Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018

Mike J Mwanga; Betty E Owor; John B Ochieng; Mwanajuma H Ngama; Billy Ogwel; Clayton Onyango; Jane Juma; Regina Njeru; Elijah Gicheru; Grieven P Otieno; Sammy Khagayi; Charles N Agoti; Godfrey M Bigogo; Richard Omore; O Yaw Addo; Seheri Mapaseka; Jacqueline E Tate; Umesh D Parashar; Elizabeth Hunsperger; Jennifer R Verani; Robert F Breiman; D James Nokes

doi:10.1186/s12879-020-05230-0

Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018

Mike J Mwanga, Betty E Owor, John B Ochieng, Mwanajuma H Ngama, Billy Ogwel, Clayton Onyango, Jane Juma, Regina Njeru, Elijah Gicheru, Grieven P Otieno, Sammy Khagayi, Charles N Agoti, Godfrey M Bigogo, Richard Omore, O Yaw Addo, Seheri Mapaseka, Jacqueline E Tate, Umesh D Parashar, Elizabeth Hunsperger, Jennifer R VeraniRobert F Breiman, D James Nokes

Virological Pathology

Research output: Contribution to journal › Article › peer-review

16 Citations (Scopus)

Abstract

BACKGROUND: Kenya introduced the monovalent G1P [8] Rotarix® vaccine into the infant immunization schedule in July 2014. We examined trends in rotavirus group A (RVA) genotype distribution pre- (January 2010-June 2014) and post- (July 2014-December 2018) RVA vaccine introduction.

METHODS: Stool samples were collected from children aged < 13 years from four surveillance sites across Kenya: Kilifi County Hospital, Tabitha Clinic Nairobi, Lwak Mission Hospital, and Siaya County Referral Hospital (children aged < 5 years only). Samples were screened for RVA using enzyme linked immunosorbent assay (ELISA) and VP7 and VP4 genes sequenced to infer genotypes.

RESULTS: We genotyped 614 samples in pre-vaccine and 261 in post-vaccine introduction periods. During the pre-vaccine introduction period, the most frequent RVA genotypes were G1P [8] (45.8%), G8P [4] (15.8%), G9P [8] (13.2%), G2P [4] (7.0%) and G3P [6] (3.1%). In the post-vaccine introduction period, the most frequent genotypes were G1P [8] (52.1%), G2P [4] (20.7%) and G3P [8] (16.1%). Predominant genotypes varied by year and site in both pre and post-vaccine periods. Temporal genotype patterns showed an increase in prevalence of vaccine heterotypic genotypes, such as the commonly DS-1-like G2P [4] (7.0 to 20.7%, P < .001) and G3P [8] (1.3 to 16.1%, P < .001) genotypes in the post-vaccine introduction period. Additionally, we observed a decline in prevalence of genotypes G8P [4] (15.8 to 0.4%, P < .001) and G9P [8] (13.2 to 5.4%, P < .001) in the post-vaccine introduction period. Phylogenetic analysis of genotype G1P [8], revealed circulation of strains of lineages G1-I, G1-II and P [8]-1, P [8]-III and P [8]-IV. Considerable genetic diversity was observed between the pre and post-vaccine strains, evidenced by distinct clusters.

CONCLUSION: Genotype prevalence varied from before to after vaccine introduction. Such observations emphasize the need for long-term surveillance to monitor vaccine impact. These changes may represent natural secular variation or possible immuno-epidemiological changes arising from the introduction of the vaccine. Full genome sequencing could provide insights into post-vaccine evolutionary pressures and antigenic diversity.

Original language	English
Pages (from-to)	504
Journal	BMC Infectious Diseases
Volume	20
Issue number	1
DOIs	https://doi.org/10.1186/s12879-020-05230-0
Publication status	Published - 13 Jul 2020

Keywords

Child
Child, Preschool
Enzyme-Linked Immunosorbent Assay
Feces/virology
Female
Gastroenteritis/etiology
Genotype
Humans
Immunization Schedule
Infant
Kenya/epidemiology
Male
Phylogeny
Prevalence
Rotavirus/genetics
Rotavirus Infections/epidemiology
Rotavirus Vaccines/adverse effects
Vaccination
Vaccines, Attenuated/adverse effects

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1186/s12879-020-05230-0

Cite this

Mwanga, M. J., Owor, B. E., Ochieng, J. B., Ngama, M. H., Ogwel, B., Onyango, C., Juma, J., Njeru, R., Gicheru, E., Otieno, G. P., Khagayi, S., Agoti, C. N., Bigogo, G. M., Omore, R., Addo, O. Y., Mapaseka, S., Tate, J. E., Parashar, U. D., Hunsperger, E., ... Nokes, D. J. (2020). Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018. BMC Infectious Diseases, 20(1), 504. https://doi.org/10.1186/s12879-020-05230-0

@article{c8a265b6f09d44a8bae2a0665881c114,

title = "Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018",

abstract = "BACKGROUND: Kenya introduced the monovalent G1P [8] Rotarix{\textregistered} vaccine into the infant immunization schedule in July 2014. We examined trends in rotavirus group A (RVA) genotype distribution pre- (January 2010-June 2014) and post- (July 2014-December 2018) RVA vaccine introduction.METHODS: Stool samples were collected from children aged < 13 years from four surveillance sites across Kenya: Kilifi County Hospital, Tabitha Clinic Nairobi, Lwak Mission Hospital, and Siaya County Referral Hospital (children aged < 5 years only). Samples were screened for RVA using enzyme linked immunosorbent assay (ELISA) and VP7 and VP4 genes sequenced to infer genotypes.RESULTS: We genotyped 614 samples in pre-vaccine and 261 in post-vaccine introduction periods. During the pre-vaccine introduction period, the most frequent RVA genotypes were G1P [8] (45.8%), G8P [4] (15.8%), G9P [8] (13.2%), G2P [4] (7.0%) and G3P [6] (3.1%). In the post-vaccine introduction period, the most frequent genotypes were G1P [8] (52.1%), G2P [4] (20.7%) and G3P [8] (16.1%). Predominant genotypes varied by year and site in both pre and post-vaccine periods. Temporal genotype patterns showed an increase in prevalence of vaccine heterotypic genotypes, such as the commonly DS-1-like G2P [4] (7.0 to 20.7%, P < .001) and G3P [8] (1.3 to 16.1%, P < .001) genotypes in the post-vaccine introduction period. Additionally, we observed a decline in prevalence of genotypes G8P [4] (15.8 to 0.4%, P < .001) and G9P [8] (13.2 to 5.4%, P < .001) in the post-vaccine introduction period. Phylogenetic analysis of genotype G1P [8], revealed circulation of strains of lineages G1-I, G1-II and P [8]-1, P [8]-III and P [8]-IV. Considerable genetic diversity was observed between the pre and post-vaccine strains, evidenced by distinct clusters.CONCLUSION: Genotype prevalence varied from before to after vaccine introduction. Such observations emphasize the need for long-term surveillance to monitor vaccine impact. These changes may represent natural secular variation or possible immuno-epidemiological changes arising from the introduction of the vaccine. Full genome sequencing could provide insights into post-vaccine evolutionary pressures and antigenic diversity.",

keywords = "Child, Child, Preschool, Enzyme-Linked Immunosorbent Assay, Feces/virology, Female, Gastroenteritis/etiology, Genotype, Humans, Immunization Schedule, Infant, Kenya/epidemiology, Male, Phylogeny, Prevalence, Rotavirus/genetics, Rotavirus Infections/epidemiology, Rotavirus Vaccines/adverse effects, Vaccination, Vaccines, Attenuated/adverse effects",

author = "Mwanga, {Mike J} and Owor, {Betty E} and Ochieng, {John B} and Ngama, {Mwanajuma H} and Billy Ogwel and Clayton Onyango and Jane Juma and Regina Njeru and Elijah Gicheru and Otieno, {Grieven P} and Sammy Khagayi and Agoti, {Charles N} and Bigogo, {Godfrey M} and Richard Omore and Addo, {O Yaw} and Seheri Mapaseka and Tate, {Jacqueline E} and Parashar, {Umesh D} and Elizabeth Hunsperger and Verani, {Jennifer R} and Breiman, {Robert F} and Nokes, {D James}",

year = "2020",

month = jul,

day = "13",

doi = "10.1186/s12879-020-05230-0",

language = "English",

volume = "20",

pages = "504",

journal = "BMC Infectious Diseases",

issn = "1471-2334",

publisher = "BioMed Central Ltd.",

number = "1",

}

Mwanga, MJ, Owor, BE, Ochieng, JB, Ngama, MH, Ogwel, B, Onyango, C, Juma, J, Njeru, R, Gicheru, E, Otieno, GP, Khagayi, S, Agoti, CN, Bigogo, GM, Omore, R, Addo, OY, Mapaseka, S, Tate, JE, Parashar, UD, Hunsperger, E, Verani, JR, Breiman, RF & Nokes, DJ 2020, 'Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018', BMC Infectious Diseases, vol. 20, no. 1, pp. 504. https://doi.org/10.1186/s12879-020-05230-0

TY - JOUR

T1 - Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018

AU - Mwanga, Mike J

AU - Owor, Betty E

AU - Ochieng, John B

AU - Ngama, Mwanajuma H

AU - Ogwel, Billy

AU - Onyango, Clayton

AU - Juma, Jane

AU - Njeru, Regina

AU - Gicheru, Elijah

AU - Otieno, Grieven P

AU - Khagayi, Sammy

AU - Agoti, Charles N

AU - Bigogo, Godfrey M

AU - Omore, Richard

AU - Addo, O Yaw

AU - Mapaseka, Seheri

AU - Tate, Jacqueline E

AU - Parashar, Umesh D

AU - Hunsperger, Elizabeth

AU - Verani, Jennifer R

AU - Breiman, Robert F

AU - Nokes, D James

PY - 2020/7/13

Y1 - 2020/7/13

N2 - BACKGROUND: Kenya introduced the monovalent G1P [8] Rotarix® vaccine into the infant immunization schedule in July 2014. We examined trends in rotavirus group A (RVA) genotype distribution pre- (January 2010-June 2014) and post- (July 2014-December 2018) RVA vaccine introduction.METHODS: Stool samples were collected from children aged < 13 years from four surveillance sites across Kenya: Kilifi County Hospital, Tabitha Clinic Nairobi, Lwak Mission Hospital, and Siaya County Referral Hospital (children aged < 5 years only). Samples were screened for RVA using enzyme linked immunosorbent assay (ELISA) and VP7 and VP4 genes sequenced to infer genotypes.RESULTS: We genotyped 614 samples in pre-vaccine and 261 in post-vaccine introduction periods. During the pre-vaccine introduction period, the most frequent RVA genotypes were G1P [8] (45.8%), G8P [4] (15.8%), G9P [8] (13.2%), G2P [4] (7.0%) and G3P [6] (3.1%). In the post-vaccine introduction period, the most frequent genotypes were G1P [8] (52.1%), G2P [4] (20.7%) and G3P [8] (16.1%). Predominant genotypes varied by year and site in both pre and post-vaccine periods. Temporal genotype patterns showed an increase in prevalence of vaccine heterotypic genotypes, such as the commonly DS-1-like G2P [4] (7.0 to 20.7%, P < .001) and G3P [8] (1.3 to 16.1%, P < .001) genotypes in the post-vaccine introduction period. Additionally, we observed a decline in prevalence of genotypes G8P [4] (15.8 to 0.4%, P < .001) and G9P [8] (13.2 to 5.4%, P < .001) in the post-vaccine introduction period. Phylogenetic analysis of genotype G1P [8], revealed circulation of strains of lineages G1-I, G1-II and P [8]-1, P [8]-III and P [8]-IV. Considerable genetic diversity was observed between the pre and post-vaccine strains, evidenced by distinct clusters.CONCLUSION: Genotype prevalence varied from before to after vaccine introduction. Such observations emphasize the need for long-term surveillance to monitor vaccine impact. These changes may represent natural secular variation or possible immuno-epidemiological changes arising from the introduction of the vaccine. Full genome sequencing could provide insights into post-vaccine evolutionary pressures and antigenic diversity.

AB - BACKGROUND: Kenya introduced the monovalent G1P [8] Rotarix® vaccine into the infant immunization schedule in July 2014. We examined trends in rotavirus group A (RVA) genotype distribution pre- (January 2010-June 2014) and post- (July 2014-December 2018) RVA vaccine introduction.METHODS: Stool samples were collected from children aged < 13 years from four surveillance sites across Kenya: Kilifi County Hospital, Tabitha Clinic Nairobi, Lwak Mission Hospital, and Siaya County Referral Hospital (children aged < 5 years only). Samples were screened for RVA using enzyme linked immunosorbent assay (ELISA) and VP7 and VP4 genes sequenced to infer genotypes.RESULTS: We genotyped 614 samples in pre-vaccine and 261 in post-vaccine introduction periods. During the pre-vaccine introduction period, the most frequent RVA genotypes were G1P [8] (45.8%), G8P [4] (15.8%), G9P [8] (13.2%), G2P [4] (7.0%) and G3P [6] (3.1%). In the post-vaccine introduction period, the most frequent genotypes were G1P [8] (52.1%), G2P [4] (20.7%) and G3P [8] (16.1%). Predominant genotypes varied by year and site in both pre and post-vaccine periods. Temporal genotype patterns showed an increase in prevalence of vaccine heterotypic genotypes, such as the commonly DS-1-like G2P [4] (7.0 to 20.7%, P < .001) and G3P [8] (1.3 to 16.1%, P < .001) genotypes in the post-vaccine introduction period. Additionally, we observed a decline in prevalence of genotypes G8P [4] (15.8 to 0.4%, P < .001) and G9P [8] (13.2 to 5.4%, P < .001) in the post-vaccine introduction period. Phylogenetic analysis of genotype G1P [8], revealed circulation of strains of lineages G1-I, G1-II and P [8]-1, P [8]-III and P [8]-IV. Considerable genetic diversity was observed between the pre and post-vaccine strains, evidenced by distinct clusters.CONCLUSION: Genotype prevalence varied from before to after vaccine introduction. Such observations emphasize the need for long-term surveillance to monitor vaccine impact. These changes may represent natural secular variation or possible immuno-epidemiological changes arising from the introduction of the vaccine. Full genome sequencing could provide insights into post-vaccine evolutionary pressures and antigenic diversity.

KW - Child

KW - Child, Preschool

KW - Enzyme-Linked Immunosorbent Assay

KW - Feces/virology

KW - Female

KW - Gastroenteritis/etiology

KW - Genotype

KW - Humans

KW - Immunization Schedule

KW - Infant

KW - Kenya/epidemiology

KW - Male

KW - Phylogeny

KW - Prevalence

KW - Rotavirus/genetics

KW - Rotavirus Infections/epidemiology

KW - Rotavirus Vaccines/adverse effects

KW - Vaccination

KW - Vaccines, Attenuated/adverse effects

U2 - 10.1186/s12879-020-05230-0

DO - 10.1186/s12879-020-05230-0

M3 - Article

C2 - 32660437

SN - 1471-2334

VL - 20

SP - 504

JO - BMC Infectious Diseases

JF - BMC Infectious Diseases

IS - 1

ER -

Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018

Abstract

Keywords

UN SDGs

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