A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS-CoV-2 in seven Sub-Saharan African countries: Lessons from the field.

BACKGROUND: The COVID-19 pandemic led to severe health systems collapse, as well as logistics and supply delivery shortages across sectors. Delivery of PCR related healthcare supplies continue to be hindered. There is the need for a rapid and accessible SARS-CoV-2 molecular detection method in low resource settings. OBJECTIVES: To validate a novel isothermal amplification method for rapid detection of SARS-CoV-2 across seven sub-Sharan African countries. STUDY DESIGN: In this multi-country phase 2 diagnostic study, 3,231 clinical samples in seven African sites were tested with two reverse transcription Recombinase-Aided Amplification (RT-RAA) assays (based on SARS-CoV-2 Nucleocapsid (N) gene and RNA-dependent RNA polymerase (RdRP) gene). The test was performed in a mobile suitcase laboratory within 15 min. All results were compared to a real-time RT-PCR assay. Extraction kits based on silica gel or magnetic beads were applied. RESULTS: Four sites demonstrated good to excellent agreement, while three sites showed fair to moderate results. The RdRP gene assay exhibited an overall PPV of 0.92 and a NPV of 0.88. The N gene assay exhibited an overall PPV of 0.93 and a NPV 0.88. The sensitivity of both RT-RAA assays varied depending on the sample Ct values. When comparing sensitivity between sites, values differed considerably. For high viral load samples, the RT-RAA assay sensitivity ranges were between 60.5 and 100% (RdRP assay) and 25 and 98.6 (N assay). CONCLUSION: Overall, the RdRP based RT-RAA test showed the best assay accuracy. This study highlights the challenges of implementing rapid molecular assays in field conditions. Factors that are important for successful deployment across countries include the implementation of standardized operation procedures, in-person continuous training for staff, and enhanced quality control measures.

Transmission transmissible hepatitis B virus markers of infection among sickle cell disease patients receiving care at a tertiary health facility in Ibadan, southwest Nigeria.

INTRODUCTION: Hepatitis B virus infection attacks the liver and can cause both acute and chronic disease. Sickle cell disease (SCD) patients are at risk of transmission transmissible viral hepatitis due to their constant need for blood transfusion. However, these patients could have been infected with HBV but may not know their status due to asymptomatic nature of the infection. Therefore, this study was designed to determine the burden of HBV markers of infection among SCD patients attending the hematology clinic at a tertiary health facility in Ibadan, Nigeria. METHODOLOGY: A cross-sectional study was investigated among 112 consenting SCD patients (M = 45; F = 67) age ranged 15-60 years (mean age = 26.9; mean PCV = 24 ± 4.8) attending a hematology clinic at the University College Hospital, Ibadan. A structured questionnaire was administered to capture demographic and other relevant information. Blood samples from each participant were tested for HBV markers by ELISA technique, while data were analyzed using SPSS version 21 with P < 0.05 considered significant. RESULTS: A total of 5 (4.5%), 0 (0.0%), and 15 (13.4%) were positive for HBsAg, HBeAg, and HBeAb, respectively. Also, 63 (56.3%) of the participants have never been transfused, while 49 (43.8%) had received blood transfusion at a point in time. No significant difference (P = 0.095) found a prevalence of HBV markers among those that had received blood transfusion and those that did not. Highest rates for HBsAg (3.6%) and HBeAb (10.7%) were observed among female than their male (HBsAg (0.9%) and HBeAb (2.8%) counterparts (P = 0.065)). No significant associations (P > 0.05) were found among those with incisions, among those who are sexually active and among the vaccinated individuals for HBV markers. There was a significant difference (P = 0.025) among the married participants for HBeAb with higher HBeAb rate (64.3%). CONCLUSION: This study reported high rates of HBV markers of infection among SCD patients. It is therefore advocated that donated blood must pass through rigorous screening processes before it is transfused.

Investigation of mother-to-child transmission of HIV in pregnancy and among HIV-exposed infants accessing care at a PMTCT clinic in southwest Nigeria.

BACKGROUND: Over 90% of infant acquired immunodeficiency syndrome (AIDS) cases have been through mother-to-child transmission (MTCT) of human immunodeficiency virus (HIV). Consequent to this, prevention of mother-to-child transmission (PMTCT) programs have instituted as dual purposes for prevention of HIV transmission from mother to child and enrollment of infected pregnant women and their families into antiretroviral treatment (ART) program. However, there are still some breakthrough infections and challenges. Therefore, this study was designed to assess risk of HIV transmission among HIV-exposed infants on follow-up at a PMTCT clinic in an antiretroviral (ARV) referral health facility in southwest Nigeria. METHODS: A cohort of 60 purposively recruited consenting pregnant women referred to PMTCT HIV clinic in Ibadan, southwest Nigeria were enrolled and followed up for 1 year (2015-2016). A well-structured epidemiological questionnaire was used to capture all relevant information. Data were then analyzed by SPSS version 21 (St. Louis, MO, USA), while bivariate and multivariate analyses were used to identify associations. RESULTS: A total of 44 mothers and their infants were available for the analysis with an attrition rate of 26.7%. The mean age of mothers at enrollment to follow-up was 32.9 years (SD = 4.2 years). Two (4.5%, 95% CI: 7.2-12.3%) of the infants were HIV positive by DNA PCR test. There was no linear relationship between age of the mothers with CD4 count or viral load both before and after delivery but there was a significant positive relationship with year on ARV (r = 0.318, 95% CI: 0.024-0.562). Infants of rural dwelling mothers were at 3.39 (adjusted odds ratio (AOR) = 3.39, 95% CI: 1.32, 2.29) times higher risk of vertical HIV transmission compared to those of urban dwelling mothers. Infants delivered at home had 2.61(AOR = 2.61, 95% CI: 1.59, 7.91) times higher risk of MTCT compared to those delivered at health institution. Mixed feeding was also another important predictor in which the risk of MTCT was about two (AOR = 2.21, 95% CI: 0.68, 9.97) times higher compared to exclusive breastfeeding. CONCLUSIONS: There was a high risk of MTCT of HIV among exposed infants on follow-up at the PMTCT clinic of Adeoyo Maternity Teaching referral hospital. Our findings will assist health policy makers in providing important information capable of enhancing assurance HIV control in such population and in raising the standard of PMTCT program in Nigeria.

Hepatitis B virus infection among asymptomatic residents of low income community in Ibadan, Southwest, Nigeria.

INTRODUCTION: Hepatitis B Virus (HBV) infection is one of the most infectious diseases worldwide and a major public health concern. In spite of efforts at controlling the scourge globally, HBV continues to thrive in developing countries, such as Nigeria due to ignorance on its mode of transmission and its asymptomatic nature in the populace. Therefore, this community-based study was carried out in Yemetu community in Ibadan, Nigeria to determine the burden of HBV infection among asymptomatic residents of this community. METHODOLOGY: Blood samples were aseptically collected from consenting 150 participants, male (m = 49) and female (f = 101), age ranged 15->55 years (Median age = 27.3 years). Astructured questionnaire was used to capture demographic data and other relevant information from these participants. Sera from these samples were tested for HBsAg using a 3rd generation Enzyme-Linked Immunosorbent-Assay (ELISA) Wantai HBV Diagnostics kit. Data were analyzed using Chi-square and ANOVA at 95% CI with P < 0.05 considered as significant. RESULTS: An overall seroprevalence rate for HBV in this study was 7.3%. HBV infection was higher among male (8.2%) than in female (6.7%), 1.4 times higher in male compared to their female counterparts (OR = 1.37, 95%CI 1.01-2.06) and also statistically significant (P = 0.043). Participants in the age groups 25-34 (10.3%) and >55 (4.2%) years had highest and lowest rates of HBV infection, respectively. Further analysis of the results by occupation shows that HBV infection was highest among Artisans (10.7%), followed by Students (6.9%) and Traders (6.9%) and lowest (5.6%) among Civil servants who are sexually active, married and unmarried. However, these differences were not statistically significant (P = 0.081). CONCLUSION: This study reported relatively high prevalence for HBV infection among asymptomatic population, which is of public health importance and this calls for urgent attention. Therefore, public sensitization on HBV transmission and control for all through voluntary counseling and testing is advocated.

Evaluation of performance testing of different rapid diagnostic kits in comparison with EIAs to validate detection of hepatitis B virus among high risk group in Nigeria.

BACKGROUND: Hepatitis B virus (HBV) causes chronic liver-associated diseases and its early detection is of high public health importance. Its diagnosis is mainly based on immunological assays among which Enzyme-Linked Immunosorbent Assay (ELISA) and rapid tests are the most common and widespread methods. However, a major challenge is the discordance of results of any two laboratory assays which cannot be easily resolved. Therefore, this study was designed to evaluate the validity and reliability of commercially available five rapid test kits in comparison with two Enzyme Immunoassays (EIAs) in Nigeria using hepatitis B surface antigen as a reference marker. METHODS: A total of 100 sera of previously diagnosed consenting HBV-positive patients from private diagnostic laboratories in Ibadan between March and August, 2011 were tested using two EIA and five rapid commercially available HBV test kits in Nigeria. Data were analyzed by SPSS version 15, while bivariate and multivariate analyses were carried out to identify associations at P < 0.05 considered significant. RESULTS: Overall, the sensitivity rates of the two EIA kits were 100% and 99.9% (95% confidence interval [CI] = 98.9-99.7) with specificity of 100% and 99.9% (95% CI = 98.9-99.7), respectively. The sensitivity of the five rapid test kits ranged from 97.5% (95% CI = 96.4-97.6) to 98.9% (95% CI = 97.9-99.9) with specificity of 80% (95% CI = 79.3-80.9) to 90% (95% CI = 89.2-91.0). Also, the positive predictive value ranged from 88% (95% CI = 88.2-89.9) to 89% (95% CI = 88.2-89.9), while the negative predictive value ranged from 80% (95% CI = 79.3-80.9) to 90% (95% CI = 89.2-91.0) for the five rapid kits. However, that of the two EIAs ranged from 99.9% (98.9-99.7) to 100%. Further analysis showed significant (P = 0.033) variations in the sensitivity and specificity of the EIAs and rapid test kits. CONCLUSIONS: The results from this study have clearly revealed the challenges of diagnosis of HBV infections in Nigeria. This study has also demonstrated that the sensitivity of most of the rapid test kits may not be adequate when compared with EIA for early detection of HBV infections. The implications of possible misdiagnosis on the various intervention strategies that rely predominantly on correct HBV status of an individual are enormous. Therefore, there is the need to further compliment the use of rapid test kits with EIAs for HBV control in Nigeria.

Seroprevalence of hepatitis B surface antigenemia and viral infectivity among liver cancer patients accessing care at a tertiary health facility in Southwest Nigeria.

INTRODUCTION: Hepatitis B virus (HBV) infection is a public health challenge globally, associated with hepatocellular carcinoma and known to be highly endemic in developing countries. Its comorbidity with cancer in infected patients poses greater challenge in their management. This study was therefore designed to determine the burden of HBV infection and its correlation among cancer patients assessing care in a tertiary health facility in southwest Nigeria. METHODOLOGY: A total of 122 plasma samples from consenting cancer patients were tested for Hepatitis B surface Antigen (HBsAg) using a commercial enzyme-linked immunosorbent (ELISA) assay and their plasma HBV DNA quantified by COBAS Amplicor HBV Monitor assay. Data were analyzed using SPSS version 21 and chi-square (χ2) test was used to determine association while p < 0.05 considered statistically significant. RESULTS: An overall HBsAg rate of 13.9% was found among the study population. The distribution of HBsAg positivity among the subjects with condition of cancer showed 9(23.7%) with chronic liver disease (CLD), 4(10.8%) in primary liver carcinoma (PLCC) and 4(8.5%) with pyrexia of unknown origin (PUO). The CLD group had highest viral infectivity (Mean=8324.3 Copies/Ml) and lowest among those with PLCC (468.4 Copies/Ml). The rate for HBsAg was higher in male (14.7%) than in their female (13.0%) counterparts with significant statistical association by gender (p>0.0314) and peaked (23.5%) among age group 20-29 years. CONCLUSION: This study identified high rate of HBV infection among the population and could be investigated as a predictor for cancer. This finding is vital in the management of cancer patients coinfected with HBV.

Development of a pan-rickettsial molecular diagnostic test based on recombinase polymerase amplification assay.

Rickettsioses are zoonotic vector-transmitted bacterial infections leading to flu-like symptoms and can progress to severe illness in humans. The gold standard for diagnosis of rickettsial infections is the indirect immunofluorescence assay, a serological method which is not suitable for pathogen identification during the acute phase of the disease. Therefore, several real-time PCR assays were developed. These assays are very sensitive, but require high-equipped laboratories and well-trained personnel. Hence, in this study, a rapid point-of-need detection method was developed to detect all Rickettsia species. The 23S and 16S rRNA genes were targeted to develop a recombinase polymerase amplification (RPA) assay. Both 23S and 16S_RPA assays required between seven to ten minutes to amplify and detect one or ten DNA molecules/reaction, respectively. The 16S_RPA assay detected all tested species, whereas the 23S_RPA assay identified only species of the spotted fever and transitional rickettsial groups. All results were compared with real-time PCR assays directed against the same rickettsial genes. The RPA assays are easy to handle and produced quicker results in comparison to real-time PCRs. Both RPA assays were implemented in a mobile suitcase laboratory to ease the use in rural areas. This method can help to provide rapid management of rickettsial infections.

Detection and circulation of hepatitis B virus immune escape mutants among asymptomatic community dwellers in Ibadan, southwestern Nigeria.

BACKGROUND: In 2012, the first Nigerian Hepatitis B Virus (HBV) immune escape mutant (IEM) case was detected in a pregnant woman in southwestern Nigeria. Consequently, this study was designed to investigate the presence and possible circulation of IEMs amongst asymptomatic community dwellers in southwestern Nigeria. METHODS: Blood specimens collected from 438 asymptomatic community dwellers were screened for HBsAg using ELISA technique. Subsequently, the S-gene was amplified in HBsAg positive samples by a nested PCR protocol, and amplicons sequenced. Isolates were then subtyped by amino acid residues at positions 122, 127, 134 and 160, and genotyped by phylogenetic analysis. RESULTS: Of the 31 (7.08%) samples positive for HBsAg, the ∼ 408 bp Sgene fragment was successfully amplified and sequenced in 27. Samples obtained from 4 patients could not be amplified due to low titres. Sequence data from only 15 of the isolates could be analysed further as eight of the remaining 12 had multiple peaks while the rest three showed no similarity to any HBV gene when subjected to BLAST analysis. Thirteen of the 15 isolates were identified as genotype E. Eleven of which were subtyped as ayw4 while the remaining two could not be subtyped due to sR122Q/P substitutions. The last two isolates that could not be genotyped and subtyped had other mutations in the "a" determinant associated with IEMs. CONCLUSIONS: This study confirmed presence and circulation of HBV IEM in Nigeria, the country's inclusion in the genotype E crescent, and the value of phylogenetic analysis in HBV identification.