023; 9:vead025. [PMID: 37207000 PMCID: PMC10190042 DOI: 10.1093/ve/vead025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/07/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
The introduction of rotavirus vaccines into the national immunization programme in many countries has led to a decline in childhood diarrhoea disease burden. Coincidentally, the incidence of some rotavirus group A (RVA) genotypes has increased, which may result from non-vaccine-type replacement. Here, we investigate the evolutionary genomics of rotavirus G2P[4] which has shown an increase in countries that introduced the monovalent Rotarix® vaccine. We examined sixty-three RVA G2P[4] strains sampled from children (aged below 13 years) admitted to Kilifi County Hospital, coastal Kenya, pre- (2012 to June 2014) and post-(July 2014 to 2018) rotavirus vaccine introduction. All the sixty-three genome sequences showed a typical DS-1-like genome constellation (G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2). Pre-vaccine G2 sequences predominantly classified as sub-lineage IVa-3 and co-circulated with low numbers of sub-lineage IVa-1 strains, whereas post-vaccine G2 sequences mainly classified into sub-lineage IVa-3. In addition, in the pre-vaccine period, P[4] sub-lineage IVa strains co-circulated with low numbers of P[4] lineage II strains, but P[4] sub-lineage IVa strains predominated in the post-vaccine period. On the global phylogeny, the Kenyan pre- and post-vaccine G2P[4] strains clustered separately, suggesting that different virus populations circulated in the two periods. However, the strains from both periods exhibited conserved amino acid changes in the known antigenic epitopes, suggesting that replacement of the predominant G2P[4] cluster was unlikely a result of immune escape. Our findings demonstrate that the pre- and post-vaccine G2P[4] strains circulating in Kilifi, coastal Kenya, differed genetically but likely were antigenically similar. This information informs the discussion on the consequences of rotavirus vaccination on rotavirus diversity.
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Affiliation(s)
- Timothy O Makori
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Kalimoni, PO Box 62000-00200, Juja, Kenya
| | - Joel L Bargul
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Kalimoni, PO Box 62000-00200, Juja, Kenya
- International Centre of Insect Physiology and Ecology, Animal Health Theme, ICIPE Road Kasarani, P.O BOX 30772-00100, Nairobi, Kenya
| | - Arnold W Lambisia
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Mike J Mwanga
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Clement S Lewa
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Martin Mutunga
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
| | - Paul Kellam
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, Exhibition Road, London SW7 2AZ, UK
- Kymab Ltd, The Bennet Building (B930), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Matthew Cotten
- Medical Research Centre (MRC)/Uganda Virus Research Institute, Plot No: 51-59 Nakiwogo Road, P.O.Box 49, Entebbe, Uganda
- MRC-University of Glasgow, Centre for Virus Research Glasgow, 464 Bearsden Road, Glasgow G61 1QH UK
| | - D James Nokes
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute (SBIDER), The University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - My Phan
- Medical Research Centre (MRC)/Uganda Virus Research Institute, Plot No: 51-59 Nakiwogo Road, P.O.Box 49, Entebbe, Uganda
- MRC-University of Glasgow, Centre for Virus Research Glasgow, 464 Bearsden Road, Glasgow G61 1QH UK
| | - Charles N Agoti
- Epidemiology and Demography Department Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Off Hospital Road, P.O BOX 230-80108, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi-Malindi Road, P.O BOX 195-80108, Kilifi, Kenya
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Rennert W, Hindiyeh M, Allahham M, Mercer LD, Hamad KI, Ghuneim NI, A. M. Eljaro Z, Abu-Awwad F, Bozya Y, Hjaija D, Bhat N, Leader T, Ramlawi A, Marzouqa H. Introducing ROTAVAC® to the occupied Palestinian Territories: Impact on diarrhea incidence, rotavirus prevalence and genotype composition. Vaccine 2023; 41:945-954. [PMID: 36585280 PMCID: PMC9880560 DOI: 10.1016/j.vaccine.2022.12.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Rotavirus infection remains an important cause of morbidity and mortality in children. The introduction of vaccination programs in more than 100 countries has contributed to a decrease in hospitalizations and mortality. This study investigates the epidemiological impact of the rotavirus vaccine ROTAVAC® in the Palestinian Territories, the first country to switch from ROTARIX® to this new vaccine. METHODS Clinical surveillance data was collected fromchildren younger than 5attendingoutpatient clinics throughout Gaza withdiarrhea between 2015 and 2020. The incidence of all-cause diarrhea was assessed using an interrupted time-series approach. Rotavirus prevalence was determined at the Caritas Baby Hospital in the West Bank usingELISA on stool specimen of children younger than 5with diarrhea. Genotyping was performed on 325 randomly selected rotavirus-positive samples from January 2015 through December 2020 using multiplex PCR analysis. RESULTS Average monthly diarrhea casesdropped by 16.7% annually fromintroduction of rotavirus vaccination in May 2016 to the beginning of the SARS-CoV-2 epidemic in March 2020 for a total of 53%. Case count declines were maintained afterthe switchto ROTAVAC® in October 2018. Rotavirus positivity in stool samples declined by 67.1% over the same period without change followingthe switch to ROTAVAC®. The distribution of predominant genotypes in rotavirus-positive stool samples changed from a pre-vaccination G1P [8] to G9P[8] and G12P[8] during the ROTARIX® period and G2P[4] after the introduction of ROTAVAC®. CONCLUSION ROTAVAC® has shown epidemiological impact on par with ROTARIX® after its introduction to the national immunization schedule in the Palestinian Territories. A molecular genotype shift from a pre-vaccination predominance of G1P[8] to a current predominance of G2P[4] requires more long-term surveillance.
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Affiliation(s)
- Wolfgang Rennert
- Rostropovich Vishnevskaya Foundation, 1776 K Street, NW, Washington, D.C. 20006, USA,MedStar Georgetown University, 4200 Wisconsin Ave NW, Suite 200, Washington D.C2. 200162, USA,Corresponding author.
| | - Musa Hindiyeh
- Caritas Baby Hospital, Caritas Street, Bethlehem, West Bank, Palestine
| | - Majd Allahham
- Caritas Baby Hospital, Caritas Street, Bethlehem, West Bank, Palestine
| | - Laina D. Mercer
- PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA
| | - Khalil I. Hamad
- Health Department, UNRWA, Al-Azhar Road, Rimal Quarter, Gaza, Palestine
| | - Nedal I. Ghuneim
- Preventive Medicine Department, Ministry of Health, Tal-Sultan-190/82, Rafah, Gaza, Palestine
| | | | - Fakhr Abu-Awwad
- Rostropovich Vishnevskaya Foundation, 1776 K Street, NW, Washington, D.C. 20006, USA
| | - Yaser Bozya
- Public Health General Directorate, Ministry of Health, Ramallah, Palestine
| | - Diaa Hjaija
- Public Health General Directorate, Ministry of Health, Ramallah, Palestine
| | - Niranjan Bhat
- PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA
| | - Troy Leader
- PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA
| | - Asad Ramlawi
- Rostropovich Vishnevskaya Foundation, 1776 K Street, NW, Washington, D.C. 20006, USA
| | - Hiyam Marzouqa
- Caritas Baby Hospital, Caritas Street, Bethlehem, West Bank, Palestine
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Farahmand M, Latifi T, Kachooei A, Jalilvand S, Shoja Z. Circulating rotavirus P[8]-lineage IV, unlike P[8]-lineage III, significantly related to nonsecretors status in Iranian children. J Med Virol 2023; 95:e28160. [PMID: 36123611 DOI: 10.1002/jmv.28160] [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: 06/06/2022] [Revised: 08/20/2022] [Accepted: 09/14/2022] [Indexed: 01/11/2023]
Abstract
Rotavirus (RV) P[8] strains are responsible for the most of the RV infections globally and are significantly associated with the secretor and Lewis positive status. Among the distinct P[8] lineages, different ligand affinities have been detected which can be linked to differences in secretor status associated histo-blood group antigens (HBGAs). Herein, we report the lineages of P[8] strains and their associated secretor and Lewis antigen phenotypes in Iranian children. The phylogenetic tree and sequence analyses showed that the most common detected RV P[8] strain belonged to P[8]-lineage III (92%) and were significantly associated with secretor and Lewis positive status. In contrast, 8% of P[8] strains clustered into the P[8]-lineage IV and were significantly associated with nonsecretor status, implying that lineage IV tends to infect nonsecretor individuals. Furthermore, protein modeling and amino acid analyses of the VP8* glycan binding site of Iranian P[8]-lineage IV strains indicated two residual substitutions (T184V and N216V/I) compared to the P[8]-lineage III strains that might have affected the glycan affinity among P[8]-lineages IV strains. The corresponding residual changes might permit their continued transmission in nonsecretor children in competition with other P[8]-lineages. Although nonsecretors show natural resistant to P[8] strains, but such residual changes might overcome this natural resistance which in turn might indirectly contribute to the decline in the vaccine efficacy in populations where HBGA polymorphism allows their circulation at high frequency.
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Affiliation(s)
- Mohammad Farahmand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Tayebeh Latifi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Atefeh Kachooei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zabihollah Shoja
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran.,Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
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Agoti CN, Curran MD, Murunga N, Ngari M, Muthumbi E, Lambisia AW, Frost SDW, Blacklaws BA, Nokes DJ, Drumright LN. Differences in epidemiology of enteropathogens in children pre- and post-rotavirus vaccine introduction in Kilifi, coastal Kenya. Gut Pathog 2022; 14:32. [PMID: 35915480 PMCID: PMC9340678 DOI: 10.1186/s13099-022-00506-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/18/2022] [Indexed: 12/03/2022] Open
Abstract
Background Kenya introduced Rotarix® (GlaxoSmithKline Biologicals, Rixensart, Belgium) vaccination into its national immunization programme beginning July 2014. The impact of this vaccination program on the local epidemiology of various known enteropathogens is not fully understood. Methods We used a custom TaqMan Array Card (TAC) to screen for 28 different enteropathogens in 718 stools from children aged less than 13 years admitted to Kilifi County Hospital, coastal Kenya, following presentation with diarrhea in 2013 (before vaccine introduction) and in 2016–2018 (after vaccine introduction). Pathogen positivity rate differences between pre- and post-Rotarix® vaccination introduction were examined using both univariate and multivariable logistic regression models. Results In 665 specimens (92.6%), one or more enteropathogen was detected, while in 323 specimens (48.6%) three or more enteropathogens were detected. The top six detected enteropathogens were: enteroaggregative Escherichia coli (EAggEC; 42.1%), enteropathogenic Escherichia coli (EPEC; 30.2%), enterovirus (26.9%), rotavirus group A (RVA; 24.8%), parechovirus (16.6%) and norovirus GI/GII (14.4%). Post-rotavirus vaccine introduction, there was a significant increase in the proportion of samples testing positive for EAggEC (35.7% vs. 45.3%, p = 0.014), cytomegalovirus (4.2% vs. 9.9%, p = 0.008), Vibrio cholerae (0.0% vs. 2.3%, p = 0.019), Strongyloides species (0.8% vs. 3.6%, p = 0.048) and Dientamoeba fragilis (2.1% vs. 7.8%, p = 0.004). Although not reaching statistical significance, the positivity rate of adenovirus 40/41 (5.8% vs. 7.3%, p = 0.444), norovirus GI/GII (11.2% vs. 15.9%, p = 0.089), Shigella species (8.7% vs. 13.0%, p = 0.092) and Cryptosporidium spp. (11.6% vs. 14.7%, p = 0.261) appeared to increase post-vaccine introduction. Conversely, the positivity rate of sapovirus decreased significantly post-vaccine introduction (7.8% vs. 4.0%, p = 0.030) while that of RVA appeared not to change (27.4% vs. 23.5%, p = 0.253). More enteropathogen coinfections were detected per child post-vaccine introduction compared to before (mean: 2.7 vs. 2.3; p = 0.0025). Conclusions In this rural Coastal Kenya setting, childhood enteropathogen infection burden was high both pre- and post-rotavirus vaccination introduction. Children who had diarrheal admissions post-vaccination showed an increase in coinfections and changes in specific enteropathogen positivity rates. This study highlights the utility of multipathogen detection platforms such as TAC in understanding etiology of childhood acute gastroenteritis in resource-limited regions. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-022-00506-z.
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9
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Elbashir I, Aldoos NF, Mathew S, Al Thani AA, Emara MM, Yassine HM. Molecular epidemiology, genetic diversity, and vaccine availability of viral acute gastroenteritis in the middle East and North Africa (MENA) region. J Infect Public Health 2022; 15:1193-1211. [PMID: 36240530 DOI: 10.1016/j.jiph.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/26/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022] Open
Abstract
Acute gastroenteritis is the cause of considerable mortality and morbidity worldwide, particularly among children under five years in underdeveloped countries. Most acute gastroenteritis (AGE) cases are attributed to viral etiologies, including rotavirus, norovirus, adenovirus, astrovirus, and sapovirus. This paper aimed to determine the prevalence rate of different viral etiologies of AGE in the Middle East and North Africa (MENA) region. Moreover, this paper explored rotavirus phylogenetic relatedness, compared VP7 and VP4 antigenic regions of rotavirus with vaccine strains, and explored the availability of vaccines in the MENA region. The literature search identified 160 studies from 18 countries from 1980 to 2019. The overall prevalence of rotavirus, norovirus, adenovirus, astrovirus, and sapovirus were 29.8 %, 13.9 %, 6.3 %, 3.5 %, and 3.2 % of tested samples, respectively. The most common rotavirus genotype combinations in the MENA region were G1P[8], G9P[9], and G2P[4], whereas GII.4 was the predominant norovirus genotype all of which were reported in almost all the studies with genotyping data. The comparison of VP7 and VP4 between circulating rotavirus in the MENA region and vaccine strains has revealed discrete divergent regions, including the neutralizing epitopes. Rotavirus vaccine was introduced to most of the countries of the MENA region; however, only a few studies have assessed the effectiveness of vaccine introduction. This paper provides a comprehensive update on the prevalence of the different viral agents of AGE in the MENA region.
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Affiliation(s)
- Israa Elbashir
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar.
| | - Noor F Aldoos
- Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.
| | - Shilu Mathew
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar.
| | - Asmaa A Al Thani
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar; Department of Biomedical Sciences, College of Health Science-QU Health, Qatar University, Doha 2713, Qatar
| | - Mohamed M Emara
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar.
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar.
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10
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Latifi T, Eybpoosh S, Afchangi A, Jalilvand S, Shoja Z. Genetic characterization of P[8] rotavirus strains circulated in Iran between 2009 and 2017. J Med Virol 2022; 94:3561-3569. [PMID: 35393690 DOI: 10.1002/jmv.27766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/24/2022] [Accepted: 04/03/2022] [Indexed: 11/07/2022]
Abstract
Group A rotavirus (RVA) is the most common cause of acute gastroenteritis (AGE) worldwide, which is responsible for causing an estimated 120,000 deaths in children under 5 years of age, which mostly occur in the lower income countries of Asia and Africa. The G1P[8] is a common genotype of RVA that has spread throughout the world, including Iran and this genotype is present in two commonly used RVA vaccines, RotarixTM and RotaTeqTM . In this study, we investigated the genetic diversity, viral evolutionary, and differences between antigenic epitopes of Iran's P[8] strains and two licensed vaccines. The phylogenetic and evolutionary analysis was carried out, using MEGA vs 6.0 and BEAST respectively. Antigenic epitopes of VP8* were compared to determine the differences between strains from Iran and RotarixTM and RotaTeqTM . The P[8]-lineages III and IV was found as the predominant P genotype that circulating in Iran. The TMRCA of P[8]-lineages III and IV was estimated at 1987 and 2009 respectively. The P[8]-lineage III strains showed 12 amino acid changes compared to RotarixTM and 10 amino acid changes compared to RotaTeqTM . The P[8]-lineage IV strains showed 10 amino acid variations for both RotarixTM and RotaTeqTM strains. The results revealed that the P[8] strains circulating in Iran differs from RotarixTM and RotaTeqTM strains. To monitor the long-term effects of vaccines on the emergence of P[8] strains with different lineages, routine and successful monitoring of these strains will be crucial. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tayebeh Latifi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sana Eybpoosh
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Atefeh Afchangi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zabihollah Shoja
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
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11
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Sadiq A, Bostan N, Aziz A. Effect of rotavirus genetic diversity on vaccine impact. Rev Med Virol 2022; 32:e2259. [PMID: 34997676 DOI: 10.1002/rmv.2259] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/05/2021] [Indexed: 11/07/2022]
Abstract
Group A rotaviruses (RVAs) are the leading cause of gastroenteritis, causing 0.2 million deaths and several million hospitalisations globally each year. Four rotavirus vaccines (RotarixTM , RotaTeqTM , Rotavac® and ROTASIIL® ) have been pre-qualified by the World Health Organization (WHO), but the two newly pre-qualified vaccines (Rotavac® and ROTASIIL® ) are currently only in use in Palestine and India, respectively. In 2009, WHO strongly proposed that rotavirus vaccines be included in the routine vaccination schedule of all countries around the world. By the end of 2019, a total of 108 countries had administered rotavirus vaccines, and 10 countries have currently been approved by Gavi for the introduction of rotavirus vaccine in the near future. With 39% of global coverage, rotavirus vaccines have had a substantial effect on diarrhoeal morbidity and mortality in different geographical areas, although efficacy appears to be higher in high income settings. Due to the segmented RNA genome, the pattern of RVA genotypes in the human population is evolving through interspecies transmission and/or reassortment events for which the vaccine might be less effective in the future. However, despite the relative increase in some particular genotypes after rotavirus vaccine use, the overall efficacy of rotavirus mass vaccination worldwide has not been affected. Some of the challenges to improve the effect of current rotavirus vaccines can be solved in the future by new rotavirus vaccines and by vaccines currently in progress.
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Affiliation(s)
- Asma Sadiq
- Department of Biosciences, Molecular Virology Laboratory, COMSATS University, Islamabad, Pakistan
| | - Nazish Bostan
- Department of Biosciences, Molecular Virology Laboratory, COMSATS University, Islamabad, Pakistan
| | - Aamir Aziz
- Sarhad University of Science and Information Technology, Institute of Biological Sciences, Sarhad University, Peshawar, Pakistan
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12
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Varghese T, Alokit Khakha S, Giri S, Nair NP, Badur M, Gathwala G, Chaudhury S, Kaushik S, Dash M, Mohakud NK, Ray RK, Mohanty P, Kumar CPG, Venkatasubramanian S, Arora R, Raghava Mohan V, E. Tate J, D. Parashar U, Kang G. Rotavirus Strain Distribution before and after Introducing Rotavirus Vaccine in India. Pathogens 2021; 10:pathogens10040416. [PMID: 33915946 PMCID: PMC8066972 DOI: 10.3390/pathogens10040416] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 12/13/2022] Open
Abstract
In April 2016, an indigenous monovalent rotavirus vaccine (Rotavac) was introduced to the National Immunization Program in India. Hospital-based surveillance for acute gastroenteritis was conducted in five sentinel sites from 2012 to 2020 to monitor the vaccine impact on various genotypes and the reduction in rotavirus positivity at each site. Stool samples collected from children under 5 years of age hospitalized with diarrhea were tested for group A rotavirus using a commercial enzyme immunoassay, and rotavirus strains were characterized by RT-PCR. The proportion of diarrhea hospitalizations attributable to rotavirus at the five sites declined from a range of 56–29.4% in pre-vaccine years to 34–12% in post-vaccine years. G1P[8] was the predominant strain in the pre-vaccination period, and G3P[8] was the most common in the post-vaccination period. Circulating patterns varied throughout the study period, and increased proportions of mixed genotypes were detected in the post-vaccination phase. Continuous long-term surveillance is essential to understand the diversity and immuno-epidemiological effects of rotavirus vaccination.
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Affiliation(s)
- Tintu Varghese
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore 632004, India; (T.V.); (S.A.K.); (S.G.); (N.P.N.)
| | - Shainey Alokit Khakha
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore 632004, India; (T.V.); (S.A.K.); (S.G.); (N.P.N.)
| | - Sidhartha Giri
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore 632004, India; (T.V.); (S.A.K.); (S.G.); (N.P.N.)
| | - Nayana P. Nair
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore 632004, India; (T.V.); (S.A.K.); (S.G.); (N.P.N.)
| | - Manohar Badur
- Department of Pediatrics, Sri Venkateshwara Medical College, Tirupati 517507, India;
| | - Geeta Gathwala
- Department of Pediatrics, Post Graduate Institute of Medical Sciences, Medical Road, Rohtak, Haryana 124001, India;
| | - Sanjeev Chaudhury
- Department of Pediatrics, Dr Rajendra Prasad Government Medical College, Tanda, Himachal Pradesh 176001, India;
| | - Shayam Kaushik
- Department of Pediatrics, Indira Gandhi Medical College, Shimla, Himachal Pradesh 171001, India;
| | - Mrutunjay Dash
- Department of Pediatrics, Institute of Medical Sciences and SUM Hospital, Bhubaneswar, Odisha 751003, India;
| | - Nirmal K. Mohakud
- Department of Pediatrics, Kalinga Institute of Medical Sciences, 5 KIIT Road, Bhubaneswar, Odisha 751024, India;
| | - Rajib K. Ray
- Department of Pediatrics, Hi-Tech Hospital, Bhubaneswar, Odisha 751025, India; (R.K.R.); (P.M.)
| | - Prasantajyoti Mohanty
- Department of Pediatrics, Hi-Tech Hospital, Bhubaneswar, Odisha 751025, India; (R.K.R.); (P.M.)
| | | | | | - Rashmi Arora
- Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India;
| | | | - Jacqueline E. Tate
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Umesh D. Parashar
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Gagandeep Kang
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore 632004, India; (T.V.); (S.A.K.); (S.G.); (N.P.N.)
- Correspondence:
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Mwanga MJ, Verani JR, Omore R, Tate JE, Parashar UD, Murunga N, Gicheru E, Breiman RF, Nokes DJ, Agoti CN. Multiple Introductions and Predominance of Rotavirus Group A Genotype G3P[8] in Kilifi, Coastal Kenya, 4 Years after Nationwide Vaccine Introduction. Pathogens 2020; 9:pathogens9120981. [PMID: 33255256 PMCID: PMC7761311 DOI: 10.3390/pathogens9120981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/10/2020] [Accepted: 11/20/2020] [Indexed: 01/22/2023] Open
Abstract
Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use of vaccines in more than 100 countries. RVA sequencing for local outbreaks facilitates investigation into strain composition, origins, spread, and vaccine failure. In 2018, we collected 248 stool samples from children aged less than 13 years admitted with diarrheal illness to Kilifi County Hospital, coastal Kenya. Antigen screening detected RVA in 55 samples (22.2%). Of these, VP7 (G) and VP4 (P) segments were successfully sequenced in 48 (87.3%) and phylogenetic analysis based on the VP7 sequences identified seven genetic clusters with six different GP combinations: G3P[8], G1P[8], G2P[4], G2P[8], G9P[8] and G12P[8]. The G3P[8] strains predominated the season (n = 37, 67.2%) and comprised three distinct G3 genetic clusters that fell within Lineage I and IX (the latter also known as equine-like G3 Lineage). Both the two G3 lineages have been recently detected in several countries. Our study is the first to document African children infected with G3 Lineage IX. These data highlight the global nature of RVA transmission and the importance of increasing global rotavirus vaccine coverage.
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Affiliation(s)
- Mike J. Mwanga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
| | - Jennifer R. Verani
- Centers for Disease Control and Prevention (CDC), KEMRI Complex, off Mbagathi Way, Village Market, Nairobi 00621, Kenya;
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Richard Omore
- KEMRI, Center for Global Health Research (KEMRI-CGHR), Kisumu 00202, Kenya;
| | - Jacqueline E. Tate
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Umesh D. Parashar
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA; (J.E.T.); (U.D.P.)
| | - Nickson Murunga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
| | - Elijah Gicheru
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
| | - Robert F. Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
| | - D. James Nokes
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
- School of Life Sciences and Zeeman Institute (SBIDER), The University of Warwick, Coventry CV4 7AL, UK
| | - Charles N. Agoti
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, off Hospital Road, Kilifi 80108, Kenya; (M.J.M.); (N.M.); (E.G.); (D.J.N.)
- School of Health and Human Sciences, Pwani University, Kilifi 80108, Kenya
- Correspondence:
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14
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Lambisia AW, Onchaga S, Murunga N, Lewa CS, Nyanjom SG, Agoti CN. Epidemiological Trends of Five Common Diarrhea-Associated Enteric Viruses Pre- and Post-Rotavirus Vaccine Introduction in Coastal Kenya. Pathogens 2020; 9:pathogens9080660. [PMID: 32824245 PMCID: PMC7459961 DOI: 10.3390/pathogens9080660] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 12/28/2022] Open
Abstract
Using real-time RT-PCR, we screened stool samples from children aged <5 years presenting with diarrhea and admitted to Kilifi County Hospital, coastal Kenya, pre- (2003 and 2013) and post-rotavirus vaccine introduction (2016 and 2019) for five viruses, namely rotavirus group A (RVA), norovirus GII, adenovirus, astrovirus and sapovirus. Of the 984 samples analyzed, at least one virus was detected in 401 (40.8%) patients. Post rotavirus vaccine introduction, the prevalence of RVA decreased (23.3% vs. 13.8%, p < 0.001) while that of norovirus GII increased (6.6% vs. 10.9%, p = 0.023). The prevalence of adenovirus, astrovirus and sapovirus remained statistically unchanged between the two periods: 9.9% vs. 14.2%, 2.4% vs. 3.2 %, 4.6% vs. 2.6%, (p = 0.053, 0.585 and 0.133), respectively. The median age of diarrhea cases was higher post vaccine introduction (12.5 months, interquartile range (IQR): 7.9–21 vs. 11.2 months pre-introduction, IQR: 6.8–16.5, p < 0.001). In this setting, RVA and adenovirus cases peaked in the dry months while norovirus GII and sapovirus peaked in the rainy season. Astrovirus did not display clear seasonality. In conclusion, following rotavirus vaccine introduction, we found a significant reduction in the prevalence of RVA in coastal Kenya but an increase in norovirus GII prevalence in hospitalized children.
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Affiliation(s)
- Arnold W. Lambisia
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi 230-80108, Kenya; (S.O.); (N.M.); (C.S.L.); (C.N.A.)
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja 62000-00200, Kenya;
- Correspondence: ; Tel.: +254-708-164-077
| | - Sylvia Onchaga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi 230-80108, Kenya; (S.O.); (N.M.); (C.S.L.); (C.N.A.)
| | - Nickson Murunga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi 230-80108, Kenya; (S.O.); (N.M.); (C.S.L.); (C.N.A.)
| | - Clement S. Lewa
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi 230-80108, Kenya; (S.O.); (N.M.); (C.S.L.); (C.N.A.)
| | - Steven Ger Nyanjom
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja 62000-00200, Kenya;
| | - Charles N. Agoti
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi 230-80108, Kenya; (S.O.); (N.M.); (C.S.L.); (C.N.A.)
- School of Health and Human Sciences, Pwani University, Kilifi 195-80108, Kenya
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