Risk factors of virologic failure and slow response to art among HIV-infected children and adolescents in Nairobi

Background: Antiretroviral therapy (ART) in resource-limited settings is effective when backed up with adequate clinical, immunological, and virologic monitoring. Undetected, virologic failure results in increased HIV-1 drug resistance mutations (DRMs), morbidity and mortality, or the need for costly second-line and third-line ART.Objective: To evaluate the prevalence, patterns, and risk factors of virologic failure and slow response to ART, among children and adolescents in resource-limited settings in Nairobi, Kenya.Design: A Retrospective study.Setting: The 8 Lea Toto Programme (LTP) Clinics in Dagoretti, Dandora, Kangemi, Kariobangi, Kawangware, Kibera, Mukuru, and Zimmerman areas of Nairobi. Subjects: One hundred and forty-six HIV-infected children and adolescents aged 1 month to 19 years of the LTP in Nairobi Kenya. Medical and demographic data including, HIV-1 viral loads, information on adherence to ART, HIV-1 DRMs and other key determinants of virologic failure, collected over a period of 2 years, was used for this study.Results: A threshold of 1,000 HIV RNA copies/ml was used to determine treatment outcome. The virologic failure rates in this cohort were 43.8% after 6 months, 32.2% after 12 months, 28.8% after 18 months, and 24.0% after 24 months of first-line ART. Twelve (8.2%) of 146 children showed a slow response to ART: they initially failed ART at 12 months, but had treatment success after 18 to 24 months. The rates of virologic rebound were 4 (2.7%) after 18 months and 3 (2.1%) after 24 months of ART. Multivariate Cox proportional hazards regression revealed that children with suboptimal adherence to ART were 37 times more likely to experience virologic failure (P = 0.000003).Conclusions: This study showed that ART implementation in resource-limited settings is effective when regular virologic monitoring, adherence counselling, and HIV-DR testing are available. Secondly, adherence to ART is a strong predictor of treatment outcome for children and adolescents in resourcelimited settings. Therefore, methods of optimizing adherence levels should be explored and implemented

Performance of selected HIV testing centers in a HIV Proficiency Testing Scheme in Kenya: a case study

Background: The Proficiency Testing (PT) for Human Immunodeficiency Virus (HIV) using Lateral flow assays provides an avenue for participating institutions/individuals to assess their technical competence in testing for HIV using LFAs that are recommended in the National HIV Testing Algorithm (NHTA) in Kenya. It also provides confidence to the participating institutions and potential users of their services besides giving the institutions an opportunity for improvement. Objective: To determine the performance of selected HIV testing centers in a HIV PT Scheme in Kenya Methods: Fifty one participants (51) in Kenya were selected from 7 sites (Kisumu, Mombasa, Kilifi, Nairobi and Malindi) to participate in this PT round. The sites comprised both private sector and institutions that do not participate in the National HIV referral Lab-PT scheme. They were provided with panels containing six samples to analyze using the current NHTA in Kenya. Obtained results were sent to our laboratory electronically. Results: Eighty nine percent (89.0%) of the panels were correctly identified by the participants as positive or negative. Of the 11.0% errors, 74.2% were committed in one or more test result obtained while 12.9% committed in failure to follow NHTA. Two minor errors repeated by participants were; failure to record the final results in spite of obtaining correct tests and correct reactive results with the first and second test kits but in conclusion the participant recorded negative (12.9%). Root cause analysis revealed that the error committed by participants were as a result of failure to observe the kit manufactures’ instructions and NHTA guidelines. Conclusion: The results of this PT Scheme enhance the need for constant training of personnel conducting HIV testing and Counseling in Kenya on proper techniques of carrying out HIV testing using Lateral flow assays in the NHTA. Key words: HIV, Proficiency Testing, errors, false negative, false positive

The Potential for DPPIV/CD26 usage as a surrogate marker for Antiretroviral Therapy Efficacy in HIV Infected populations

Background: Human Immunodeficiency Virus (HIV) viral load and CD4+ cell counts are the most commonly used markers for monitoring efficacy of anti-retroviral therapy (ART) in HIV infected individuals. The high cost of viral load monitoring limits its usage in resource limited countries, often leaving the use of CD4+ T cell counts as the only alternative. Though cheaper and more readily available, CD4+ cell counts as a measure of detecting treatment failure, is an unreliable predictor of disease progression. Hence, there is a need for more sensitive alternative, but less costly techniques for detecting treatment failure which can be used in resource limited settings. Objective: To evaluate the feasibility of using plasma CD26/Dipeptidyl peptidase IV (DPPIV) as a novel marker for clinical evaluation of treatment efficacy in HIV infected children. Method: Blood samples collected from HIV+ children (n=76) before and after initiation on ART, were assessed for HIV RNA (viral load), CD4+ T-cell count and DPPIV/CD26 levels. Viral load levels were analyzed using Roche Amplicor HIV-1 Monitor Test kit; CD4+ T-Cell Counts were analyzed using BD FACS Calibur flow cytometer while DPPIV/CD 26 levels were analyzed using Human DPPIV/CD26 Quantikine ELISA kit (R&D Systems, Minneapolis MN). Results: The plasma DPPIV/CD26 levels increased significantly in children after ART initiation (p = 0.017), while the viral load levels declined after ART initiation with subsequent CD4+ cell counts increase. The DPPIV/CD 26 increase positively correlated with viral load decrease while negatively correlating to the CD4+ cell count increase. Conclusion: These findings demonstrate an inverse relationship between DPPIV/CD26 levels and HIV viral load and the direct proportionality of CD4+ Cell counts and DPPIV/CD26 levels, suggesting potential for use of DPPIV/CD26 as a surrogate marker for evaluating HIV disease progression in children receiving anti-retroviral therapy. Key words: CD26/Dipeptidyl peptidase IV (DPPIV), ELISA, Surrogate marker, Viral Load, CD4 Count, antiretroviral

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Cytoarchitecture of ex vivo midgut cultures of unfed Ixodes scapularis infected with a tick-borne flavivirus

A bite from an infected tick is the primary means of transmission for tick-borne flaviviruses (TBFV). Ticks ingest the virus while feeding on infected blood. The traditional view is that the virus first replicates in and transits the tick midgut prior to dissemination to other organs, including salivary glands. Thus, understanding TBFV infection in the tick midgut is a key first step in identifying potential countermeasures against infection. Ex vivo midgut cultures prepared from unfed adult female Ixodes scapularis ticks were viable and remained morphologically intact for more than 8 days. The midgut consisted of two clearly defined cell layers separated by a basement membrane: an exterior network of smooth muscle cells and an internal epithelium composed of digestive generative cells. The smooth muscle cells were arranged in a stellate circumferential pattern spaced at regular intervals along the long axis of midgut diverticula. When the cultures were infected with the TBFV Langat virus (LGTV), virus production increased by two logs with a peak at 96 hours post-infection. Infected cells were readily identified by immunofluorescence staining for the viral envelope protein, nonstructural protein 3 (NS3) and dsRNA. Microscopy of the stained cultures suggested that generative cells were the primary target for virus infection in the midgut. Infected cells exhibited an expansion of membranes derived from the endoplasmic reticulum; a finding consistent with TBFV infected cell cultures. Electron microscopy of infected cultures revealed virus particles in the basolateral region between epithelial cells. These results demonstrated LGTV replication in midgut generative cells of artificially infected, ex vivo cultures of unfed adult female I. scapularis ticks