Understanding multilevel barriers to childhood vaccination uptake among Internally Displaced Populations (IDPs) in Mogadishu, Somalia: a qualitative study.

BACKGROUND: Disparities in vaccination coverage exist in Somalia with Internally Displaced Persons (IDPs) being among the groups with the lowest coverage. We implemented an adapted Participatory Learning and Action (PLA) intervention, which focused on routine vaccinations among displaced populations living in Mogadishu IDP camps. The intervention was successful in improving maternal knowledge and vaccination coverage but unsuccessful in improving timely vaccination. We conducted a qualitative study to understand this result and analyze the multi-level barriers to routine childhood immunization uptake. METHOD: In this qualitative study we used observation data from 40 PLA group discussions with female caregivers and purposively sampled nine vaccination service providers and six policy makers for interview. We also reviewed national-level vaccine policy documents and assessed the quality of health facilities in the study area. We used the socioecological framework to structure our analysis and analyzed the data in NVivo. RESULTS: The barriers to childhood vaccination among IDPs at the individual level were fear due to lack of knowledge, mistrust of vaccines, concerns about side effects and misinformation; opportunity costs; and costs of transportation. At the interpersonal level, family members played an important role as did the extent of decision-making autonomy. Community factors such as cultural practices, gender roles, and household evictions influenced vaccination. Organizational issues at health facilities such as waiting times, vaccine stock-outs, distance to the facility, language differences, and hesitancy of health workers to open multi-dose vials affected vaccination. At the policy level, confusion about the eligible age for routine vaccination and age restrictions for catch-up vaccination and certain antigens such as BCG were important barriers. CONCLUSION: Complex and interrelated factors affect childhood vaccination uptake among IDPs in Somalia. Interventions that address multiple barriers simultaneously will have the greatest impact given the complex nature of vulnerabilities in this population. There is a need to strengthen the health system and connect it with existing community structures to increase demand for services. Our research highlights the importance of formative research before implementing interventions. Further research on the integration of health service strengthening with PLA to improve childhood vaccination among IDPs is recommended. TRIAL REGISTRATION NUMBER: ISRCTN-83,172,390. Date of registration: 03/08/2021.

Use of an adapted participatory learning and action cycle to increase knowledge and uptake of child vaccination in internally displaced persons camps (IVACS): A cluster-randomised controlled trial.

BACKGROUND: Vaccination is a key public health intervention that can reduce excess mortality in humanitarian contexts. Vaccine hesitancy is thought to be a significant problem requiring demand side interventions. Participatory Learning and Action (PLA) approaches have proven effective in reducing perinatal mortality in low income settings and we aimed to apply an adapted approach in Somalia. METHODS: A randomised cluster trial was implemented in camps for internally displaced people near Mogadishu, from June to October 2021. An adapted PLA approach (hPLA) was used in partnership with indigenous 'Abaay-Abaay' women's social groups. Trained facilitators ran 6 meeting cycles that addressed topics of child health and vaccination, analysed challenges, and planned and implemented potential solutions. Solutions included a stakeholder exchange meeting involving Abaay-Abaay group members and services providers from humanitarian organisations. Data was collected at baseline and after completion of the 3 month intervention cycle. RESULTS: Overall, 64.6% of mothers were group members at baseline and this increased in both arms during the intervention (p = 0.016). Maternal preference for getting young children vaccinated was >95% at baseline and did not change. The hPLA intervention improved the adjusted maternal/caregiver knowledge score by 7.9 points (maximum possible score 21) compared to the control (95% CI 6.93, 8.85; p < 0.0001). Coverage of both measles vaccination (MCV1) (aOR 2.43 95% CI 1.96, 3.01; p < 0.001) and completion of the pentavalent vaccination series (aOR 2.45 95% CI 1.27, 4.74; p = 0.008) also improved. However, adherence to timely vaccination did not (aOR 1.12 95% CI 0.39, 3.26; p = 0.828). Possession of a home-based, child health record card increased in the intervention arm from 18 to 35% (aOR 2.86 95% CI 1.35, 6.06; p = 0.006). CONCLUSION: A hPLA approach, run in partnership with indigenous social groups, can achieve important changes in public health knowledge and practice in a humanitarian context. Further work to scale up the approach and address other vaccines and population groups is warranted.

Clinical evaluation of a Hepatitis C Virus whole-genome sequencing pipeline for genotyping and resistance testing.

OBJECTIVES: We sought to evaluate clinically a hepatitis C virus (HCV) whole-genome, next-generation sequencing (NGS) pipeline that is agnostic to viral genotype. METHODS: Performance of the NGS pipeline was assessed through comparison of results with Sanger sequencing (SS) of partial HCV genomes. RESULTS: There was 98.7% (376/381) concordance for viral subtype between SS and NGS. The positive and negative per cent agreements for determination of resistance-associated substitutions were 97.8% (95% CI 92.5-99.4%) and 99.9% (95% CI 99.5-100.0%), respectively. The NGS pipeline was also able to detect novel subtypes, mixtures, recombinants, transiently occurring resistance mutations and distinguish re-infection with the same subtype from relapse. DISCUSSION: Particular scenarios where NGS may be used include settings without universal access to pan-genotypic antiviral regimens, those infected with a 'rare' subtype or who have been failed by first-line therapy, and in cases of suspected re-infection.

Technical Validation of a Hepatitis C Virus Whole Genome Sequencing Assay for Detection of Genotype and Antiviral Resistance in the Clinical Pathway.

Choice of direct acting antiviral (DAA) therapy for Hepatitis C Virus (HCV) in the United Kingdom and similar settings usually requires knowledge of the genotype and, in some cases, antiviral resistance (AVR) profile of the infecting virus. To determine these, most laboratories currently use Sanger technology, but next-generation sequencing (NGS) offers potential advantages in throughput and accuracy. However, NGS poses unique technical challenges, which require idiosyncratic development and technical validation approaches. This applies particularly to virology, where sequence diversity is high and the amount of starting genetic material is low, making it difficult to distinguish real data from artifacts. We describe the development and technical validation of a sequence capture-based HCV whole genome sequencing (WGS) assay to determine viral genotype and AVR profile. We use clinical samples of known subtypes and viral loads, and simulated FASTQ datasets to validate the analytical performances of both the wet laboratory and bioinformatic pipeline procedures. We show high concordance of the WGS assay compared to current "gold standard" Sanger assays. Specificity was 92.3 and 96.1% for AVR and genotyping, respectively. Discordances were due to the inability of Sanger assays to assign the correct subtype or accurately call mixed drug-resistant variants. We show high repeatability and reproducibility with >99.8% sequence similarity between sequence runs as well as high precision for variant frequency detection at >98.8% in the 95th percentile. Post-sequencing bioinformatics quality control workflows allow the accurate distinction between mixed infections, cross-contaminants and recombinant viruses at a threshold of >5% for the minority population. The sequence capture-based HCV WGS assay is more accurate than legacy AVR and genotyping assays. The assay has now been implemented in the clinical pathway of England's National Health Service HCV treatment programs, representing the first validated HCV WGS pipeline in clinical service. The data generated will additionally provide granular national-level genomic information for public health policy making and support the WHO HCV elimination strategy.

Enhanced Detection of DNA Viruses in the Cerebrospinal Fluid of Encephalitis Patients Using Metagenomic Next-Generation Sequencing.

The long and expanding list of viral pathogens associated with causing encephalitis confounds current diagnostic procedures, and in up to 50% of cases, the etiology remains undetermined. Sequence-agnostic metagenomic next-generation sequencing (mNGS) obviates the need to specify targets in advance and thus has great potential in encephalitis diagnostics. However, the low relative abundance of viral nucleic acids in clinical specimens poses a significant challenge. Our protocol employs two novel techniques to selectively remove human material at two stages, significantly increasing the representation of viral material. Our bioinformatic workflow using open source protein- and nucleotide sequence-matching software balances sensitivity and specificity in diagnosing and characterizing any DNA viruses present. A panel of 12 cerebrospinal fluid (CSFs) from encephalitis cases was retrospectively interrogated by mNGS, with concordant results in seven of nine samples with a definitive DNA virus diagnosis, and a different herpesvirus was identified in the other two. In two samples with an inconclusive diagnosis, DNA viruses were detected and in a virus-negative sample, no viruses were detected. This assay has the potential to detect DNA virus infections in cases of encephalitis of unknown etiology and to improve the current screening tests by identifying new and emerging agents.

PCR Assembly of Synthetic Promoters.

In this chapter, we describe a two-step assembly PCR method to construct synthetic promoters. Essentially, this method takes advantage of specific annealing between complimentary DNA sequences to build random TFBS combinations within the assembled PCR products. A DNA polymerase is then employed to fill in the unpaired nucleotides in the generated sequences and also to amplify the assembled PCR products. We have used this method to generate synthetic promoters whereby the orientation of the TFBS can be controlled, the spacing between TFBS can be predetermined, and also the full diversity of the consensus TFBS can be covered through the use of degenerate oligonucleotides .