Challenges in conducting population-based seroepidemiology survey of COVID-19 in Lagos State, Nigeria

Population-based study is known to be a very essential type of study during and after a pandemic or epidemic, as it provides crucial information on the incidence, prevalence, and risk factors of the disease in question. There has been limited information about the challenges faced in conducting such surveys in Nigeria. In this paper, we will share our experience, and describe the challenges faced in conducting a population-based seroepidemiological study of COVID-19 in Lagos, Nigeria. Some challenges were peculiar to specific Local Government Areas (LGAs) while others were general. The challenges include general misconceptions of community members about health research, difficulties in mapping houses, planning for data collection, standardizing data collection, working in hard-to-reach communities when resources were limited as well as difficulty in collection of blood and naso-oropharyngeal swabs. Ways of overcoming these problems, lessons learnt, and recommendations are hereby discussed.

Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria

Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates.

The use of DIY (Do it yourself) sampling and telemonitoring model for COVID-19 qPCR testing scale up

The first case of COVID-19 in Nigeria was recorded on February 27, 2020, being an imported case by an Italian expatriate, to the country. Since then, there has been steady increase in the number of cases. However, the number of cases in Nigeria is low in comparison to cases reported by other countries with similar large populations, despite the poor health system prevailing in the country. This has been mainly attributed to the low testing capacity in Nigeria among other factors. Therefore, there is a need for innovative ways to increase the number of persons testing for COVID-19. The aim of the study was to pilot a nasopharyngeal swab self-sample collection model that would help increase COVID-19 testing while ensuring minimal person-to-person contact being experienced at the testing center. 216 participants took part in this study which was carried out at the Nigerian Institute of Medical Research between June and July 2020. Amongst the 216 participants, 174 tested negatives for both self-collected samples and samples collected by Professionals, 30 tested positive for both arms, with discrepancies occurring in 6 samples where the self-collected samples were positive while the ones collected by the professionals were negative. The same occurred in another set of 6 samples with the self-collected samples being negative and the professional-collected sample coming out positive, with a sensitivity of 83.3% and a specificity of 96.7%. The results of the interrater analysis are Kappa = 0.800 (95% CI, 0.690 to 0.910) which implies an outstanding agreement between the two COVID-19 sampling methods. Furthermore, since p< 0.001 Kappa (k) coefficient is statistically different from zero, our findings have shown that self-collected samples can be reliable in the diagnosis of COVID-19.

Low levels of HIV-1 drug resistance mutations in patients who achieved viral re-suppression without regimen switch: a retrospective study

BACKGROUND

We identified a HIV-positive cohort in virologic failure (VF) who re-suppressed without drug switch. We characterized their drug resistance mutations (DRM) and adherence profiles to learn how to better manage HIV drug resistance. A retrospective cohort study utilizing clinical data and stored samples. Patients received ART at three Nigerian treatment centres. Plasma samples stored when they were in VF were genotyped.

RESULT

Of 126 patients with samples available, 57 were successfully genotyped. From ART initiation, the proportion of patients with adherence ≥90% increased steadily from 54% at first high viral load (VL) to 67% at confirmed VF, and 81% at time of re-suppressed VL. Sixteen (28%) patients had at least one DRM. Forty-six (81%) patients had full susceptibility to the three drugs in their first-line (1 L) regimen. Thirteen (23%) were resistant to at least one antiretroviral drug but three were resistant to drugs not used in Nigeria. Ten patients had resistance to their 1 L drug(s) and six were fully susceptible to the three drugs in the recommended second-line regimen.

CONCLUSION

This cohort had little drug resistance mutations. We conclude that if adherence is not assured, patients could exhibit virologic failure without having developed mutations associated with drug resistance.

Development and implementation challenges of a quality assured HIV infant diagnosis program in Nigeria using dried blood spots and DNA polymerase chain reaction

Nigeria has one of the highest HIV burdens as well as mother-to-infant transmission rates in the world. A pilot program using polymerase chain reaction (PCR)-based testing of dried blood spot (DBS) specimens was implemented to enable early identification of HIV-infected infants and timely referral and linkage to care. From February 2007 to October 2008, whole blood was collected by finger prick to prepare DBS from infants <18 months presenting in six public mother-and-child health facilities in Lagos, Nigeria. The DBS were tested using the Roche Amplicor HIV-1 DNA Test, v1.5. To monitor laboratory testing quality, all of the PCR-positive and 10% of the PCR-negative DBS were retested by the same method at another reference laboratory. Three hundred and sixty-five randomly selected infants were screened using HIV rapid tests (RT) according to the national algorithm and RT-negative and PCR-positive specimens were also tested using Genscreen enzyme-linked immunosorbent assay (EIA) (Bio-Rad, France). The turnaround time (TAT) from sample collection, testing, and dispatching of results from each health facility was monitored. A total of 1,273 infants with a median age of 12.6 weeks (1 day to 71.6 weeks) participated in the program and 280 (22.0%) were PCR positive. HIV transmission levels varied greatly in the different health facilities ranging from 7.1% to 38.4%. Infants aged 48 to 72 weeks had the highest level of PCR positivity (41.1%). All PCR-positive specimens were confirmed by retesting. The mean turnaround time from DBS collection to returning of the laboratory result to the health facilities was 25 days. Three infants were found to be HIV antibody negative by rapid tests but were positive by both PCR and the fourth generation EIA. The DBS-based PCR program accurately identified all of the HIV-infected infants. However, many programmatic challenges related to the laboratory and TAT were identified.

Sero-prevalence and factors associated with Hepatitis B and C co-infection in pregnant Nigerian women living with HIV infection

Introduction

Perinatal and horizontal transmission of Hepatitis B occur in areas of high endemicity as most infections are acquired in the first 5 years of life. Unless Hepatitis B and C infected pregnant women identified, and appropriate treatment provided, children born to these women are at high risk of chronic Hepatitis B (and C) virus infection. The objecive of this study was to determined the prevalence and the factors associated with Hepatitis B and C Virus infection in pregnant HIV positive Nigerians.

Methods

A cross sectional study among HIV Positive pregnant women seen at a large PMTCT clinic in Lagos Nigeria. The women were screened for Hepatitis B and C Virus infection at enrollment. HIV viral load, CD4 count, liver transaminases and hemoglobin levels were also determined. Data were managed with SPSS for windows version. Ethical approval was obtained from the Institutions Ethical Review Board.

Results

Of the 2391 studied subjects, 101(4.2%) and 37(1.5%) respectively were seropositive for Hepatitis B and C Virus infection. Twowomen (0. 08%) had triple infections. blood transfusion, (cOR: 2.3; 95% CI:1.1 - 4.6), history of induced abortion (cOR:2. 2;95% CI:1.3 - 3.6), and elevated baseline ALT (cOR:2. 2; 95%CI:2. 2;4.2) were significantly associated with HBV. History of induced abortion was the only factor found to be associated with HIV/ HCV (cOR: 1.9;95%CI:1. 3-3.9).

Conclusion

Hepatitis B Virus infection (4.2%) is relatively common in our environment and associated with induced abortion, blood transfusion and elevated baseline transaminase. Hepatitis C Virus infection (1.5%) is less common and associated with only history of induced abortion.