Evaluation of quality control viral load HIV results from two laboratories in Maputo, after the 3rd Congress of Laboratory Quality Control for Portuguese-Speaking Countries, Mozambique

The Project of Laboratory Quality Improvement for Portuguese Speaking Countries (ProMeQuaLab) is based on three major work tools: education, training and monitoring of quality control measures, in order to build capacity to implement and sustain good laboratory practices. Since 2015, a biennial congress on quality control is organised which includes also courses in this field. The third edition of the Congress was held in Mozambique in May 2019. Theoretical and practical courses concerning internal (CQI) and external quality control (EQA), calculation of Total Error (TE) and Measurement Uncertainty (MU) were held. Two practical work sessions were organized, with the trainers of the quality control courses and trainees from two laboratories, Centro Criança Dream (Dream) and Laboratório de Virologia Molecular (INS) in Maputo (Mozambique), to applied the statistical tools to evaluate their quality control results of viral load HIV from 2018. Evaluation of viral load is strongly recommended by WHO for monitoring response to retroviral treatment. The objective of this work was the implementation of the concepts and tools of the assessment of bias and uncertainty presented in the quality control courses and their application on the quantitative quality control results from 2018 of RNA viral load HIV-1 from two laboratories from Maputo. The concepts and tools presented in quality control courses were applied to quality control results of two laboratories in Maputo (Mozambique) for the measure of imprecision, bias and measurement uncertainty. The courses and the work sessions have proved to be very effective in transferring knowledge and skills and therefore should be continued with other laboratories. The results of the bias and measurement uncertainty show that the INS laboratory (Cobas Ampliprep TaqMan96) had a better performance in comparison to the Dream laboratory (Abbott m2000). Effort must be made to continue the education program, namely the interpretation of the quality control results to achieve an improvement of the evaluation of patient results.N/

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

Hepatitis B virus genotypes and drug resistance mutations circulating in blood donors in Beira, Mozambique.

Hepatitis B virus (HBV) infects nearly 300 million people and is the leading cause of hepatitis and hepatocellular carcinoma worldwide. Despite the high burden of HBV in sub-Saharan Africa, countries such as Mozambique have limited data available on circulating HBV genotypes and the presence of drug resistance mutations. Blood donors from Beira, Mozambique were tested for HBV surface antigen (HBsAg) and HBV DNA at the Instituto Nacional de Saúde in Maputo, Mozambique. Regardless of HBsAg status, donors with detectable HBV DNA were evaluated for HBV genotype. PCR was performed with primers amplifying a 2.1-2.2 kilobase fragment of the HBV genome. PCR products were submitted for next generation sequencing (NGS), and consensus sequences were evaluated for HBV genotype, recombination, and the presence or absence of drug resistance mutations. Of the 1281 blood donors tested, 74 had quantifiable HBV DNA. The polymerase gene could be amplified from 45 of 58 (77.6%) individuals with chronic HBV infection and 12 of 16 (75%) with occult HBV infection. Among these 57, 51 (89.5%) sequences belonged to HBV genotype A1, while 6 (10.5%) were HBV genotype E. All genotype E sequences were E/A recombinants, and clustered separately from other genotype E references. Genotype A samples had a median viral load of 637 IU/mL, while genotype E samples had a median viral load of 476,084 IU/mL. No drug resistance mutations were observed in the consensus sequences. The current study demonstrates the genotypic diversity of HBV in blood donors in Mozambique, but the absence of dominant (consensus) drug resistance mutations. Studies in other at-risk populations are essential for understanding the epidemiology, risk of liver disease, and likelihood of treatment resistance in resource-limited settings

Nucleic acid testing identifies high prevalence of blood borne viruses among approved blood donors in Mozambique.

BackgroundAlthough blood transfusion is an intervention that saves lives, it poses significant risks to the blood receivers, including the transmission of bloodborne pathogens. We aimed at determining the prevalence of Human Immunodeficiency Virus (HIV), Hepatitis B virus (HBV), and Hepatitis C virus (HCV) in candidates approved for blood donation, and in samples considered to be negative in reference blood banks in Mozambique.MethodsA cross-sectional study was performed between November 2014 and October 2015 in Maputo and Beira cities. Demographic information was obtained from all consenting blood donors using a structured questionnaire. Plasma samples were screened for HIVAb/Ag combinations, HBsAg and Anti-HCV. Blood donors considered to be negative by serological testing were re-tested in pools of six plasma samples using nucleic acid testing (NAT).ResultsMost blood donors were male 2,320 (83.4%) with an age range of 18 to 34 years. The overall seroprevalence of HIV, HBV and HCV infections among blood donors approved for donation was 4.6% (127; 95% CI 3.8-5.4), 4.5% (124; 95% CI 3.7-5.3) and 0.4% (11; 95% CI 0.2-0.7), respectively. The overall frequency by NAT of HIV RNA, HBV DNA, and HCV RNA in serologically negative blood donor samples was 2.6 per 1000 blood donors (7; 95% CI 1.1-5.4); 12.5 per 1000 blood donors (33; 95% CI 8.6-17.5) and 2.6 per 1000 blood donors (6; 95% CI 1.0-5.7), respectively.ConclusionOur results show high seroprevalence of HIV and HBV infections in blood donors approved for donation, and high frequency of molecular biomarkers of HIV, HBV, and HCV in blood considered to be safe. These results suggest the need for a new blood screening policy in Mozambique, including the use of NAT to detect infectious blood donations during the immunologically negative window

First report of occult hepatitis B infection among ART naïve HIV seropositive individuals in Maputo, Mozambique.

The prevalence of hepatitis B virus (HBV) infection and human immunodeficiency virus (HIV) infection in Mozambique is one of the highest in the world, though in spite of this the prevalence of occult hepatitis B infection (OBI) is unknown.This study was conducted with the aim to investigate the prevalence of OBI and frequency of isolated hepatitis B core antibody (anti-HBc alone) among antiretroviral (ART) naïve HIV-positive patients in Mozambique.A cross-sectional study was conducted in two health facilities within Maputo city. All ART-naive HIV seropositive patients attending outpatient clinics between June and October 2012 were consecutively enrolled. Blood samples were drawn from each participant and used for serological measurement of HBV surface antigen (HBsAg), antibodies against HBV surface antigen (anti-HBs) and antibodies against core antigen (anti-HBc) using ELISA. Quantification of HBV DNA was performed by real time PCR. A questionnaire was used to obtain demographics and clinical data.Of the 518 ART-naive HIV-positive subjects enrolled in the study, 90.9% (471/518) were HBsAg negative. Among HBsAg negative, 45.2% (213/471) had isolated anti-HBc antibodies, and the frequency of OBI among patients with anti-HBc alone was 8.3% (17/206). OBI was not correlated either with CD4+ T cells count or transaminases levels. A total of 11.8% of patients with OBI presented elevated HBV DNA level. Frequency of individuals with APRI score > 2 and FIB-4 score > 3.25 was higher in patients with OBI as compared not exposed, immune and anti-HBc alone patients.Our data demonstrate for the first time that OBI is prevalent among HIV patients in Mozambique, and will be missed using the commonly available serological assays that measures HBsAg

Accurate HIV viral load measurement in primary health care settings using the cobas® plasma separation card.

INTRODUCTION:Plasma is considered the gold standard for HIV viral load (VL) testing, however its use is challenging due to the need for phlebotomy and centrifugation services, as well as cold chain for transporting to laboratories for testing. The use of Dried Blood Spot (DBS) specimen has allowed a rapid expansion of antiretroviral therapy (ART) monitoring in remote areas in many African countries, however, the VL in DBS may overestimate the copies of viral RNA result at the clinically relevant range of 1000 copies/ml, due to proviral DNA and intracellular RNA. The characteristics of the cobas® Plasma Separation Card (PSC) specimen are similar to fresh plasma (gold standard), so a better performance of HIV VL is expetected in PSC specimen and can be an alternative to DBS. This study aims to evaluate the performance of cobas® PSC for VL testing at primary health care facilities in Mozambique. METHODOLOGY:HIV-1 infected adults on ART were enrolled consecutively in two health facilities in Mozambique, between August 2018 and October 2018. Capillary and venous cobas® PSC, DBS and fresh plasma specimens were collected from each patient. All specimens were tested for VL using CAP/CTM v2.0. Sensitivity and specificity of viral load using DBS, capillary and venous PSC specimens were estimated. Viral load obtained in fresh plasma specimen was used as reference and a threshold of 1000 copies/ml was considered for the analyses. RESULTS:From the total 613 patients included for the study, 2444 specimens including DBS (613), plasma (613), venous cobas® PSC (609) and capillary cobas® PSC (609) were collected and 2407 results were obtained. Sensitivity and specificity of the VL using venous cobas®PSC specimen at 1000 copies/ml threshold were 99.8% and 98.1% respectively, whereas for capillary cobas® PSC sensitivity was 99.6% and specificity was 97.2%. For DBS VL, sensitivity was 96.9% and specificity was 81.8%. Misclassification rate was more prominent in DBS specimens (5.9%), but lower in venous and capillary cobas®PSC with a rate of 0.3% and 0.7% respectively. CONCLUSION:The cobas® PSC specimen has improved performance over DBS for more accurate VL testing aligned with plasma testing. The use of this specimen type can increase the rates of reliable VL results and this will improve the quality of VL monitoring of HIV-positive patients in low-income settings

HBV infection in untreated HIV-infected adults in Maputo, Mozambique.

HIV/ HBV coinfected patients are at high risk of developing chronic HBV infection, liver cirrhosis and hepatocellular carcinoma. In Mozambique, where HIV prevalence is one of the highest in the world, HIV-infected patients are scarcely characterized in terms of HBV coinfection and 3TC-resistance mutations profile.To characterize ART-naïve HIV-infected adults, with and without HBV coinfection, a cross-sectional study was conducted between May and November 2012 in two health centers from Maputo city, Mozambique. Subjects were consecutively enrolled in the study and, then, tested for hepatitis B surface antigen (HBsAg). Moreover, CD4+ T cells count, HBV DNA in plasma, HBV genotyping and 3TC-resistance mutations profile of HBV were assessed in HIV/HBV coinfected patients.In total, 518 patients were enrolled in the study. The median age was 33 years old and 66.8% were women. The median CD4+ T cells count was 361 cells/mm3 and 47 (9.1%) were coinfected with HBV. Out of 46 coinfected patients, 24 (55.2%) had HBV DNA ≥ 20 - 2.0 was reported in 4.3% of coinfected and 1.7% of monoinfected patients (p = 0.228), while FIB-4 > 3.25 was reported in 4.4% of coinfected and 1.3% of monoinfected patients (p = 0.112). Genotype A was the most frequent, identified in 25/27 (92.6%) patients, whereas genotype E was present in 2/27 (7.4%) patients. No patient had 3TC-resistance mutations.This study showed that HBV coinfection was prevalent among ART-naïve HIV-infected adults in Mozambique. Overall, these data highlight the importance of screening HBV coinfection as an integrated measure of HIV routine care to improve health conditions and treatment of HIV/HBV coinfected patients

Flowchart of recruitment and testing of study participants.

<p>anti-HBc- − antibody against HBV core antigen. anti-HBs- − antibody against HBV surface antigen. DNA–desoxirribonucleic acid. HBsAg- HBV surface antigen. HBV–hepatitis B virus. HIV–human immunodeficiency virus. OBI- occult hepatitis B virus infection.</p

Serum viral load (DNA of HBV) in 17 HIV patients, with occult hepatitis B infection.

<p>Serum viral load (DNA of HBV) in 17 HIV patients, with occult hepatitis B infection.</p