Long term outcomes of highly active antiretroviral therapy in HIV infected Nigerians and those co-infected with hepatitis B and C viruses

Background: HIV co-infection with hepatitis B (HBV) and/or hepatitis C virus (HCV) is common, largely due to shared routes of transmission, but paucity of data exists for long term treatment outcomes of HIV infected patients, and those co-infected with HBV and HCV despite the high burden in Nigeria. The aim of study was to describe the longterm treatment outcomes in HIV infected Nigerians and to assess the effect of HBV and HCV co-infections on longterm response to antiretroviral therapy (ART).Methodology: This was a retrospective study of HIV infected adults (> 18 years old) consecutively initiating ART between July 2004 and December 2007, who were followed up for 7 years (2011 and 2014). HBV and HCV infections were diagnosed by detection of serum hepatitis B surface antigen (HBsAg) and HCV antibody (HCVAb) respectively. HIV viral load and CD4 count were monitored 3-monthly after initiating ART, and treatment outcomes based on these were compared between patients with HIV mono-infection, HIV/HBV, HIV/HCV and HIV/HBV/HCV co-infections. Clinical and laboratory data of the patients were abstracted from the medical databases, FileMaker Pro, v 10, entered into Microsoft Excel, and analyzed using SPSS version 20.0.Results: A total of 2,800 adults were evaluated (median age of 35.5 years; 64.2% female), of whom 197 (7.0%) were co-infected with HBV, 53 (1.9%) with HCV, and 15 (0.5%) with HBV and HCV. During the 7-year period, 369 (13.2%) patients were lost to follow up. Immune reconstitution, measured by CD4 recovery, was lower in both HBV and HCV co-infections compared to HIV mono-infection, but this was not statistically significant (p>0.05). Median baseline HIV viral load was 4.63 log copies/ml for all groups, which decreased to undetectable level at a median time of 6 months and remained so for the study duration.Conclusion: This study revealed a higher virologic failure among HIV/HCV co-infected group compared to other groups. No immunological difference in ART treatment outcomes between HIV mono-infected and those co-infected with HBV and HCV after 7-year follow-up. Gradual rise in CD4 was found to be an immunological evidence of the body’s recovery from HIV, buttressed by the drop in viral load over the 7-year period. Keywords: ART, HIV, HBV, HCV co-infection, long term outcomes   English title: Résultats à long terme du traitement antirétroviral hautement actif chez les Nigérians infectés par le VIH et ceux co-infectés par les virus des hépatites B et C Contexte: La co-infection par le VIH avec l'hépatite B (VHB) et/ou le virus de l'hépatite C (VHC) est courante, engrande partie en raison des voies de transmission partagées, mais il existe peu de données sur les résultats dutraitement à long terme des patients infectés par le VIH, et ceux co -infectés par le VHB et le VHC malgré le fardeau élevé au Nigéria. Le but de l'étude était de décrire les résultats du traitement à long terme chez les Nigérians infectés par le VIH et d'évaluer l'effet des co-infections par le VHB et le VHC sur la réponse à long terme au traitement antirétroviral (TAR).Méthodologie: Il s'agissait d'une étude rétrospective sur des adultes infectés par le VIH (>18 ans) ayant commencé un traitement antirétroviral consécutivement entre juillet 2004 et décembre 2007, suivis pendant 7 ans (2011 et 2014). Les infections par le VHB et le VHC ont été diagnostiquées par détection de l'antigène de surface sérique de l'hépatite B (AgHBs) et des anticorps anti-VHC (HCVAb) respectivement. La charge virale du VIH et la numération des CD4 ont été surveillées tous les trois mois après le début du TAR, et les résultats du traitement basés sur ceuxci ont été comparés entre les patients atteints de mono-infection VIH, VIH/VHB, VIH/VHC et VIH/VHB/VHC. Les données cliniques et de laboratoire des patients ont été extraites des bases de données médicales, FileMaker Pro, v 10, saisies dans Microsoft Excel et analysées à l'aide de SPSS version 20.0.Résultats: Un total de 2800 adultes ont été évalués (âge médian de 35,5 ans; 64,2% de femmes), dont 197 (7,0%) étaient co-infectés par le VHB, 53 (1,9%) par le VHC et 15 (0,5%) par le VHB et VHC. Au cours de la période de 7 ans, 369 (13,2%) patients ont été perdus de vue. La reconstitution immunitaire, mesurée par la récupération des CD4, était plus faible dans les co-infections par le VHB et le VHC que dans la mono-infection par le VIH, mais cela n'était pas statistiquement significatif (p>0,05). La charge virale VIH de base médiane était de 4,63 log copies / ml pour tous les groupes, ce qui a diminué à un niveau indétectable à une période médiane de 6 mois et le reste pendant toute la durée de l'étude.Conclusion: Cette étude a révélé un échec virologique plus élevé parmi le groupe co-infecté par le VIH / VHC par rapport aux autres groupes. Aucune différence immunologique dans les résultats du traitement TAR entre le VIH mono-infecté et ceux co-infectés par le VHB et le VHC après un suivi de 7 ans. L’augmentation progressive des CD4 s’est avérée être une preuve immunologique de la guérison du corps du VIH, étayée par la baisse de la charge virale au cours de la période de 7 ans. Mots clés: TAR, VIH, VHB, co-infection par le VHC, résultats à long terme     &nbsp

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

Communication: Implementation of biosafety in infection control: a 10-year review

Biosafety is an important issue globally, as a line of defence that protects health personnel, public and the environment from exposure to hazardous agents. Most developing nations have weak health systems and consequently weak biosafety. Engaging in an external quality program such as an accreditation process will help build capacity and competence in all areas. The Centre for Human Virology and Genomics (CHVG) laboratory of the Nigerian Institute of Medical Research, Lagos, Nigeria started its biosafety program in compliance to international standards stipulated by ISO 15189:2012, in its journey towards laboratory accreditation. Accreditation is widely used to attest for laboratory competence. In the quest for laboratory accreditation, several processes were implemented to ensure compliance, one of which was biosafety. Simple remedial actions and policies that have worked in other climes were applied over a 10-year period in the CHVG laboratory. A significant drop in nonconforming incidences and laboratory accidents was seen while biosafety audits showed improvement in safety practices. Keywords: Biosafety, Infection control, audit   French Title: Mise en œuvre de la biosécurité dans la lutte contre les infections: un examen décennal La biosécurité est une question importante à l'échelle mondiale, en tant que ligne de défense qui protège le personnel de santé, le public et l'environnement de l'exposition à des agents dangereux. La plupart des pays en développement ont des systèmes de santé faibles et, par conséquent, une faible sécurité biologique. S'engager dans un programme de qualité externe tel qu'un processus d'accréditation aidera à renforcer les capacités et les compétences dans tous les domaines. Le laboratoire du Centre de virologie humaine et de génomique (CHVG) de l'Institut nigérian de recherche médicale de Lagos, au Nigéria, a commencé son programme de biosécurité conformément aux normes internationales stipulées par ISO 15189: 2012, dans son parcours vers l'accréditation des laboratoires. L'accréditation est largement utilisée pour attester la compétence du laboratoire. Dans la recherche de l'accréditation des laboratoires, plusieurs processus ont été mis en œuvre pour assurer la conformité, dont l'un était la biosécurité. Des mesures  correctives simples et des politiques qui ont fonctionné sous d'autres climats ont été appliquées sur une période de 10 ans dans le laboratoire du CHVG. Une baisse significative des incidents non conformes et des accidents de laboratoire a été observée tandis que les audits de biosécurité ont montré une amélioration des pratiques de sécurité. Mots clés: Biosécurité, Contrôle des infections, audi

Genetic studies in the nigerian population implicate an MSX1 mutation in complex oral facial clefting disorders

BACKGROUND: Orofacial clefts are the most common malformations of the head and neck with a World-wide prevalence of 1/700 births. They are commonly divided into CL(P) and CP based on anatomical, genetic and embryological findings. A Nigerian craniofacial anomalies study “NigeriaCRAN” was set up in 2006 to investigate the role of gene-environment interaction in the etiology of orofacial clefts in Nigeria. SUBJECTS AND METHODS: DNA isolated from saliva from the Nigerian probands was used for genotype association studies and direct sequencing on the cleft candidate genes: MSX1, IRF6, FOXE1, FGFR1, FGFR2, BMP4, MAFB, ABCA4, PAX7 and VAX1, and the chromosome 8q region. RESULTS: A missense mutation A34G in MSX1 was observed in nine cases and four hap map controls. No other apparent etiologic variations were identified. A deviation from HWE was observed in the cases (p= 0.00002). There was a significant difference between the affected side for unilateral CL (p=0.03) and, between bilateral clefts and clefts on either side (p=0.02). A significant gender difference was also observed for CP (p=0.008). CONCLUSIONS: The replication of a mutation previously implicated in other populations suggests a role for the MSX1 A34G variant in the etiology of CL(P)