scholarly journals Multiple Introductions and Predominance of Rotavirus Group A Genotype G3P[8] in Kilifi, Coastal Kenya, 4 Years after Nationwide Vaccine Introduction

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 981
Author(s):  
Mike J. Mwanga ◽  
Jennifer R. Verani ◽  
Richard Omore ◽  
Jacqueline E. Tate ◽  
Umesh D. Parashar ◽  
...  
Keyword(s):  
Vaccine Coverage ◽  
Childhood Diarrhea ◽  
Vaccine Failure ◽  
Multiple Introductions ◽  
Vaccine Introduction ◽  
Coastal Kenya ◽  
Group A ◽  
Genetic Clusters ◽  
Global Nature ◽  
Stool Samples

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.

scholarly journals Multiple Introductions and Predominance of Rotavirus Group A Genotype G3P[8] in Coastal Kenya in 2018, 4 Years After Nationwide Vaccine Introduction

2020 ◽  
Author(s):  
Mike J. Mwanga ◽  
Jennifer R. Verani ◽  
Richard Omore ◽  
Jacqueline E. Tate ◽  
Umesh D. Parashar ◽  
...  
Keyword(s):  
Vaccine Coverage ◽  
Childhood Diarrhea ◽  
Vaccine Failure ◽  
Multiple Introductions ◽  
Vaccine Introduction ◽  
Coastal Kenya ◽  
Group A ◽  
Genetic Clusters ◽  
Global Nature ◽  
Stool Samples

Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use of vaccines in > 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 <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 G3 genetic clusters that fell within Lineage I and IX (the latter also known as equine-like G3 lineage). Both two G3 lineages have been recently detected in several countries. Our study is the first to document African children infection with G3 lineage IX. These data highlight the global nature of RVA transmission and the importance of increasing global rotavirus vaccine coverage.

scholarly journals Epidemiological Trends of Five Common Diarrhea-Associated Enteric Viruses Pre- and Post-Rotavirus Vaccine Introduction in Coastal Kenya

Pathogens ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 660
Author(s):  
Arnold W. Lambisia ◽  
Sylvia Onchaga ◽  
Nickson Murunga ◽  
Clement S. Lewa ◽  
Steven Ger Nyanjom ◽  
...  
Keyword(s):  
Rainy Season ◽  
Hospitalized Children ◽  
Rotavirus Vaccine ◽  
Rt Pcr ◽  
Vaccine Introduction ◽  
Coastal Kenya ◽  
Group A ◽  
Stool Samples ◽  
Norovirus Gii ◽  
Epidemiological Trends

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.

Molecular characterization of rotaviruses in mid-western Turkey, 2006–2007

Open Medicine ◽  
2010 ◽  
Vol 5 (5) ◽  
pp. 640-645
Author(s):  
Mustafa Altindis ◽  
Krisztián Bányai ◽  
Raike Kalayci ◽  
Cihangir Gulamber ◽  
Resit Koken ◽  
...  
Keyword(s):  
Immune Escape ◽  
Local Strain ◽  
Western Turkey ◽  
Vaccine Introduction ◽  
Rotavirus Vaccines ◽  
Group A ◽  
Stool Samples ◽  
Commercial Enzyme Immunoassay ◽  
P Type

AbstractVaccines against rotaviruses are now available in numerous countries, including Turkey. As the vaccines may show various efficiencies against different type specificities and routine vaccination in infants might result in selection and immune escape of wild-type rotavirus strains, strain surveillance has been initiated before and during the vaccine introduction. We aimed to provide corresponding information on local strain prevalence in Anatolia, mid-western Turkey during the introduction of rotavirus vaccines. Stool samples positive for group A rotavirus by commercial enzyme immunoassay were subjected to reverse transcription-polymerase chain reaction based genotyping of the outer capsid antigens, VP7 and VP4, determining G and P type specificities respectively. Among 36 fully and 5 partially typeable strains we detected genotype G1, G2, and G9 VP7 specificities and genotype P[4], P[6] and P[8] VP4 specificities in 5 individual and 4 mixed combinations. The most common strain was G2P[4] (n=17), followed by G9P[8] (n=9). Other strains were G1P[8] (n=2), G2P[8] (n=2), G1+2P[8] (n=2), G9P[4] (n=1), G2+9P[8] (n=1), G4+9P[6] (n=1), and G2P[4+8] (n=1). Partially typed strains included 2 G1P[NT] and 3 G2P[NT] strains. Our data may help determine a baseline of the rotavirus genotype prevalence in Turkey and see if changes in the incidence of individual strains will be observed after routine use of vaccine.

scholarly journals Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013

2019 ◽  
Vol 3 ◽  
pp. 150
Author(s):  
Betty E. Owor ◽  
Mike J. Mwanga ◽  
Regina Njeru ◽  
Robert Mugo ◽  
Mwanajuma Ngama ◽  
...  
Keyword(s):  
Temporal Fluctuations ◽  
Consensus Sequences ◽  
Vaccine Introduction ◽  
Coastal Kenya ◽  
Circulation Patterns ◽  
Sequencing Method ◽  
Group A ◽  
Wide Scale ◽  
Classification Tool ◽  
The Impact

Background: Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014.  Long-term surveillance data is important prior to wide-scale vaccine use to assess the impact on disease and to investigate the occurrence of heterotypic strains arising through immune selection. This report presents baseline data on RVA genotype circulation patterns and intra-genotype genetic diversity over a 7-year period in the pre-vaccine era in Kilifi, Kenya, from 2002 to 2004 and from 2010 to 2013. Methods: A total of 745 RVA strains identified in children admitted with acute gastroenteritis to a referral hospital in Coastal Kenya, were sequenced using the di-deoxy sequencing method in the VP4 and VP7 genomic segments (encoding P and G proteins, respectively). Sequencing successfully generated 569 (76%) and 572 (77%) consensus sequences for the VP4 and VP7 genes respectively. G and P genotypes were determined by use of BLAST and the online RotaC v2 RVA classification tool. Results: The most common GP combination was G1P[8] (51%), similar to the Rotarix® strain, followed by G9P[8] (15%) , G8P[4] (14%) and G2P[4] (5%).  Unusual GP combinations—G1P[4], G2P[8], G3P[4,6], G8P[8,14], and G12P[4,6,8]—were observed at frequencies of <5%. Phylogenetic analysis showed that the infections were caused by both locally persistent strains as evidenced by divergence of local strains occurring over multiple seasons from the global ones, and newly introduced strains, which were closely related to global strains. The circulating RVA diversity showed temporal fluctuations both season by season and over the longer-term. None of the unusual strains increased in frequency over the observation period.   Conclusions: The circulating RVA diversity showed temporal fluctuations with several unusual strains recorded, which rarely caused major outbreaks.  These data will be useful in interpreting genotype patterns observed in the region during the vaccine era.

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

2020 ◽  
Author(s):  
Mike Mwanga ◽  
Betty Owor ◽  
John Ocheing ◽  
Mwanajuma Ngama ◽  
Billy Ogwel ◽  
...  
Keyword(s):  
Enzyme Linked Immunosorbent Assay ◽  
Genotype Distribution ◽  
Vaccine Introduction ◽  
Circulation Patterns ◽  
Before And After ◽  
Epidemiological Changes ◽  
Group A ◽  
Vaccine Impact ◽  
Stool Samples

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, 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 G and P 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 heterotypic 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.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 length sequencing could provide insights into post-vaccine evolutionary pressures and antigenic diversity.

scholarly journals Rotavirus breakthrough infections responsible for gastroenteritis in vaccinated infants who presented with acute diarrhoea at University Teaching Hospitals, Children’s Hospital in 2016, in Lusaka Zambia

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246025
Author(s):  
Julia Simwaka ◽  
Mapaseka Seheri ◽  
Gina Mulundu ◽  
Patrick Kaonga ◽  
Jason M. Mwenda ◽  
...  
Keyword(s):  
Acute Diarrhoea ◽  
Clinical Score ◽  
University Teaching ◽  
Teaching Hospitals ◽  
Mixed Infections ◽  
Rotavirus Vaccine ◽  
Vaccine Introduction ◽  
Rotavirus Vaccines ◽  
Group A ◽  
Stool Samples

Background In Zambia, before rotavirus vaccine introduction, the virus accounted for about 10 million episodes of diarrhoea, 63 000 hospitalisations and 15 000 deaths in 2015, making diarrhoea the third leading cause of death after pneumonia and malaria. In Zambia, despite the introduction of the vaccine acute diarrhoea due to rotaviruses has continued to affect children aged five years and below. This study aimed to characterise the rotavirus genotypes which were responsible for diarrhoeal infections in vaccinated infants aged 2 to 12 months and to determine the relationship between rotavirus strains and the severity of diarrhoea in 2016. Methods Stool samples from infants aged 2 to 12 months who presented to the hospital with acute diarrhoea of three or more episodes in 24 hours were tested for group A rotavirus. All positive specimens that had enough sample were genotyped using reverse transcriptase Polymerase Chain Reaction (RT-PCR). A 20-point Vesikari clinical score between 1–5 was considered as mild, 6–10 as moderate and greater or equal to 11 as severe. Results A total of 424 stool specimens were tested of which 153 (36%, 95% CI 31.5% to 40.9%) were positive for VP6 rotavirus antigen. The age-specific rotavirus infections decreased significantly (p = 0.041) from 2–4 months, 32.0% (49/118) followed by a 38.8% (70/181) infection rate in the 5–8 months’ category and subsequently dropped in the infants aged 9–12 months with a positivity rate of 27.2%. 38.5% of infants who received a single dose, 34.5% of those who received a complete dose and 45.2% (19/42) of the unvaccinated tested positive for rotavirus. The predominant rotavirus genotypes included G2P[6] 36%, G1P[8] 32%, mixed infections 19%, G2P[4] 6%, G1P[6] 4% and G9P[6] 3%. Discussion and conclusion Results suggest breakthrough infection of heterotypic strains (G2P[6] (36%), homotypic, G1P[8] (32%) and mixed infections (19%) raises concerns about the effects of the vaccination on the rotavirus diversity, considering the selective pressure that rotavirus vaccines could exert on viral populations. This data indicates that the rotavirus vaccine has generally reduced the severity of diarrhoea despite the detection of the virus strains.

scholarly journals Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013

2018 ◽  
Vol 3 ◽  
pp. 150 ◽  
Author(s):  
Betty E. Owor ◽  
Mike J. Mwanga ◽  
Regina Njeru ◽  
Robert Mugo ◽  
Mwanajuma Ngama ◽  
...  
Keyword(s):  
Temporal Fluctuations ◽  
Consensus Sequences ◽  
Vaccine Introduction ◽  
Coastal Kenya ◽  
Circulation Patterns ◽  
Sequencing Method ◽  
Group A ◽  
Wide Scale ◽  
Classification Tool ◽  
The Impact

Background: Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014.  Long-term surveillance data is important prior to wide-scale vaccine use to assess the impact on disease and to investigate the occurrence of heterotypic strains arising through immune selection. This report presents baseline data on RVA genotype circulation patterns and intra-genotype genetic diversity over a 7-year period in the pre-vaccine era in Kilifi, Kenya, from 2002 to 2004 and from 2010 to 2013. Methods: A total of 745 RVA strains identified in children admitted with acute gastroenteritis to a referral hospital in Coastal Kenya, were sequenced using the di-deoxy sequencing method in the VP4 and VP7 genomic segments (encoding P and G proteins, respectively). Sequencing successfully generated 569 (76%) and 572 (77%) consensus sequences for the VP4 and VP7 genes respectively. G and P genotypes were determined by use of BLAST and the online RotaC v2 RVA classification tool. Results: The most common GP combination was G1P[8] (51%), similar to the Rotarix® strain, followed by G9P[8] (15%) , G8P[4] (14%) and G2P[4] (5%).  Unusual GP combinations—G1P[4], G2P[8], G3P[4,6], G8P[8,14], and G12P[4,6,8]—were observed at frequencies of <5%. Phylogenetic analysis showed that the infections were caused by both locally persistent strains as evidenced by divergence of local strains occurring over multiple seasons from the global ones, and newly introduced strains, which were closely related to global strains. The circulating RVA diversity showed temporal fluctuations both season by season and over the longer-term. None of the unusual strains increased in frequency over the observation period.   Conclusions: The circulating RVA diversity showed temporal fluctuations with several unusual strains recorded, which rarely caused major outbreaks.  These data will be useful in interpreting genotype patterns observed in the region during the vaccine era.

Molecular Detection of Group A Rotavirus in under Five Years Old Children with Acute Diarrhoea Admitted to Yangon Children’s Hospital

2019 ◽  
Vol 31 (1) ◽  
pp. 87-92
Keyword(s):  
Acute Diarrhoea ◽  
Enzyme Linked Immunosorbent Assay ◽  
Viral Gastroenteritis ◽  
Cross Sectional ◽  
Under Five ◽  
Group A Rotavirus ◽  
Rotavirus Vaccination ◽  
Group A ◽  
Stool Samples ◽  
Considerable Morbidity

Rotaviruses are regarded as the most common cause of viral gastroenteritis and are responsible for considerable morbidity and mortality among children especially under five years of age worldwide. In developing countries like Myanmar, where diarrhoea is in the priority childhood disease, rotavirus surveillance and detection of rotavirus genotypes are utmost important. A hospital-based, cross-sectional descriptive study was conducted at Yangon Children‟s Hospital among under five children admitted for acute diarrhoea from January to October 2016. This study includes detection of Group A rotavirus antigen by commercial enzyme-linked immunosorbent assay (ELISA) and genotyping by multiplex RT-PCR. From a total of 488 collected samples, rotavirus antigen was detected in 219 samples (45%). Rotavirus diarrhoea was most common among the age of 6-11 months (38.8%) followed by 12-23 months (37.9%). The results showed that boys were more commonly affected than girls. Detection of rotavirus positivity was peak in February (57.6 %). Out of 219 stool samples with positive ELISA result, 40 stool samples with high optical density value were proceeded for further determination of G and P genotypes. Regarding distribution of G genotypes, the most common G genotype was G9 which comprised 45%, and that of P genotype was P[8] which comprised 92.5%. Regarding combination of G and P genotypes, the most frequent combination is G9P[8], and it constituted 42.5%. Untypable genotypes were seen in 30% of G and 2.5% of P typing. As rotavirus infection can be prevented by vaccine, WHO recommended that rotavirus vaccination should be included in national immunization program especially in countries where prevalence of rotavirus is high. The distribution of G and P genotypes is important in consideration of appropriate vaccine in pre-vaccination and evaluation of effectiveness of vaccine in post-vaccination period. Therefore, the information on currently circulating genotypes of rotavirus in this study will serve as valuable data for vaccination programme.

scholarly journals Evidence for multiple introductions of an invasive wild bee species currently under rapid range expansion in Europe

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Julia Lanner ◽  
Fabian Gstöttenmayer ◽  
Manuel Curto ◽  
Benoît Geslin ◽  
Katharina Huchler ◽  
...  
Keyword(s):  
Cluster Formation ◽  
Invasion History ◽  
European Continent ◽  
Multiple Introductions ◽  
Wild Bee ◽  
Invasion Stage ◽  
Middle Europe ◽  
History Of ◽  
Genetic Clusters ◽  
Colonization Dynamics

Abstract Background Invasive species are increasingly driving biodiversity decline, and knowledge of colonization dynamics, including both drivers and dispersal modes, are important to prevent future invasions. The bee species Megachile sculpturalis (Hymenoptera: Megachilidae), native to East-Asia, was first recognized in Southeast-France in 2008, and has since spread throughout much of Europe. The spread is very fast, and colonization may result from multiple fronts. Result To track the history of this invasion, codominant markers were genotyped using Illumina sequencing and the invasion history and degree of connectivity between populations across the European invasion axis were investigated. Distinctive genetic clusters were detected with east–west differentiations in Middle-Europe. Conclusion We hypothesize that the observed cluster formation resulted from multiple, independent introductions of the species to the European continent. This study draws a first picture of an early invasion stage of this wild bee and forms a foundation for further investigations, including studies of the species in their native Asian range and in the invaded range in North America.

scholarly journals The history of introduction of the African baobab ( Adansonia digitata , Malvaceae: Bombacoideae) in the Indian subcontinent

2015 ◽  
Vol 2 (9) ◽  
pp. 150370 ◽  
Author(s):  
Karen L. Bell ◽  
Haripriya Rangan ◽  
Christian A. Kull ◽  
Daniel J. Murphy
Keyword(s):  
West Africa ◽  
Indian Subcontinent ◽  
Central India ◽  
Adansonia Digitata ◽  
Multiple Introductions ◽  
Human Interactions ◽  
Time Period ◽  
History Of ◽  
Genetic Clusters ◽  
Southeast India

To investigate the pathways of introduction of the African baobab, Adansonia digitata , to the Indian subcontinent, we examined 10 microsatellite loci in individuals from Africa, India, the Mascarenes and Malaysia, and matched this with historical evidence of human interactions between source and destination regions. Genetic analysis showed broad congruence of African clusters with biogeographic regions except along the Zambezi (Mozambique) and Kilwa (Tanzania), where populations included a mixture of individuals assigned to at least two different clusters. Individuals from West Africa, the Mascarenes, southeast India and Malaysia shared a cluster. Baobabs from western and central India clustered separately from Africa. Genetic diversity was lower in populations from the Indian subcontinent than in African populations, but the former contained private alleles. Phylogenetic analysis showed Indian populations were closest to those from the Mombasa-Dar es Salaam coast. The genetic results provide evidence of multiple introductions of African baobabs to the Indian subcontinent over a longer time period than previously assumed. Individuals belonging to different genetic clusters in Zambezi and Kilwa may reflect the history of trafficking captives from inland areas to supply the slave trade between the fifteenth and nineteenth centuries. Baobabs in the Mascarenes, southeast India and Malaysia indicate introduction from West Africa through eighteenth and nineteenth century European colonial networks.

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