Evaluation of Intussusception Following Pentavalent Rotavirus Vaccine (RotaTeq) Administration in 5 African Countries.

BACKGROUND: A low-level risk of intussusception following rotavirus vaccination has been observed in some settings and may vary by vaccine type. We examined the association between RotaTeq vaccination and intussusception in low-income settings in a pooled analysis from 5 African countries that introduced RotaTeq into their national immunization program. METHODS: Active surveillance was conducted at 20 hospitals to identify intussusception cases. A standard case report form was completed for each enrolled child, and vaccination status was determined by review of the child's vaccination card. The pseudo-likelihood adaptation of self-controlled case-series method was used to assess the association between RotaTeq administration and intussusception in the 1-7, 8-21, and 1-21 day periods after each vaccine dose in infants aged 28-245 days. RESULTS: Data from 318 infants with confirmed rotavirus vaccination status were analyzed. No clustering of cases occurred in any of the risk windows after any of the vaccine doses. Compared with the background risk of naturally occurring intussusception, no increased risk was observed after dose 1 in the 1-7 day (relative incidence = 2.71; 95% confidence interval [CI] = 0.47-8.03) or the 8-21 day window (relative incidence = 0.77; 95%CI = 0.0-2.69). Similarly, no increased risk of intussusception was observed in any risk window after dose 2 or 3. CONCLUSIONS: RotaTeq vaccination was not associated with increased risk of intussusception in this analysis from 5 African countries. This finding mirrors results from similar analyses with other rotavirus vaccines in low-income settings and highlights the need for vaccine-specific and setting-specific risk monitoring.

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.

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.

The Role of Molecular Testing in Pediatric Meningitis Surveillance in Southern and East African Countries, 2008-2017.

BACKGROUND: As part of the global Invasive Bacterial Vaccine-Preventable Diseases Surveillance Network, 12 African countries referred cerebrospinal fluid (CSF) samples to South Africa's regional reference laboratory. We evaluated the utility of real-time polymerase chain reaction (PCR) in detecting and serotyping/grouping Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pneumoniae (HNS). METHODS: From 2008 to 2017, CSF samples collected from children <5 years old with suspected meningitis underwent routine microbiology testing in-country, and 11 680 samples were submitted for HNS PCR at the regional reference laboratory. Unconditional logistic regression, with adjustment for geographic location, was performed to identify factors associated with PCR positivity. RESULTS: The overall HNS PCR positivity rate for all countries was 10% (1195 of 11 626 samples). In samples with both PCR and culture results, HNS PCR positivity was 11% (744 of 6747 samples), and HNS culture positivity was 3% (207 of 6747). Molecular serotype/serogroup was assigned in 75% of PCR-positive specimens (762 of 1016). Compared with PCR-negative CSF samples, PCR-positive samples were more often turbid (adjusted odds ratio, 6.80; 95% confidence interval, 5.67-8.17) and xanthochromic (1.72; 1.29-2.28), had elevated white blood cell counts (6.13; 4.71-7.99) and high protein concentrations (5.80; 4.34-7.75), and were more often HNS culture positive (32.70; 23.18-46.12). CONCLUSION: PCR increased detection of vaccine-preventable bacterial meningitis in countries where confirmation of suspected meningitis cases is impeded by limited culture capacity.

Whole-Genome Analyses Identifies Multiple Reassortant Rotavirus Strains in Rwanda Post-Vaccine Introduction.

Children in low-and middle-income countries, including Rwanda, experience a greater burden of rotavirus disease relative to developed countries. Evolutionary mechanisms leading to multiple reassortant rotavirus strains have been documented over time which influence the diversity and evolutionary dynamics of novel rotaviruses. Comprehensive rotavirus whole-genome analysis was conducted on 158 rotavirus group A (RVA) samples collected pre- and post-vaccine introduction in children less than five years in Rwanda. Of these RVA positive samples, five strains with the genotype constellations G4P[4]-I1-R2-C2-M2-A2-N2-T1-E1-H2 (n = 1), G9P[4]-I1-R2-C2-M2-A1-N1-T1-E1-H1 (n = 1), G12P[8]-I1-R2-C2-M1-A1-N2-T1-E2-H3 (n = 2) and G12P[8]-I1-R1-C1-M1-A2-N2-T2-E1-H1 (n = 1), with double and triple gene reassortant rotavirus strains were identified. Phylogenetic analysis revealed a close relationship between the Rwandan strains and cognate human RVA strains as well as the RotaTeq® vaccine strains in the VP1, VP2, NSP2, NSP4 and NSP5 gene segments. Pairwise analyses revealed multiple differences in amino acid residues of the VP7 and VP4 antigenic regions of the RotaTeq® vaccine strain and representative Rwandan study strains. Although the impact of such amino acid changes on the effectiveness of rotavirus vaccines has not been fully explored, this analysis underlines the potential of rotavirus whole-genome analysis by enhancing knowledge and understanding of intergenogroup reassortant strains circulating in Rwanda post vaccine introduction.

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.

Adherence to isoniazid preventive therapy among child contacts in Rwanda: A mixed-methods study.

BACKGROUND: The World Health Organization recommends isoniazid preventive therapy (IPT) for six months for child contacts without tuberculosis (TB), who are exposed to an adult with active TB. The effectiveness of IPT depends on 80% or greater adherence to medication. In the current study, we assessed IPT adherence and explored barriers to and facilitators of adherence among eligible child contacts in Kigali, Rwanda. METHODS: A mixed method study design was used to prospectively assess adherence to IPT among eligible child contacts and its associated factors through a quantitative, observational cohort study, and to explore barriers to and facilitators of adherence to IPT through a descriptive qualitative study. RESULTS: Of the 84 child contacts who started IPT, 74 (88%) had complete adherence and ten (12%) had incomplete adherence. There were no factors (individual characteristics of index cases, households and or health facility characteristics) found to be significantly associated with IPT adherence in the bivariate and multivariate analysis. In the qualitative analysis, we identified factors relating to parents/caregivers, disease, household and health-care providers as major themes determining IPT adherence. CONCLUSION: There was a high rate of IPT completion in this cohort of eligible child contacts living in Kigali. However, structural factors (poverty and relocation) were found to be the main barriers to IPT adherence that could be addressed by health-care providers.

Xpert MTB/RIF assay did not improve diagnosis of pulmonary tuberculosis among child contacts in Rwanda.

INTRODUCTION: To report on the diagnostic yield using the Xpert MTB/RIF assay on gastric lavage samples from children (<15 years) who were household contacts of tuberculosis (TB) cases in Kigali, Rwanda. METHODS: A cross-sectional study was conducted among 216 child contacts of index cases with sputum smear-positive TB over a 7 month period, from 1st August 2015 to 29th February 2016. Child contacts with tuberculosis-related symptoms or abnormal chest X-ray had sputum collected by gastric lavage on two consecutive days and samples were examined by smear microscopy, Xpert MTB/RIF assay and solid culture. RESULTS: Of the 216 child contacts, 94 (44%) were less than 5 years of age. Most of them 84 (89%) were receiving isoniazid preventive therapy at the time of screening. Thirty seven out of 216 children had TB-related symptoms. Only 4 (10.8%) were clinically diagnosed with TB; and none had bacteriologically confirmed tuberculosis. CONCLUSION: The use of Xpert MTB/RIF assay did not contribute to bacteriological confirmation of active TB in child contacts in this study. The low prevalence of tuberculosis in child contacts in this study may reflect the high coverage of preventive therapy in young (<5 years) child contacts. The low sensitivity of Xpert MTB/RIF assay in contacts may also suggest likely reflection of paucibacillary disease.

Assessment of the Isoniazid Preventive Therapy Uptake and Associated Characteristics: A Cross-Sectional Study.

OBJECTIVE: To assess the uptake of isoniazid preventive therapy (IPT) by eligible children in Kigali, Rwanda, and associated individual, households, and healthcare systems characteristics. METHODS: A cross-sectional study was conducted among child contacts of index cases having sputum smear-positive pulmonary tuberculosis. Data were collected from 13 selected primary health centres. Descriptive statistics were used to generate frequency tables and figures. Logistic regression models were performed to determine characteristics associated with IPT uptake. RESULTS: Of 270 children (under 15 years), who were household contacts of 136 index cases, 94 (35%) children were less than 5 years old and eligible for IPT; and 84 (89%, 95% CI 81-94) were initiated on IPT. The reasons for not initiating IPT in the remaining 10 children were parents/caregivers' lack of information on the need for IPT, refusal to give IPT to their children, and poor quality services offered at health centres. Factors associated with no uptake of IPT included children older than 3 years, unfriendly healthcare providers, HIV infected index cases, and the index case not being the child's parent. CONCLUSION: The National Tuberculosis Program's policy on IPT delivery was effectively implemented. Future interventions should find strategies to manage factors associated with IPT uptake.

Etiology of Severe Acute Watery Diarrhea in Children in the Global Rotavirus Surveillance Network Using Quantitative Polymerase Chain Reaction.

Background: The etiology of acute watery diarrhea remains poorly characterized, particularly after rotavirus vaccine introduction. Methods: We performed quantitative polymerase chain reaction for multiple enteropathogens on 878 acute watery diarrheal stools sampled from 14643 episodes captured by surveillance of children <5 years of age during 2013-2014 from 16 countries. We used previously developed models of the association between pathogen quantity and diarrhea to calculate pathogen-specific weighted attributable fractions (AFs). Results: Rotavirus remained the leading etiology (overall weighted AF, 40.3% [95% confidence interval {CI}, 37.6%-44.3%]), though the AF was substantially lower in the Americas (AF, 12.2 [95% CI, 8.9-15.6]), based on samples from a country with universal rotavirus vaccination. Norovirus GII (AF, 6.2 [95% CI, 2.8-9.2]), Cryptosporidium (AF, 5.8 [95% CI, 4.0-7.6]), Shigella (AF, 4.7 [95% CI, 2.8-6.9]), heat-stable enterotoxin-producing Escherichia coli (ST-ETEC) (AF, 4.2 [95% CI, 2.0-6.1]), and adenovirus 40/41 (AF, 4.2 [95% CI, 2.9-5.5]) were also important. In the Africa Region, the rotavirus AF declined from 54.8% (95% CI, 48.3%-61.5%) in rotavirus vaccine age-ineligible children to 20.0% (95% CI, 12.4%-30.4%) in age-eligible children. Conclusions: Rotavirus remained the leading etiology of acute watery diarrhea despite a clear impact of rotavirus vaccine introduction. Norovirus GII, Cryptosporidium, Shigella, ST-ETEC, and adenovirus 40/41 were also important. Prospective surveillance can help identify priorities for further reducing the burden of diarrhea.

Use of administrative records to assess pneumococcal conjugate vaccine impact on pediatric meningitis and pneumonia hospitalizations in Rwanda.

BACKGROUND: Ongoing surveillance is critical to assessing pneumococcal conjugate vaccine (PCV) impact over time. However, robust prospective studies are difficult to implement in resource-poor settings. We evaluated retrospective use of routinely collected data to estimate PCV impact in Rwanda. METHODS: We collected data from admission registers at five district hospitals on children age <5yearsadmitted for suspected meningitis and pneumonia during 2002-2012. We obtained clinical and laboratory data on meningitis from sentinel surveillance at the national reference hospital in Kigali. We developed multivariable logistic regression models to estimate PCV effectiveness (VE) against severe pneumonia and probable bacterial meningitis and Poisson models to estimate absolute rate reductions. Haemophilus influenzae type b vaccine was introduced in January 2002, PCV7 in April 2009 and PCV13 in August 2011. RESULTS: At the district hospitals, the severe pneumonia and suspected meningitis hospitalization rates decreased by 70/100,000 and 11/100,000 children for 2012 compared to baseline, respectively. VE against severe pneumonia calculated from logistic regression was 54% (95% CI 42-63%). In Kigali, from 2002 to 2012, annual suspected meningitis cases decreased from 170 pre-PCV7 to 40 post-PCV13 and confirmed pneumococcal meningitis cases from 7 to 0. VE against probable bacterial meningitis was 42% (95% CI -4% to 68%). CONCLUSION: In a resource-poor African setting, analysis of district hospital admission logbooks and routine sentinel surveillance data produced results consistent with more sophisticated impact studies conducted elsewhere. Our findings support applying this methodology in other settings and confirm the benefits of PCV in Rwanda.

Effectiveness of Pentavalent Rotavirus Vaccine Under Conditions of Routine Use in Rwanda.

BACKGROUND: Rotavirus vaccine efficacy is lower in low-income countries than in high-income countries. Rwanda was one of the first low-income countries in sub-Saharan Africa to introduce rotavirus vaccine into its national immunization program. We sought to evaluate rotavirus vaccine effectiveness (VE) in this setting. METHODS: VE was assessed using a case-control design. Cases and test-negative controls were children who presented with a diarrheal illness to 1 of 8 sentinel district hospitals and 10 associated health centers and had a stool specimen that tested positive (cases) or negative (controls) for rotavirus by enzyme immunoassay. Due to high vaccine coverage almost immediately after vaccine introduction, the analysis was restricted to children 7-18 weeks of age at time of rotavirus vaccine introduction. VE was calculated as (1 - odds ratio) × 100, where the odds ratio was the adjusted odds ratio for the rotavirus vaccination rate among case-patients compared with controls. RESULTS: Forty-eight rotavirus-positive and 152 rotavirus-negative children were enrolled. Rotavirus-positive children were significantly less likely to have received rotavirus vaccine (33/44 [73%] unvaccinated) compared with rotavirus-negative children (81/136 [59%] unvaccinated) (P= .002). A full 3-dose series was 75% (95% confidence interval [CI], 31%-91%) effective against rotavirus gastroenteritis requiring hospitalization or a health center visit and was 65% (95% CI, -80% to 93%) in children 6-11 months of age and 81% (95% CI, 25%-95%) in children ≥12 months of age. CONCLUSIONS: Rotavirus vaccine is effective in preventing rotavirus disease in Rwandan children who began their rotavirus vaccine series from 7 to 18 weeks of age. Protection from vaccination was sustained after the first year of life.

Engagement of non-government organisations and community care workers in collaborative TB/HIV activities including prevention of mother to child transmission in South Africa: opportunities and challenges.

BACKGROUND: The implementation of collaborative TB/HIV activities may help to mitigate the impact of the dual epidemic on patients and communities. Such implementation requires integrated interventions across facilities and levels of government, and with communities. Engaging Community Care Workers (CCWs) in the delivery of integrated TB/HIV services may enhance universal coverage and treatment outcomes, and address human resource needs in sub-Saharan Africa. METHODS: Using pre-intervention research in Sisonke district, KwaZulu-Natal, South Africa as a case study, we report on three study objectives: (1) to determine the extent of the engagement of NGOs and CCWs in the implementation of collaborative TB/HIV including PMTCT; (2) to identify constraints related to provision of TB/HIV/PMTCT integrated care at community level; and (3) to explore ways of enhancing the engagement of CCWs to provide integrated TB/HIV/PMTCT services. Our mixed method study included facility and NGO audits, a household survey (n = 3867), 33 key informant interviews with provincial, district, facility, and NGO managers, and six CCW and patient focus group discussions. RESULTS: Most contracted NGOs were providing TB or HIV support and care with little support for PMTCT. Only 11% of facilities' TB and HIV patients needing care and support at the community level were receiving support from CCWs. Only 2% of pregnant women reported being counseled by CCWs on infant feeding options and HIV testing. Most facilities (83%) did not have any structural linkage with NGOs. Major constraints identified were system-related: structural, organizational and managerial constraints; inadequate CCW training and supervision; limited scope of CCW practice; inadequate funding; and inconsistency in supplies and equipment. Individual and community factors, such as lack of disclosure, stigma related to HIV, and cultural beliefs were also identified as constraints. CONCLUSIONS: NGO/CCW engagement in the implementation of collaborative TB/HIV/PMTCT activities is sub-optimal, despite its potential benefits. Effective interventions that address contextual and health systems challenges are required. These should combine systematic skills-building, an enhanced scope of practice and consistent CCW supervision with a reliable referral and monitoring and evaluation system.

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.