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Item T7 expression plasmids for producing a recombinant human G1P[8] rotavirus comprising RIX4414 sequences of the RV1 (Rotarix , GSK) vaccine strain(Microbiology Resource Announcements, 2023) Philip, A.A.; Agbemabiese, C.A.; Patton, J.T.; et al.The live oral rotavirus RV1 (Rotarix) vaccine is formulated from the human G1P[8] RIX4414 virus. Based on RIX4414 sequences, T7 expression plasmids were constructed that supported recovery of recombinant RIX4414-like viruses by reverse genetics. These plasmids will advance the study of the RV1 vaccine, possibly allowing improvements to its efficacy.Item Vaccine value profile for norovirus(Vaccine, 2023) Armah, G.; Vinjé, J.; Lopman, B.A.; et al.Norovirus is attributed to nearly 1 out of every 5 episodes of diarrheal disease globally and is estimated to cause approximately 200,000 deaths annually worldwide, with 70,000 or more among children in devel oping countries. Noroviruses remain a leading cause of sporadic disease and outbreaks of acute gastroen teritis even in industrialized settings, highlighting that improved hygiene and sanitation alone may not be fully effective in controlling norovirus. Strengths in global progress towards a Norovirus vaccine include a diverse though not deep pipeline which includes multiple approaches, including some with proven technology platforms (e.g., VLP-based HPV vaccines). However, several gaps in knowledge persist, including a fulsome mechanistic understanding of how the virus attaches to human host cells, internal izes, and induces disease.Item Prevalence, Awareness, and Control of Hypertensive Disorders amongst Pregnant Women Seeking Healthcare in Ghana(Hindawi Journal of Pregnancy, 2023) Boachie-Ansah, P; Anto, B.P.; Asiamah, M.; et al.Hypertensive disorders in pregnancy (HDPs) are no longer seen as “transitory diseases cured by delivery.” It accounts for up to 50% of maternal deaths. Information concerning HDPs is less in developing countries like Ghana. This study was conducted to find out the prevalence, awareness, risk factors, control, and the birth outcomes of HDPs. This was a retrospective cohort study conducted among pregnant women seeking care in selected health facilities in the Ashanti Region. Data on demographics, HDPs, and its associated birth outcomes were collected. Logistic regression models were used to examine the association of the independent variables with HDPs. The burden of HDPs was 37.2% among the 500 mothers enrolled with chronic hypertension superimposed with preeclampsia accounting for 17.6%, chronic hypertension, 10.2%, and preeclampsia 6.8% whilst gestational hypertension was 2.6%. It was observed that 44% (220) of the mothers had excellent knowledge on HDPs. Oral nifedipine and methyldopa were frequently used for HDP management, and it resulted in a significant reduction in HDP burden from 37.2% to 26.6%. Factors that influenced the increased risk of HDPs were grand multigravida (AOR = 4 53; CI = 1 42–14.42), family history of hypertension (AOR = 3 61; CI = 1 89–6.90), and the consumption of herbal preparations (AOR = 2 92; CI = 1 15–7.41) and alcohol (AOR = 4 10; CI = 1 34-12.62) during pregnancy. HDPs increased the risk of preterm delivery (AOR = 2 66; CI = 1 29–5.89), stillbirth (AOR = 12 47; CI = 2 72–57.24), and undergoing caesarean section (AOR = 1 70; CI = 1 10–2.61) amongst mothers during delivery. The burden of HDPs is high amongst pregnant mothers seeking care in selected facilities. There is the need for intensified campaign on HDPs in the Ashanti Region of Ghana.Item Prevalence, Awareness, and Control of Hypertensive Disorders amongst Pregnant Women Seeking Healthcare in Ghana(Journal of Pregnancy, 2023) Boachie-Ansah, P.; Anto, B.P.; Asiamah, M.; et al.Hypertensive disorders in pregnancy (HDPs) are no longer seen as “transitory diseases cured by delivery.” It accounts for up to 50% of maternal deaths. Information concerning HDPs is less in developing countries like Ghana. This study was conducted to find out the prevalence, awareness, risk factors, control, and the birth outcomes of HDPs. This was a retrospective cohort study conducted among pregnant women seeking care in selected health facilities in the Ashanti Region. Data on demographics, HDPs, and its associated birth outcomes were collected. Logistic regression models were used to examine the association of the independent variables with HDPs. The burden of HDPs was 37.2% among the 500 mothers enrolled with chronic hypertension superimposed with preeclampsia accounting for 17.6%, chronic hypertension, 10.2%, and preeclampsia 6.8% whilst gestational hypertension was 2.6%. It was observed that 44% (220) of the mothers had excellent knowledge on HDPs. Oral nifedipine and methyldopa were frequently used for HDP management, and it resulted in a significant reduction in HDP burden from 37.2% to 26.6%. Factors that influenced the increased risk of HDPs were grand multigravida (AOR = 4 53; CI = 1 42–14.42), family history of hypertension (AOR = 3 61; CI = 1 89–6.90), and the consumption of herbal preparations (AOR = 2 92; CI = 1 15–7.41) and alcohol (AOR = 4 10; CI = 1 34-12.62) during pregnancy. HDPs increased the risk of preterm delivery (AOR = 2 66; CI = 1 29–5.89), stillbirth (AOR = 12 47; CI = 2 72–57.24), and undergoing caesarean section (AOR = 1 70; CI = 1 10–2.61) amongst mothers during delivery. The burden of HDPs is high amongst pregnant mothers seeking care in selected facilities. There is the need for intensified campaign on HDPs in the Ashanti Region of Ghana.Item Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi(Oxford University Press., 2023) Dennis, F. E.; Chimwemwe, M.; Akuzike, B.; et al.Abstract G3 rotaviruses rank among the most common rotavirus strains worldwide in humans and animals. However, despite a robust long term rotavirus surveillance system from 1997 at Queen Elizabeth Central Hospital in Blantyre, Malawi, these strains were only detected from 1997 to 1999 and then disappeared and re-emerged in 2017, 5 years after the introduction of the Rotarix rotavirus vaccine. Here, we analysed representative twenty-seven whole genome sequences (G3P[4], n = 20; G3P[6], n = 1; and G3P[8], n = 6) randomly selected each month between November 2017 and August 2019 to understand how G3 strains re-emerged in Malawi. We found four geno type constellations that were associated with the emergent G3 strains and co-circulated in Malawi post-Rotarix vaccine introduction: G3P[4] and G3P[6] strains with the DS-1-like genetic backbone genes (G3-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and G3-P[6]-I2-R2-C2-M2-A2- N2-T2-E2-H2), G3P[8] strains with the Wa-like genetic backbone genes (G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1), and reassortant G3P[4] strains consisting of the DS-1-like genetic backbone genes and a Wa-like NSP2 (N1) gene (G3-P[4]-I2-R2-C2-M2-A2-N1-T2-E2-H2). Time resolved phylogenetic trees demonstrated that the most recent common ancestor for each ribonucleic acid (RNA) segment of the emer gent G3 strains was between 1996 and 2012, possibly through introductions from outside the country due to the limited genetic similarity with G3 strains which circulated before their disappearance in the late 1990s. Further genomic analysis revealed that the reassortant DS-1-like G3P[4] strains acquired a Wa-like NSP2 genome segment (N1 genotype) through intergenogroup reassortment; an artiodactyl like VP3 through intergenogroup interspecies reassortment; and VP6, NSP1, and NSP4 segments through intragenogroup reassortment likely before importation into Malawi. Additionally, the emergent G3 strains contain amino acid substitutions within the antigenic regions of the VP4 proteins which could potentially impact the binding of rotavirus vaccine–induced antibodies. Altogether, our fnd ings show that multiple strains with either Wa-like or DS-1-like genotype constellations have driven the re-emergence of G3 strains. The fndings also highlight the role of human mobility and genome reassortment events in the cross-border dissemination and evolution of rotavirus strains in Malawi necessitating the need for long-term genomic surveillance of rotavirus in high disease–burden settings to inform disease prevention and controlItem The Full Impact of Rotavirus Vaccines in Africa Has Yet to Be Realized(Clinical Infectious Diseases, 2023) Steele, A.D.; Armah, G.E.; Mwenda, J.M.; Kirkwood, C.D.Africa bears the brunt of diarrheal mortality globally. Rotavirus vaccination rates are high across the continent and demonstrate impact on diarrheal disease reduction. Nevertheless, there is room for significant improvement in managing rotavirus vaccine coverage, in access to recognized public services such as appropriate medical care, including oral rehydration therapy and improved water and sanitation.Item Evolutionary changes between pre- and post-vaccine South African group A G2P[4] rotavirus strains, 2003–2017(Microbiology Society, 2022) Mwangi, P.N.; Page, N.A.; Seheri, M.L.; Mphahlele, M.J.; Nadan, S.; Esona, M.D.; Kumwenda, B.; Kamng’ona, A.W.; Donato, C.M.; Steele, D.A.; Ndze, V.N.; Dennis, F.E.; Jere, K.C.; Nyaga, M.M.The transient upsurge of G2P[4] group A rotavirus (RVA) after Rotarix vaccine introduction in several countries has been a matter of concern. To gain insight into the diversity and evolution of G2P[4] strains in South Africa pre and post-RVA vaccination introduction, whole-genome sequencing was performed for RVA positive faecal specimens collected between 2003 and 2017 and samples previously sequenced were obtained from GenBank (n=103; 56 pre- and 47 post-vaccine). Pre-vaccine G2 sequences predominantly clustered within sub- lineage IVa-1. In contrast, post-vaccine G2 sequences clustered mainly within sub-lineage IVa-3, whereby a radical amino acid (AA) substitution, S15F, was observed between the two sub- lineages. Pre-vaccine P[4] sequences predominantly segregated within sub-lineage IVa while post-vaccine sequences clustered mostly within sub-lineage IVb, with a radical AA substitution R162G. Both S15F and R162G occurred outside recognised antigenic sites. The AA residue at position 15 is found within the signal sequence domain of Viral Protein 7 (VP7) involved in translocation of VP7 into endoplasmic reticulum during infection process. The 162 AA residue lies within the hemagglutination domain of Viral Protein 4 (VP4) engaged in interaction with sialic acid- containing structure during attachment to the target cell. Free energy change analysis on VP7 indicated accumulation of stable point mutations in both antigenic and non-antigenic regions. The segregation of South African G2P[4] strains into pre and post-vaccination sub-lineages is likely due to erstwhile hypothesized step-wise lineage/sub-lineage evolution of G2P[4] strains rather than RVA vaccine introduction. Our findings reinforce the need for continuous whole- genome RVA surveillance and investigation of contribution of AA substitutions in understanding the dynamic G2P[4] epidemiology.Item Enterotoxigenic Escherichia coli (ETEC) vaccines: Priority activities to enable product development, licensure, and global access(Elsevier, 2021) Khalil, I.; Walker, R.; Porter, C.K.; Muhib, F.; Chilengi, R.; Cravioto, A.; Guerrant, R.; Svennerholm, A.; Qadri, F.; Baqar, S.; Kosek, M.; Kang, G.; Lanata, C.; Armah, G.; Wierzba, T.; Hasso-Agopsowicz, M.; Giersing, B.; Bourgeois, L.A.Diarrhoeal disease attributable to enterotoxigenic Escherichia coli (ETEC) causes substantial morbidity and mortality predominantly in paediatric populations in low- and middle-income countries. In addition to acute illness, there is an increasing appreciation of the long-term consequences of enteric infections, including ETEC, on childhood growth and development. Provision of potable water and sanitation and appropriate clinical care for acute illness are critical to reduce the ETEC burden. However, these interven tions are not always practical and may not achieve equitable and sustainable coverage. Vaccination may be the most cost-effective and equitable means of primary prevention; however, additional data are needed to accelerate the investment and guide the decision-making process for ETEC vaccines. First, to understand and quantify the ETEC disease burden, additional data are needed on the associa tion between ETEC infection and physical and cognitive stunting as well as delayed educational attain ment. Furthermore, the role of inappropriate or inadequate antibiotic treatment of ETEC-attributable diarrhoea may contribute to the development of antimicrobial resistance (AMR) and needs further eluci dation. An ETEC vaccine that mitigates acute diarrhoeal illness and minimizes the longer-term disease manifestations could have significant public health impact and be a cost-effective countermeasure. Herein we review the ETEC vaccine pipeline, led by candidates compatible with the general parameters of the Preferred Product Characteristics (PPC) recently developed by the World Health Organization. Additionally, we have developed an ETEC Vaccine Development Strategy to provide a framework to underpin priority activities for researchers, funders and vaccine manufacturers, with the goal of address ing globally unmet data needs in the areas of research, product development, and policy, as well as com mercialization and delivery. The strategy also aims to guide prioritization and co-ordination of the priority activities needed to minimize the timeline to licensure and use of ETEC vaccines, especially in in low- and middle-income countries, where they are most urgently neededItem Report of the 1st African Enteric Viruses Genome Initiative data and Bioiniformatics workshop on whole genome analysis of some African rotavirus strains held in Bloemfontein, South Africa(Vaccine, 2020-07-22) Dennis, F.E.; Nyaga, M.M.; Sabiu, S.; Ndze, V.N.; Jere, K.C.The University of the Free State - Next Generation Sequencing (NGS) Unit, Bloemfontein, South Africa, hosted a data and bioinformatics workshop from 19 to 22 June 2018. The workshop was coordinated by the African Enteric Viruses Genome Initiative (AEVGI) with support from the Bill & Melinda Gates Foundation. The event introduced technologies in NGS and data analysis with focus on the rotavirus (RV) genome. The workshop fostered interactions and networking between professionals, scientific experts, technicians and students. The courses provided an overview of RV diarrhoea and its burden in Africa, while highlighting the key resources and methodologies in NGS and advanced bioinformatics in deciphering vaccine impact. It was concluded that, despite the reported significant decline in RV associated-diarrhoea mortality and morbidity in Africa due to RV vaccine impact, the need for continuous surveillance and genomic characterization to better understand the ever-changing dynamics of RV strains is imperative.Item Modeling of rotavirus transmission dynamics and impact of vaccination in Ghana(Vaccine, 2020-06-05) Armah, G.E.; Asare, E.O.; Al-Mamun, M.A.; Lopman, B.A.; Parashar, U.D.; Binka, F.; Pitzer, V.E.Background: Rotavirus incidence remains relatively high in low-income countries (LICs) compared to high-income countries (HICs) after vaccine introduction. Ghana introduced monovalent rotavirus vaccine in April 2012 and despite the high coverage, vaccine performance has been modest compared to developed countries. The predictors of low vaccine effectiveness in LICs are poorly understood, and the drivers of subnational heterogeneity in rotavirus vaccine impact are unknown. Methods: We used mathematical models to investigate variations in rotavirus incidence in children <5 years old in Ghana. We fit models to surveillance and case-control data from three different hospitals: Korle-Bu Teaching Hospital in Accra, Komfo Anokye Teaching Hospital in Kumasi, and War Memorial Hospital in Navrongo. The models were fitted to both pre- and post-vaccine data to estimate parameters describing the transmission rate, waning of maternal immunity, and vaccine response rate. Results: The seasonal pattern and age distribution of rotavirus cases varied among the three study sites in Ghana. Our model was able to capture the spatio-temporal variations in rotavirus incidence across the three sites and showed good agreement with the age distribution of observed cases. The rotavirus transmission rate was highest in Accra and lowest in Navrongo, while the estimated duration of maternal immunity was longer (~5 months) in Accra and Kumasi and shorter (~3 months) in Navrongo. The proportion of infants who responded to the vaccine was estimated to be high in Accra and Kumasi and low in Navrongo. Conclusions: Rotavirus vaccine impact varies within Ghana. A low vaccine response rate was estimated for Navrongo, where rotavirus is highly seasonal and incidence limited to a few months of the year. Our findings highlight the need to further explore the relationship between rotavirus seasonality, maternal immunity, and vaccine response rate to determine how they influence vaccine effectiveness and to develop strategies to improve vaccine impact.Item Endemic Burkitt lymphoma – an aggressive childhood cancer linked to Plasmodium falciparum exposure, but not to exposure to other malaria parasites(JOURNAL OF PATHOLOGY, MICROBIOLOGY AND IMMUNOLOGY, 2020-03-04) Smith‐Togobo, C.; Quintana, M.DP.; Moormann, A.; Hviid, L.Burkitt lymphoma (BL) is an aggressive non‐Hodgkin lymphoma. The prevalence of BL is ten‐fold higher in areas with stable transmission of Plasmodium falciparum malaria, where it is the most common childhood cancer, and is referred to as endemic BL (eBL). In addition to its association with exposure to P. falciparum infection, eBL is strongly associated with Epstein–Barr virus (EBV) infection (>90%). This is in contrast to BL as it occurs outside P. falciparum ‐endemic areas (sporadic BL), where only a minority of the tumours are EBV‐positive. Although the striking geographical overlap in the distribution of eBL and P. falciparum was noted shortly after the first detailed description of eBL in 1958, the molecular details of the interaction between malaria and eBL remain unresolved. It is furthermore unexplained why exposure to P. falciparum appears to be essentially a prerequisite to the development of eBL, whereas other types of malaria parasites that infect humans have no impact. In this brief review, we summarize how malaria exposure may precipitate the malignant transformation of a B‐cell clone that leads to eBL, and propose an explanation for why P. falciparum uniquely has this capacity.Item Next-generation sequencing of a human-animal reassortant G6P[14] rotavirus A strain from a child hospitalized with diarrhoea(Archives of Virology, 2020-02-10) Damanka, S.A.; Dennis, F.E.; Lartey, B.L.; Nyarko, K.M.; Agbemabiese, C.A.; Armah, G.E.We previously reported the VP4 and the VP7 genotypes of the first G6P[14] rotavirus strain (RVA/Human-wt/GHA/M0084/2010/G6P[14]) from the stool of an infant with diarrhoea in Ghana. In the current study, we obtained the complete genome sequences using Illumina MiSeq next-generation sequencing to enable us to determine the host species origin of the genes by phylogenetic analysis. The genotype constellation was G6-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3. Phylogenetic analysis showed that M0084 was a reassortant strain from RVAs of both artiodactyl and human host species origin. The level of sequence identity of the individual genes of M0084 to other sequences in the GenBank ranged from 95.2 to 99.5%; however, there was no single strain from the GenBank database with a complete genome sequence that was highly similar to that of M0084. To help trace the source of such unique gene pools being introduced into human RVAs, it will be useful to examine RVA sequences from potential reservoirs such as sheep and goats, which are common domestic animals in this locality.Item Risk Factors Associated with Increased Mortality from Intussusception in African Infants(Journal of Pediatric Gastroenterology and Nutrition, 2019-09-11) Armah, G.; Pindyck, T.; Parashar, U.; Mwenda, J.; Tadesse, A.; Omore, R.; Ngwira, B.; Jani, B.; Mpabalwani, E.; Mbuwayesango, B.; Tate, J.OBJECTIVES: Morbidity and mortality from intussusception, the leading cause of bowel obstruction in infants, is higher in Africa than in other regions of the world, but the reasons have not been well examined. We sought to identify risk and protective factors associated with death or intestinal resection following intussusception. METHODS: Infants with intussusception from 7 sub-Saharan African countries (Ethiopia, Ghana, Kenya, Malawi, Tanzania, Zambia, and Zimbabwe) were enrolled through active, hospital-based surveillance from February 2012 to December 2016. We examined demographic, clinical, and socioeconomic factors associated with death or intestinal resection following intussusception, using multivariable logistic regression. RESULTS: A total of 1017 infants <1 year of age with intussusception were enrolled. Overall, 13% of children (133/1017) died during the hospitalization, and 48% (467/966) required intestinal resection. In multivariable analyses, female sex (OR 1.8, 95% CI 1.2-3.3), longer duration of symptoms prior to presentation (OR 1.1; 95% CI 1.0-1.2), and undergoing intestinal resection (OR 3.4; 95% CI 1.9-6.1) were associated with death after intussusception. Diagnosis by ultrasound or enema (OR 0.4; 95% CI 0.3-0.7), and employment of a household member (OR 0.7; 95% CI 0.4-1.0) were protective against intestinal resection. CONCLUSION: Delays in hospital presentation and female sex were significantly associated with death, whereas higher socioeconomic status and availability of radiologic diagnosis reduced likelihood of undergoing resection. Efforts should be intensified to improve the awareness, diagnosis, and management of intussusception in sub-Saharan African countries to reduce morbidity and mortality from intussusception in these resource limited settings.Item Genetic analysis of Ghanaian G1P[8] and G9P [8] rotavirus A strains reveals the impact of P [8] VP4 gene polymorphism on P-genotyping(PLOS ONE, 2019-06-10) Damanka, S.A.; Agbemabiese, C.A.; Dennis, F.E.; Lartey, 'B.L.; Adiku, T.K.; Enweronu-Laryea, C.C.; Armah, G.E.The World Health Organisation rotavirus surveillance networks have documented and shown eclectic geographic and temporal diversity in circulating G- and P- genotypes identified in children <5 years of age. To effectively monitor vaccine performance and effectiveness, robust molecular and phylogenetic techniques are essential to detect novel strain variants that might emerge due to vaccine pressure. This study inferred the phylogenetic history of the VP7 and VP4 genes of previously non-typeable strains and provided insight into the diversity of P[8] VP4 sequences which impacted the outcome of our routine VP4 genotyping method. Near-full-length VP7 gene and the VP8* fragment of the VP4 gene were obtained by Sanger sequencing and genotypes were determined using RotaC v2.0 web-based genotyping tool. The genotypes of the 57 rotavirus-positive samples with sufficient stool was determined. Forty-eight of the 57 (84.2%) had the P[8] specificity, of which 43 (89.6%) were characterized as P[8]a subtype and 5 (10.4%) as the rare OP354-like subtype. The VP7 gene of 27 samples were successfully sequenced and their G-genotypes confirmed as G1 (18/27) and G9 (9/27). Phylogenetic analysis of the P[8]a sequences placed them in subcluster IIIc within lineage III together with contemporary G1P[8], G3P[8], G8P[8], and G9P[8] strains detected globally from 2006–2016. The G1 VP7 sequences of the study strains formed a monophyletic cluster with African G1P[8] strains, previously detected in Ghana and Mali during the RotaTeq vaccine trial as well as Togo. The G9 VP7 sequences of the study strains formed a monophyletic cluster with contemporary African G9 sequences from neighbouring Burkina Faso within the major sub-cluster of lineage III. Mutations identified in the primer binding region of the VP8* sequence of the Ghanaian P[8]a strains may have resulted in the genotyping failure since the newly designed primer successfully genotyped the previously non-typeable P[8] strains. In summary, the G1, G9, and P[8]a sequences were highly similar to contemporary African strains at the lineage level. The study also resolved the methodological challenges of the standard genotyping techniques and highlighted the need for regular evaluation of the multiplex PCR-typing method especially in the post-vaccination era. The study further highlights the need for regions to start using sequencing data from local rotavirus strains to design and update genotyping primers.Item Timeliness of rotavirus vaccination at sentinel sites in four early-adopter African countries(Vaccine, 2019-08-07) Armah, G.; Pindyck, T.; Tate, J.E.; Bonkoungou, I.J.O.; Mujuru, H.A.; Rugambwa, C.; Mwenda, J.M.; Parashar, U.Background: The majority of countries with the highest rotavirus-associated death rates are in sub- Saharan Africa. In 2009, the World Health Organization (WHO) recommended routine vaccination against rotavirus worldwide, with unique age recommendations to administer the first dose before 15 weeks of age and last dose by 32 weeks of age. These age restrictions were relaxed in January 2013, but they may still lead to lower rotavirus vaccine coverage. Methods: Children age-eligible to have received rotavirus vaccine that were enrolled in Ghana, Zimbabwe, Rwanda or Burkina Faso0s active rotavirus surveillance platforms from 2013 to 2017 and had a stool specimen that tested rotavirus-negative were included in the analysis. Proportion vaccinated and timeliness of rotavirus vaccine versus DTPw-HepB-Hib (pentavalent) first dose and last dose were compared at weeks 15 and 32, respectively, using Chi-square analyses. Odds ratios were calculated using logistic regression. Results: Among children who received rotavirus vaccine dose 1, 96–99% received this dose by 15 weeks of age and among children who received the last dose, 98–99% received it by 32 weeks of age. In all four countries, there was no significant difference in the proportion of children who received first dose rotavirus versus pentavalent vaccine by week 15, or last dose rotavirus versus concordant pentavalent vaccine by week 32. Delayed administration of first dose pentavalent vaccine was significantly associated with missing first dose of rotavirus vaccine in 3 of the 4 countries studied, although delays in administration were rare (1–4%). Conclusions: Rotavirus vaccination was timely among sentinel sites in these four early rotavirus vaccineintroducing countries in Africa. Late presentation for vaccination may have resulted in some children with access to care missing first dose of rotavirus vaccine; however, vaccination delays were infrequent and therefore the potential impact of the age restrictions on overall proportion vaccinated was minimal.Item Genetic analysis of Ghanaian G1P[8] and G9P [8] rotavirus A strains reveals the impact of P [8] VP4 gene polymorphism on P-genotyping(PLOS ONE, 2019-06-10) Damanka, S.A.; Agbemabiese, C.A.; Dennis, F.E.; Lartey, B.L.; Adiku, T.K.; Enweronu-Laryea, C.C.; Armah, G.E.The World Health Organisation rotavirus surveillance networks have documented and shown eclectic geographic and temporal diversity in circulating G- and P- genotypes identified in children <5 years of age. To effectively monitor vaccine performance and effectiveness, robust molecular and phylogenetic techniques are essential to detect novel strain variants that might emerge due to vaccine pressure. This study inferred the phylogenetic history of the VP7 and VP4 genes of previously non-typeable strains and provided insight into the diversity of P[8] VP4 sequences which impacted the outcome of our routine VP4 genotyping method. Near-full-length VP7 gene and the VP8* fragment of the VP4 gene were obtained by Sanger sequencing and genotypes were determined using RotaC v2.0 web-based genotyping tool. The genotypes of the 57 rotavirus-positive samples with sufficient stool was determined. Forty-eight of the 57 (84.2%) had the P[8] specificity, of which 43 (89.6%) were characterized as P[8]a subtype and 5 (10.4%) as the rare OP354-like subtype. The VP7 gene of 27 samples were successfully sequenced and their G-genotypes confirmed as G1 (18/27) and G9 (9/27). Phylogenetic analysis of the P[8]a sequences placed them in subcluster IIIc within lineage III together with contemporary G1P[8], G3P[8], G8P[8], and G9P[8] strains detected globally from 2006–2016. The G1 VP7 sequences of the study strains formed a monophyletic cluster with African G1P[8] strains, previously detected in Ghana and Mali during the RotaTeq vaccine trial as well as Togo. The G9 VP7 sequences of the study strains formed a monophyletic cluster with contemporary African G9 sequences from neighbouring Burkina Faso within the major sub-cluster of lineage III. Mutations identified in the primer binding region of the VP8* sequence of the Ghanaian P[8]a strains may have resulted in the genotyping failure since the newly designed primer successfully genotyped the previously non-typeable P[8] strains. In summary, the G1, G9, and P[8]a sequences were highly similar to contemporary African strains at the lineage level. The study also resolved the methodological challenges of the standard genotyping techniques and highlighted the need for regular evaluation of the multiplex PCR-typing method especially in the post-vaccination era. The study further highlights the need for regions to start using sequencing data from local rotavirus strains to design and update genotyping primers.Item Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains(PLoS ONE, 2019-05-10) Agbemabiese, C.A.; Nakagom, T.; Damanka, S.A.; Dennis, F.E.; Lartey, B.L.; Armah, G.E.; Nakagomi, O.Recent increase in the detection of unusual G1P[8], G3P[8], G8P[8], and G9P[4] Rotavirus A (RVA) strains bearing the DS-1-like constellation of the non-G, non-P genes (hereafter referred to as the genotype 2 backbone) requires better understanding of their evolutionary relationship. However, within a genotype, there is lack of a consensus lineage designation framework and a set of common sequences that can serve as references. Phylogenetic analyses were carried out on over 8,500 RVA genotype 2 genes systematically retrieved from the rotavirus database within the NCBI Virus Variation Resource. In line with previous designations, using pairwise comparison of cogent nucleotide sequences and stringent bootstrap support, reference lineages were defined. This study proposes a lineage framework and provides a dataset ranging from 34 to 145 sequences for each genotype 2 gene for orderly lineage designation of global genotype 2 genes of RVAs detected in human and animals. The framework identified five to 31 lineages depending on the gene. The least number of lineages (five to seven) were observed in genotypes A2 (NSP1), T2 (NSP3) and H2 (NSP5) which are limited to human RVA whereas the most number of lineages (31) was observed in genotype E2 (NSP4). Sharing of the same lineage constellations of the genotype 2 backbone genes between recently-emerging, unusual G1P[8], G3P[8], G8P[8] and G9P[4] reassortants and many contemporary G2P[4] strains provided strong support to the hypothesis that unusual genotype 2 strains originated primarily from reassortment events in the recent past involving contemporary G2P[4] strains as one parent and ordinary genotype 1 strains or animal RVA strains as the other. The lineage framework with selected reference sequences will help researchers to identify the lineage to which a given genotype 2 strain belongs, and trace the evolutionary history of common and unusual genotype 2 strains in circulation.Item Whole genome characterization and evolutionary analysis of OP354-like P[8] Rotavirus A strains isolated from Ghanaian children with diarrhoea(PLOS ONE, 2019-05-30) Damanka, S.A.; Kwofie, S.; Dennis, F.E.; Lartey, B.L.; Agbemabiese, C.A.; Doan, Y.H.; Adiku, T.K.; Katayama, K.; Enweronu-Laryea, C.C.; Armah, G.E.In 2010, the rare OP354-like P[8]b rotavirus subtype was detected in children less than 2 years old in Ghana. In this follow-up study, to provide insight into the evolutionary history of the genome of Ghanaian P[8]b strains RVA/Human-wt/GHA/GHDC949/2010/G9P[8] and RVA/Human-wt/GHA/GHM0094/2010/G9P[8] detected in an infant and a 7-month old child hospitalised for acute gastroenteritis, we sequenced the complete genome using both Sanger sequencing and Illumina MiSeq technology followed by phylogenetic analysis of the near-full length sequences. Both strains possessed the Wa-like/genotype 1 constellation G9P[8]b-I1-R1-C1-M1-A1-N1-T1-E1-H1. Sequence comparison and phylogenetic inference showed that both strains were identical at the lineage level throughout the 11 genome segments. Their VP7 sequences belonged to the major sub-lineage of the G9-lineage III whereas their VP4 sequences belonged to P[8]b cluster I. The VP7 and VP4 genes of the study strains were closely related to a Senegalese G9P[8]b strain detected in 2009. In the remaining nine genome segments, both strains consistently clustered together with Wa-like RVA strains possessing either P[8]a or P[8]b mostly of African RVA origin. The introduction of a P[8]b subtype VP4 gene into the stable Wa-like strain backbone may result in strains that might propagate easily in the human population, with a potential to become an important public health concern, especially because it is not certain if the monovalent rotavirus vaccine (Rotarix) used in Ghana will be efficacious against such strains. Our analysis of the full genomes of GHM0094 and GHDC949 adds to knowledge of the genetic make-up and evolutionary dynamics of P[8]b rotavirus strainsItem Efficacy of two PBO long lasting insecticidal nets against natural populations of Anopheles gambiae s.l. in experimental huts, Kolokopé, Togo(PLoS ONE, 2018-07) Ketoh, G.K.; Ahadji-Dabla, K.M.; Chabi, J.; Amoudji, A.D.; Apetogbo, G.Y.; Awokou, F.; Glitho, I.A.LLINs containing an insecticide plus the synergist, piperonyl butoxide (PBO) have been designed for increased efficacy against pyrethroid-resistant malaria vectors. In this study, two LLINs with PBO, PermaNet® 3.0 and Olyset® Plus, and a pyrethroid-only LLIN, Yorkool®, were evaluated in experimental huts against a free-flying, wild population of Anopheles gambiae s.l. in Kolokopé, a cotton cultivated area of Togo. WHO susceptibility tube tests and subsequent molecular assays determine the An. gambiae s.l. populations to be resistant to pyrethroids and DDT with both target site kdr and metabolic resistance mechanisms involved in the resistance observed. Anopheles gambiae s.s. and An. coluzzi were present in sympatry though the kdr (L1014F) mutation was observed at a higher frequency in An. gambiae s.s. The experimental hut results showed that both PermaNet® 3.0 and Olyset® Plus nets induced similar levels of deterrence, exophily, and reduced blood feeding rate against wild An. gambiae s.l. in contrast to the pyrethroid only LLIN, Yorkool®. The proportion of wild An. gambiae s.l. killed by unwashed PermaNet® 3.0 was significantly higher than unwashed Olyset® Plus (corrected mortality 80.5% compared to 66.6%). Similar blood feeding inhibition rates were observed for unwashed PermaNet® 3.0 and Olyset® Plus; however, PermaNet® 3.0 washed 20 times demonstrated significantly higher blood feeding inhibition rate than Olyset® Plus washed 20 times (91.1% compared with 85.6% respectively). Yorkool® performed the worst for all the parameters evaluated. In an area of pyrethroid resistance of An. gambiae s.l involving kdr target site and metabolic resistance mechanisms, LLINs with PBO can provide additional protection in terms of reduction in blood feeding and increase in mosquito mortality compared to a pyrethroid-only net, and should be considered in malaria vector control strategies.Item Identification of Amino Acid Substitutions Within the VP7 Genes of G2 Rotavirus Strains in Ghana(The Pediatric infectious disease journal, 2018-11) Damanka, S.A.; Agbemabiese, C.A.; Lartey, B.L.; Dennis, F.E.; Asamoah, F.K.; Adiku, T.K.; Enweronu-Laryea, C.C.; Sagoe, K.W.; Ofori, M.F.; Armah, G.E.We used the dideoxynucleotide chain termination method to determine the strains of nine non-typeable rotavirus enzyme immunoassay–positive samples, which were identified as G2. We detected nucleotide changes in the primer-binding region and amino acid substitutions within the VP7 protein of the G2 rotavirus strains. Genotyping primers need to be updated regularly.