COVID-19 in Nigeria: Implications for Management of Related Co-morbidities, Prevalent Public Health Challenges, and Future Epidemic Preparedness

The Coronavirus Disease-2019 (COVID-19) pandemic is now well-established in Africa with cases reported from all countries on the continent. Despite the significant progress that has been made in the response to the pandemic in Nigeria, relative to the period of Ebola epidemic, the currently reported number of COVID-19 cases are likely under-estimates of the true number of cases. This is attributable to restricted testing capacity due to limited technical, infrastructural, financial, and logistical capacity to rapidly scale-up testing. In this article, we explore the impact of the COVID-19 pandemic on management of related co-morbidities and the major prevalent public health challenges, including mental health, in Nigeria, Africa’s most populous country. We also discuss the most current knowledge about candidate vaccines for the control of the novel coronavirus (SARS-CoV-2) strain. The interactions between COVID-19 and the endemic public health challenges in Nigeria further highlight the linkage between infectious diseases and poverty, and emphasise the need for a sustained increase in investments in the general public health system that is geared toward achieving Universal Health Coverage in Nigeria

Sequence analysis of Plasmodium vivax Duffy binding proteins reveals the presence of unique haplotypes and diversifying selection in Ethiopian isolates.

BACKGROUND: Red blood cell invasion by the Plasmodium vivax merozoite requires interaction between the Duffy antigen receptor for chemokines (DARC) and the P. vivax Duffy-binding protein II (PvDBPII). Given that the disruption of this interaction prevents P. vivax blood-stage infection, a PvDBP-based vaccine development has been well recognized. However, the polymorphic nature of PvDBPII prevents a strain transcending immune response and complicates attempts to design a vaccine. METHODS: Twenty-three P. vivax clinical isolates collected from three areas of Ethiopia were sequenced at the pvdbpII locus. A total of 392 global pvdbpII sequences from seven P. vivax endemic countries were also retrieved from the NCBI archive for comparative analysis of genetic diversity, departure from neutrality, linkage disequilibrium, genetic differentiation, PvDBP polymorphisms, recombination and population structure of the parasite population. To establish a haplotype relationship a network was constructed using the median joining algorithm. RESULTS: A total of 110 variable sites were found, of which 44 were parsimony informative. For Ethiopian isolates there were 12 variable sites of which 10 were parsimony informative. These parsimony informative variants resulted in 10 nonsynonymous mutations. The overall haplotype diversity for global isolates was 0.9596; however, the haplotype diversity was 0.874 for Ethiopia. Fst values for genetic revealed Ethiopian isolates were closest to Indian isolates as well as to Sri Lankan and Sudanese isolates but further away from Mexican, Papua New Guinean and South Korean isolates. There was a total of 136 haplotypes from the 415 global isolates included for this study. Haplotype prevalence ranged from 36.76% to 0.7%, from this 74.2% were represented by single parasite isolates. None of the Ethiopian isolates grouped with the Sal I reference haplotype. From the total observed nonsynonymous mutations 13 mapped to experimentally verified epitope sequences. Including 10 non-synonymous mutations from Ethiopia. However, all the polymorphic regions in Ethiopian isolates were located away from DARC, responsible for junction formation. CONCLUSION: The results of this study are concurrent with the multivalent vaccine approach to design an effective treatment. However, the presence of novel haplotypes in Ethiopian isolates that were not shared by other global sequences warrant further investigation

Diagnostic performance of a novel loop-mediated isothermal amplification (LAMP) assay targeting the apicoplast genome for malaria diagnosis in a field setting in sub-Saharan Africa.

BACKGROUND: New diagnostic tools to detect reliably and rapidly asymptomatic and low-density malaria infections are needed as their treatment could interrupt transmission. Isothermal amplification techniques are being explored for field diagnosis of malaria. In this study, a novel molecular tool (loop-mediated isothermal amplification-LAMP) targeting the apicoplast genome of Plasmodium falciparum was evaluated for the detection of asymptomatic malaria-infected individuals in a rural setting in The Gambia. METHODS: A blood was collected from 341 subjects (median age 9 years, range 1-68 years) screened for malaria. On site, a rapid diagnostic test (RDT, SD Bioline Malaria Antigen P.f) was performed, thick blood films (TBF) slides for microscopy were prepared and dry blood spots (DBS) were collected on Whatman(®) 903 Specimen collection paper. The TBF and DBS were transported to the field laboratory where microscopy and LAMP testing were performed. The latter was done on DNA extracted from the DBS using a crude (methanol/heating) extraction method. A laboratory-based PCR amplification was done on all the samples using DNA extracted with the Qiagen kit and its results were taken as reference for all the other tests. RESULTS: Plasmodium falciparum malaria prevalence was 37 % (127/341) as detected by LAMP, 30 % (104/341) by microscopy and 37 % (126/341) by RDT. Compared to the reference PCR method, sensitivity was 92 % for LAMP, 78 % for microscopy, and 76 % for RDT; specificity was 97 % for LAMP, 99 % for microscopy, and 88 % for RDT. Area under the receiver operating characteristic (ROC) curve in comparison with the reference standard was 0.94 for LAMP, 0.88 for microscopy and 0.81 for RDT. Turn-around time for the entire LAMP assay was approximately 3 h and 30 min for an average of 27 ± 9.5 samples collected per day, compared to a minimum of 10 samples an hour per operator by RDT and over 8 h by microscopy. CONCLUSION: The LAMP assay could produce reliable results the same day of the screening. It could detect a higher proportion of low density malaria infections than the other methods tested and may be used for large campaigns of systematic screening and treatment

Beyond SARS-CoV-2: Lessons That African Governments Can Apply in Preparation for Possible Future Epidemics.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has placed unprecedented pressure on healthcare systems, even in advanced economies. While the number of cases of SARS-CoV-2 in Africa compared to other continents has so far been low, there are concerns about under-reporting, inadequate diagnostic tools, and insufficient treatment facilities. Moreover, proactiveness on the part of African governments has been under scrutiny. For instance, issues have emerged regarding the responsiveness of African countries in closing international borders to limit trans-continental transmission of the virus. Overdependence on imported products and outsourced services could have contributed to African governments' hesitation to shut down international air and seaports. In this era of emerging and re-emerging pathogens, we recommend that African nations should consider self-sufficiency in the health sector as an urgent priority, as this will not be the last outbreak to occur. In addition to the Regional Disease Surveillance Systems Enhancement fund (US$600 million) provided by the World Bank for strengthening health systems and disease surveillance, each country should further establish an epidemic emergency fund for epidemic preparedness and response. We also recommend that epidemic surveillance units should create a secure database of previous and ongoing pandemics in terms of aetiology, spread, and treatment, as well as financial management records. Strategic collection and analysis of data should also be a central focus of these units to facilitate studies of disease trends and to estimate the scale of requirements in preparation and response to any future pandemic or epidemic

Comparison of surveillance methods applied to a situation of low malaria prevalence at rural sites in The Gambia and Guinea Bissau

BACKGROUND: Health record-based observations from several parts of Africa indicate a major decline in malaria, but up-to-date information on parasite prevalence in West-Africa is sparse. This study aims to provide parasite prevalence data from three sites in the Gambia and Guinea Bissau, respectively, and compares the usefulness of PCR, rapid diagnostic tests (RDT), serology and slide-microscopy for surveillance. METHODS: Cross-sectional surveys in 12 villages at three rural sites were carried out in the Gambia and Guinea Bissau in January/February 2008, shortly following the annual transmission season. RESULTS: A surprisingly low microscopically detectable parasite prevalence was detected in the Gambia (Farafenni: 10.9%, CI95%: 8.7-13.1%; Basse: 9.0%, CI95%: 7.2-10.8%), and Guinea Bissau (Caio: 4%, CI95%: 2.6-5.4%), with low parasite densities (geometric mean: 104 parasites/microl, CI95%: 76-143/microl). In comparison, PCR detected a more than three times higher proportion of parasite carriers, indicating its usefulness to sensitively identify foci where malaria declines, whereas the RDT had very low sensitivity. Estimates of force of infection using age sero-conversion rates were equivalent to an EIR of approximately 1 infectious bite/person/year, significantly less than previous estimates. The sero-prevalence profiles suggest a gradual decline of malaria transmission, confirming their usefulness in providing information on longer term trends of transmission. A greater variability in parasite prevalence among villages within a site than between sites was observed with all methods. The fact that serology equally captured the inter-village variability, indicates that the observed heterogeneity represents a stable pattern. CONCLUSION: PCR and serology may be used as complementary tools to survey malaria in areas of declining malaria prevalence such as the Gambia and Guinea Bissau

Comparative analysis of four malaria diagnostic tools and implications for malaria treatment in southwestern Nigeria.

OBJECTIVES: One of the problems encountered in malaria control and elimination is inaccurate diagnosis, resulting from the degree of sensitivity of the different malaria diagnostic tools. Even though microscopy remains the gold standard for malaria diagnosis, more sensitive and robust diagnostic tools such as polymerase chain reactions (PCR) are used in research settings to monitor interventions and track sub-microscopic infections due to some of the drawbacks of microscopy. Since diagnosis is a critical determinant for rational malaria treatment, it is imperative that accurate diagnosis must be assured for an effective treatment plan. Therefore, this study compared two routinely used point of care malaria diagnostic tools with two molecular tools and discussed their implication for malaria treatment. DESIGN: In this study, 436 individuals with suspected malaria were sampled and systematically tested using four methods, namely rapid diagnostic test (henceforth referred to as malaria RDT- mRDT), microscopy, nested PCR (nPCR), and quantitative PCR (qPCR). Test sensitivities and specificities were compared, and their level of concordance was determined. RESULTS: With nPCR as the gold standard, a false positivity rate of 42.2%, 8.9%, and 57.8% was obtained for mRDT, microscopy, and qPCR. Similarly, false negativity rates of 12.5%, 62.5%, and 0.8% were obtained for each of the methods mentioned above, respectively. Of all the tools assessed, qPCR gave the highest sensitivity (99.2%) and moderate specificity (42.2%), followed by the mRDT kit used (87.5%). CONCLUSIONS: With the detection of a high false positivity rate based on mRDT and a substantial proportion of sub-microscopic carriers in this study area by nested/quantitative PCR, we recommend that these molecular tools should be in specialized laboratories within the region to (i) track and treat sub-microscopic carriers to prevent their contribution to malaria transmission; (ii) provide reliable epidemiological data using high throughput testing tools for evaluating malaria interventions

Seroprevalence and Parasite Rates of Plasmodium malariae in a High Malaria Transmission Setting of Southern Nigeria.

Although Plasmodium falciparum continues to be the main target for malaria elimination, other Plasmodium species persist in Africa. Their clinical diagnosis is uncommon, whereas rapid diagnostic tests (RDTs), the most widely used malaria diagnostic tools, are only able to distinguish between P. falciparum and non-falciparum species, the latter as "pan-species." Blood samples from health facilities were collected in southern Nigeria (Lagos and Calabar) in 2017 (October-December) and Calabar only in 2018 (October-November), and analyzed by several methods, namely, microscopy, quantitative real-time PCR (qPCR), and peptide serology targeting candidate antigens (Plasmodium malariae apical membrane antigen, P. malariae lactose dehydrogenase, and P. malariae circumsporozoite surface protein). Both microscopy and qPCR diagnostic approaches detected comparable proportions (∼80%) of all RDT-positive samples infected with the dominant P. falciparum malaria parasite. However, higher proportions of non-falciparum species were detected by qPCR than microscopy, 10% against 3% infections for P. malariae and 3% against 0% for Plasmodium ovale, respectively. No Plasmodium vivax infection was detected. Infection rates for P. malariae varied between age-groups, with the highest rates in individuals aged > 5 years. Plasmodium malariae-specific seroprevalence rates fluctuated in those aged < 10 years but generally reached the peak around 20 years of age for all peptides. The heterogeneity and rates of these non-falciparum species call for increased specific diagnosis and targeting by elimination strategies

High genetic complexity but low relatedness in Plasmodium falciparum infections from Western Savannah Highlands and coastal equatorial Lowlands of Cameroon.

To determine the diversity and connectivity of infections in Northwestern and Southwestern Cameroon, 232 Plasmodium falciparum infections, collected in 2018 from the Ndop Health District (NHD) in the western savannah highlands in the Northwest and the Limbe Health District (LHD) in the coastal lowland forests in the Southwest of Cameroon were genotyped for nine neutral microsatellite markers. Overall infection complexity and genetic diversity was significantly (p < 0.05) lower in NHD than LHD, (Mean MOI = 2.45 vs. 2.97; Fws = 0.42 vs. 0.47; Mean He = 0.84 vs. 0.89, respectively). Multi-locus linkage disequilibrium was generally low but significantly higher in the NHD than LHD population (mean ISA= 0.376 vs 0.093). Consequently, highly related pairs of isolates were observed in NHD (mean IBS = 0.086) compared to those from the LHD (mean IBS = 0.059). Infections from the two regions were mostly unrelated (mean IBS = 0.059), though the overall genetic differentiation across the geographical range was low. Indices of differentiation between the populations were however significant (overall pairwise Fst = 0.048, Jost's D = 0.133, p < 0.01). Despite the high human migration across the 270km separating the study sites, these results suggest significant restrictions to gene flow against contiguous geospatial transmission of malaria in west Cameroon. Clonal infections in the highland sites could be driven by lower levels of malaria prevalence and seasonal transmission. How these differences in genetic diversity and complexity affect responses to interventions such as drugs will require further investigations from broader community sampling

Plasmodium malariae structure and genetic diversity in sub-Saharan Africa determined from microsatellite variants and linked SNPs in orthologues of antimalarial resistance genes

Plasmodium malariae, a neglected human malaria parasite, contributes up to 10% of malaria infections in sub-Saharan Africa (sSA). Though P. malariae infection is considered clinically benign, it presents mostly as coinfections with the dominant P. falciparum. Completion of its reference genome has paved the way to further understand its biology and interactions with the human host, including responses to antimalarial interventions. We characterized 75 P. malariae isolates from seven endemic countries in sSA using highly divergent microsatellites. The P. malariae infections were highly diverse and five subpopulations from three ancestries (independent of origin of isolates) were determined. Sequences of 11 orthologous antimalarial resistance genes, identified low frequency single nucleotide polymorphisms (SNPs), strong linkage disequilibrium between loci that may be due to antimalarial drug selection. At least three sub-populations were detectable from a subset of denoised SNP data from mostly the mitochondrial cytochrome b coding region. This evidence of diversity and selection calls for including P. malariae in malaria genomic surveillance towards improved tools and strategies for malaria elimination

Detecting Foci of Malaria Transmission with School Surveys: A Pilot Study in the Gambia.

BACKGROUND: In areas of declining malaria transmission such as in The Gambia, the identification of malaria infected individuals becomes increasingly harder. School surveys may be used to identify foci of malaria transmission in the community. METHODS: The survey was carried out in May-June 2011, before the beginning of the malaria transmission season. Thirty two schools in the Upper River Region of The Gambia were selected with probability proportional to size; in each school approximately 100 children were randomly chosen for inclusion in the study. Each child had a finger prick blood sample collected for the determination of antimalarial antibodies by ELISA, malaria infection by microscopy and PCR, and for haemoglobin measurement. In addition, a simple questionnaire on socio-demographic variables and the use of insecticide-treated bed nets was completed. The cut-off for positivity for antimalarial antibodies was obtained using finite mixture models. The clustered nature of the data was taken into account in the analyses. RESULTS: A total of 3,277 children were included in the survey. The mean age was 10 years (SD = 2.7) [range 4-21], with males and females evenly distributed. The prevalence of malaria infection as determined by PCR was 13.6% (426/3124) [95% CI = 12.2-16.3] with marked variation between schools (range 3-25%, p<0.001), while the seroprevalence was 7.8% (234/2994) [95%CI = 6.4-9.8] for MSP119, 11.6% (364/2997) [95%CI = 9.4-14.5] for MSP2, and 20.0% (593/2973) [95% CI = 16.5-23.2) for AMA1. The prevalence of all the three antimalarial antibodies positive was 2.7% (79/2920). CONCLUSIONS: This survey shows that malaria prevalence and seroprevalence before the transmission season were highly heterogeneous