The Evolution of Post-Vaccine G8P[4] Group a Rotavirus Strains in Rwanda; Notable Variance at the Neutralization Epitope Sites.

Africa has a high level of genetic diversity of rotavirus strains, which is suggested to be a possible reason contributing to the suboptimal effectiveness of rotavirus vaccines in this region. One strain that contributes to this rotavirus diversity in Africa is the G8P[4]. This study aimed to elucidate the entire genome and evolution of Rwandan G8P[4] strains. Illumina sequencing was performed for twenty-one Rwandan G8P[4] rotavirus strains. Twenty of the Rwandan G8P[4] strains had a pure DS-1-like genotype constellation, and one strain had a reassortant genotype constellation. Notable radical amino acid differences were observed at the neutralization sites when compared with cognate regions in vaccine strains potentially playing a role in neutralization escape. Phylogenetic analysis revealed that the closest relationship was with East African human group A rotavirus (RVA) strains for five of the genome segments. Two genome sequences of the NSP4 genome segment were closely related to bovine members of the DS-1-like family. Fourteen VP1 and eleven VP3 sequences had the closest relationships with the RotaTeq™ vaccine WC3 bovine genes. These findings suggest that the evolution of VP1 and VP3 might have resulted from reassortment events with RotaTeq™ vaccine WC3 bovine genes. The close phylogenetic relationship with East African G8P[4] strains from Kenya and Uganda suggests co-circulation in these countries. These findings highlight the need for continued whole-genomic surveillance to elucidate the evolution of G8P[4] strains, especially after the introduction of rotavirus vaccination.

Genomic Analysis of Rwandan G9P[8] Rotavirus Strains Pre- and Post-RotaTeq® Vaccine Reveals Significant Distinct Sub-Clustering in a Post-Vaccination Cohort.

Although the introduction of rotavirus vaccines has substantially contributed to the reduction in rotavirus morbidity and mortality, concerns persist about the re-emergence of variant strains that might alter vaccine effectiveness in the long term. The G9 strains re-emerged in Africa during the mid-1990s and have more recently become predominant in some countries, such as Ghana and Zambia. In Rwanda, during the 2011 to 2015 routine surveillance period, G9P[8] persisted during both the pre- and post-vaccine periods. The pre-vaccination cohort was based on the surveillance period of 2011 to 2012, and the post-vaccination cohort was based on the period of 2013 to 2015, excluding 2014. The RotaTeq® vaccine that was first introduced in Rwanda in 2012 is genotypically heterologous to Viral Protein 7 (VP7) G9. This study elucidated the whole genome of Rwandan G9P[8] rotavirus strains pre- and post-RotaTeq® vaccine introduction. Fecal samples from Rwandan children under the age of five years (pre-vaccine n = 23; post-vaccine n = 7), conventionally genotyped and identified as G9P[8], were included. Whole-genome sequencing was then performed using the Illumina® MiSeq platform. Phylogenetic analysis and pair-wise sequence analysis were performed using MEGA6 software. Distinct clustering of three post-vaccination study strains was observed in all 11 gene segments, compared to the other Rwandan G9P[8] study strains. Specific amino acid differences were identified across the gene segments of these three 2015 post-vaccine strains. Important amino acid differences were identified at position N242S in the VP7 genome segment of the three post-vaccine G9 strains compared to the other G9 strains. This substitution occurs at a neutralization epitope site and may slightly affect protein interaction at that position. These findings indicate that the Rwandan G9P[8] strains revealed a distinct sub-clustering pattern among post-vaccination study strains circulating in Rwanda, with changes at neutralization epitopes, which may play a role in neutralization escape from vaccine candidates. This emphasizes the need for continuous whole-genome surveillance to better understand the evolution and epidemiology of the G9P[8] strains post-vaccination.

Whole genome and in-silico analyses of G1P[8] rotavirus strains from pre- and post-vaccination periods in Rwanda.

Rwanda was the first low-income African country to introduce RotaTeq vaccine into its Expanded Programme on Immunization in May 2012. To gain insights into the overall genetic make-up and evolution of Rwandan G1P[8] strains pre- and post-vaccine introduction, rotavirus positive fecal samples collected between 2011 and 2016 from children under the age of 5 years as part of ongoing surveillance were genotyped with conventional RT-PCR based methods and whole genome sequenced using the Illumina MiSeq platform. From a pool of samples sequenced (n = 158), 36 were identified as G1P[8] strains (10 pre-vaccine and 26 post-vaccine), of which 35 exhibited a typical Wa-like genome constellation. However, one post vaccine strain, RVA/Human-wt/RWA/UFS-NGS:MRC-DPRU442/2012/G1P[8], exhibited a RotaTeq vaccine strain constellation of G1-P[8]-I2-R2-C2-M2-A3-N2-T6-E2-H3, with most of the gene segments having a close relationship with a vaccine derived reassortant strain, previously reported in USA in 2010 and Australia in 2012. The study strains segregated into two lineages, each containing a paraphyletic pre- and post-vaccine introduction sub-lineages. In addition, the study strains demonstrated close relationship amongst each other when compared with globally selected group A rotavirus (RVA) G1P[8] reference strains. For VP7 neutralization epitopes, amino acid substitutions observed at positions T91A/V, S195D and M217T in relation to the RotaTeq vaccine were radical in nature and resulted in a change in polarity from a polar to non-polar molecule, while for the VP4, amino acid differences at position D195G was radical in nature and resulted in a change in polarity from a polar to non-polar molecule. The polarity change at position T91A/V of the neutralizing antigens might play a role in generating vaccine-escape mutants, while substitutions at positions S195D and M217T may be due to natural fluctuation of the RVA. Surveillance of RVA at whole genome level will enhance further assessment of vaccine impact on circulating strains, the frequency of reassortment events under natural conditions and epidemiological fitness generated by such events.

Preparing for safety monitoring after rotavirus vaccine implementation: a retrospective review of intussusception cases among children at a large teaching hospital in Rwanda, 2009-2012.

BACKGROUND: In some settings, rotavirus vaccines have been associated with a small risk of intussusception. This study describes the demographics, clinical characteristics and outcomes of children with intussusception in Rwanda before vaccine introduction in May 2012. METHODS: We retrospectively reviewed data on pediatric patients treated for intussusception at University Teaching Hospital of Kigali from January 2009 to June 2012. Hospital registries were reviewed to identify intussusception cases. Archived patient files were abstracted to collect data on demographics, clinical presentation, surgery and outcome. RESULTS: During the study period, 70 children ≤19 years of age were treated for intussusception and patient files were retrieved for 60 (86%) cases. Over half of patients (58%) were <1 year of age and 90% were transferred from a district hospital. Only 30% of patients presented within 3 days of symptom onset and 35% experienced a delay of ≥6 hours between surgical review and surgery. Surgical complications were experienced by 35% of children. Over 1 quarter (28%) of children died. Compared with children who survived, children who died were significantly more likely to have experienced complications (21% vs. 71%; P < 0.001) and to be female (28% vs. 65%; P = 0.009). DISCUSSION: Mortality due to intussusception was high among Rwanda children. Delays in presentation and treatment were common. Assessing trends in the number of cases to monitor for vaccine-associated intussusception will be difficult. Additional work is needed to further understand risk factors for mortality, to calculate incidence rates and to monitor the safety of the rotavirus vaccination program.

Long-term effectiveness of combination antiretroviral therapy and prevalence of HIV drug resistance in HIV-1-infected children and adolescents in Rwanda.

OBJECTIVE: To determine the long-term outcomes of treatment and prevalence of genotypic drug resistance in children and adolescents on combination antiretroviral therapy. METHODS: A cross-sectional study (September 2009 to October 2010) in which clinical, immunologic and virologic outcomes were assessed at a single-study visit and through patient records in a cohort of HIV-infected children and adolescents. Risk factors for clinical and immunologic responses and virologic outcome were evaluated using logistic regression, and the accuracy of clinical and immunologic criteria in identifying virologic failure was assessed. RESULTS: Four hundred twenty-four patients were enrolled with a median age of 10.8 years (range: 1.7-18.8) and a median duration on combination antiretroviral therapy of 3.4 years (range: 1.0-8.1). Thirty-three percent were stunted and 17% underweight. Eighty-four percent (95% confidence interval: 79-87) of children >5 years had CD4 ≥350 cells/mm and in 74% (95% confidence interval: 62-84) of younger children CD4% was ≥25. CD4 values and age at combination antiretroviral therapy initiation were independently associated with CD4 outcomes; 124 (29%) had HIV-1 RNA ≥1000 copies/mL, with no significant predictors. Sensitivity for weight-for-age and height-for-age and CD4 cells (<350/mm) remained under 50% (15-42%); CD4 cells showed the best specificity, ranging from 91% to 97%. Of 52 samples tested, ≥1 mutations were observed in 91% (nucleoside reverse transcriptase inhibitors) and 95% (non-nucleoside reverse transcriptase inhibitors); 1 to 2 thymidine analogue-associated mutations were detected in 16 (31%) and ≥3 thymidine analogue-associated mutations in 7 (13%). CONCLUSION: Nearly 1 in 3 children showed virologic failure, and >10% of the subgroup of children with treatment failure in whom genotyping was performed demonstrated multiple HIV drug resistance mutations. Neither clinical condition nor CD4 cells were good indicators for treatment failure.

Safety and effectiveness of combination antiretroviral therapy during the first year of treatment in HIV-1 infected Rwandan children: a prospective study.

BACKGROUND: With increased availability of paediatric combination antiretroviral therapy (cART) in resource limited settings, cART outcomes and factors associated with outcomes should be assessed. METHODS: HIV-infected children <15 years of age, initiating cART in Kigali, Rwanda, were followed for 18 months. Prospective clinical and laboratory assessments included weight-for-age (WAZ) and height-for-age (HAZ) z-scores, complete blood cell count, liver transaminases, creatinine and lipid profiles, CD4 T-cell count/percent, and plasma HIV-1 RNA concentration. Clinical success was defined as WAZ and WAZ >-2, immunological success as CD4 cells ≥500/mm3 and ≥25% for respectively children over 5 years and under 5 years, and virological success as a plasma HIV-1 RNA concentration <40 copies/mL. RESULTS: Between March 2008 and December 2009, 123 HIV-infected children were included. The median (interquartile (IQR) age at cART initiation was 7.4 (3.2, 11.5) years; 40% were <5 years and 54% were female. Mean (95% confidence interval (95%CI)) HAZ and WAZ at baseline were -2.01 (-2.23, -1.80) and -1.73 (-1.95, -1.50) respectively and rose to -1.75 (-1.98, -1.51) and -1.17 (-1.38, -0.96) after 12 months of cART. The median (IQR) CD4 T-cell values for children <5 and ≥5 years of age were 20% (13, 28) and 337 (236, 484) cells/mm3 respectively, and increased to 36% (28, 41) and 620 (375, 880) cells/mm3. After 12 months of cART, 24% of children had a detectable viral load, including 16% with virological failure (HIV-RNA>1000 c/mL). Older age at cART initiation, poor adherence, and exposure to antiretrovirals around birth were associated with virological failure. A third (33%) of children had side effects (by self-report or clinical assessment), but only 9% experienced a severe side effect requiring a cART regimen change. CONCLUSIONS: cART in Rwandan HIV-infected children was successful but success might be improved further by initiating cART as early as possible, optimizing adherence and optimizing management of side effects.

Pattern of congenital heart diseases in Rwandan children with genetic defects.

INTRODUCTION: Congenital heart diseases (CHD) are commonly associated with genetic defects. Our study aimed at determining the occurrence and pattern of CHD association with genetic defects among pediatric patients in Rwanda. METHODS: A total of 125 patients with clinical features suggestive of genetic defects were recruited. Echocardiography and standard karyotype studies were performed in all patients. RESULTS: CHDs were detected in the majority of patients with genetic defects. The commonest isolated CHD was ventricular septal defect found in many cases of Down syndrome. In total, chromosomal abnormalities represented the majority of cases in our cohort and were associated with various types of CHDs. CONCLUSION: Our findings showed that CHDs are common in Rwandan pediatric patients with genetic defects. These results suggest that a routine echocardiography assessment combined with systematic genetic investigations including standard karyotype should be mandatory in patients presenting characteristic clinical features in whom CHD is suspected to be associated with genetic defect.

Hepatitis B virus prevalence and vaccine response in HIV-infected children and adolescents on combination antiretroviral therapy in Kigali, Rwanda.

OBJECTIVE: The aim of this study was to determine the prevalence of hepatitis B virus (HBV) infection in a cohort of HIV-infected Rwandan children and adolescents on combination antiretroviral therapy (cART), and the success rate of HBV vaccination in those children found to be HBV negative. METHODS: HIV-infected children and adolescents (age 8-17 years) receiving cART with CD4 T-cells count ≥200 cells/mm and/or ≥15% and without prior HBV vaccination (by history, vaccination cards and clinic records) underwent serologic testing for past (negative HBV surface antigen [HBsAg] with positive antibody to HBV core antigen [cAb] and to HBsAg [anti-HBs]) or active HBV infection (positive HBsAg). Children with any positive HBV serologic tests were excluded from further vaccination; all others completed 3 HBV immunizations with 10 µg of ENGERIX-B. Anti-HBs titer was measured 4-6 weeks after the last immunization. RESULTS: Of 88 children, 6 (7%) children had active HBV infection and 8 (9%) had past HBV infection. The median (interquartile range) age, CD4 T-cell count and cART duration were 12.3 (10.1-13.9) years, 626 (503 to 942) cells/mm and 1.9 (1.5-2.7) years, respectively. Seventeen children had detectable plasma HIV-1 RNA. Seventy-3 children completed 3 immunizations with median (interquartile range) postimmunization anti-HBs concentration of 151 mIU/mL (1.03-650). Overall, 52 children (71%, 95% confidence interval: 61-82) developed a protective anti-HBs response. HIV-1 RNA and CD4 T-cell count were independent predictors of a protective anti-HBs response. Protective anti-HBs response was achieved in 82% of children with undetectable HIV-1 RNA and 77% with CD4 T cells ≥350/mm. CONCLUSIONS: The substantial HBV prevalence in this cohort suggests that HIV-infected Rwandan children should be screened for HBV before cART initiation. HIV viral suppression and CD4 T cells ≥350/mm favored the likelihood of a protective response after HBV vaccination.

Mid-dosing interval efavirenz plasma concentrations in HIV-1-infected children in Rwanda: treatment efficacy, tolerability, adherence, and the influence of CYP2B6 polymorphisms.

This study evaluated mid-dosing interval efavirenz plasma concentrations and the influence of CYP2B6 polymorphisms in relation to efficacy, tolerability, and adherence in 97 Rwandan HIV-infected children (3-16 years). Plasma drug concentrations and CYP2B6 polymorphisms were determined. Ten children were excluded for nonadherence. Large intersubject variability in efavirenz plasma concentrations was found. Of the 87 remaining, efavirenz concentrations were therapeutic, supratherapeutic, and subtherapeutic in 67%, 20%, and 14%, respectively. No associations were found between efavirenz concentrations and central nervous system disturbances or virologic failure. Minor allele frequencies were 0.32 (516G>T), 0.33 (785A>G), and 0.09 (983T>C). Polymorphisms in CYP2B6 were strongly associated with high efavirenz levels.

Evaluation of latent class analysis and decision thresholds to guide the diagnosis of pediatric tuberculosis in a Rwandan reference hospital.

SETTING: A pediatric ward of a university hospital in Kigali, Rwanda, a region with a high HIV seroprevalence. OBJECTIVE: To estimate the diagnostic accuracy of symptoms, signs, and paraclinical investigations for tuberculosis in children, and to propose a clinical rule based on the results. DESIGN: During a 2-year period all children with cough for more than 2 weeks and/or fever for more than 2 weeks and/or reported weight loss were prospectively included. A set of clinical and paraclinical data were analyzed with latent class analysis. Comparison of post-test probability based on this analysis with a therapeutic threshold for TB was used to develop a guideline. RESULTS: In the 309 children HIV prevalence was 56%, bacteriology was positive in 9%, and the tuberculin skin test (TST) was >10 mm in 20%. TB prevalence was 32%. Bacteriology and TST had a specificity of 97% and cough had a sensitivity of 91%. Decision analysis suggests treating children presenting one of the inclusion criteria, combined with positive bacteriology or TST >10 mm or contact with a TB patient. CONCLUSIONS: Latent class analysis confirmed earlier identified predictors for TB and allowed development of an easy to use clinical rule, applicable in reference hospitals of countries with high HIV endemicity.

Validation of 2006 WHO prediction scores for true HIV infection in children less than 18 months with a positive serological HIV test.

INTRODUCTION: All infants born to HIV-positive mothers have maternal HIV antibodies, sometimes persistent for 18 months. When Polymerase Chain Reaction (PCR) is not available, August 2006 World Health Organization (WHO) recommendations suggest that clinical criteria may be used for starting antiretroviral treatment (ART) in HIV seropositive children <18 months. Predictors are at least two out of sepsis, severe pneumonia and thrush, or any stage 4 defining clinical finding according to the WHO staging system. METHODS AND RESULTS: From January 2005 to October 2006, we conducted a prospective study on 236 hospitalized children <18 months old with a positive HIV serological test at the national reference hospital in Kigali. The following data were collected: PCR, clinical signs and CD4 cell count. Current proposed clinical criteria were present in 148 of 236 children (62.7%) and in 95 of 124 infected children, resulting in 76.6% sensitivity and 52.7% specificity. For 87 children (59.0%), clinical diagnosis was made based on severe unexplained malnutrition (stage 4 clinical WHO classification), of whom only 44 (50.5%) were PCR positive. Low CD4 count had a sensitivity of 55.6% and a specificity of 78.5%. CONCLUSION: As PCR is not yet widely available, clinical diagnosis is often necessary, but these criteria have poor specificity and therefore have limited use for HIV diagnosis. Unexplained malnutrition is not clearly enough defined in WHO recommendations. Extra pulmonary tuberculosis (TB), almost impossible to prove in young children, may often be the cause of malnutrition, especially in HIV-affected families more often exposed to TB. Food supplementation and TB treatment should be initiated before starting ART in children who are staged based only on severe malnutrition.

Molecular analysis in two siblings African patients with severe form of Hunter Syndrome: identification of a novel (p.Y54X) nonsense mutation.

Hunter syndrome (or Mucopolysaccharidosis type II, MPS II) is an X-linked recessive disorder due to the deficiency of the iduronate-2-sulfatase (IDS) enzyme, resulting in the accumulation of heparan and dermatan sulfates in the lysosomes. The heterogeneity of clinical phenotypes, ranging from mild-to-severe forms, is a result of different mutations in the IDS gene. We report here, a novel nonsense mutation (p.Y54X) in two siblings MPS II African patients affected with a severe form of the disease. We postulated that the p.Y54X mutation which causes a loss of the IDS region highly conserved among sulfatase enzymes, could be predicted as a severe disease-causing mutation for Hunter syndrome.

Haemophilus influenzae type b conjugate vaccine impact against purulent meningitis in Rwanda.

Rwanda introduced Haemophilus influenzae type b (Hib) conjugate vaccine in January 2002 and simultaneously implemented pediatric bacterial meningitis surveillance at a major referral hospital in the capital Kigali. We reviewed clinical and laboratory information collected during January 2002 to June 2006. Due to a variety of laboratory limitations, only eight confirmed Hib cases were identified, all before 2004. However, the proportion of cerebrospinal fluid with purulence decreased from 26.0% during 2002, to 15.9% during 2003, 9.7% during 2004 and 8.4% in 2005 (p<0.001). Vaccine effectiveness of two or three doses of Hib vaccine against purulent meningitis was 52% (95% confidence interval, 5-75%). In an African setting with few resources and in which few confirmed Hib meningitis cases were identified, Hib vaccine impact nevertheless could be demonstrated against the outcome of purulent meningitis and was found to be high.