Immunological insights into COVID-19 in Southern Nigeria.

Introduction: One of the unexpected outcomes of the COVID-19 pandemic was the relatively low levels of morbidity and mortality in Africa compared to the rest of the world. Nigeria, Africa's most populous nation, accounted for less than 0.01% of the global COVID-19 fatalities. The factors responsible for Nigeria's relatively low loss of life due to COVID-19 are unknown. Also, the correlates of protective immunity to SARS-CoV-2 and the impact of pre-existing immunity on the outcome of the COVID-19 pandemic in Africa are yet to be elucidated. Here, we evaluated the natural and vaccine-induced immune responses from vaccinated, non-vaccinated and convalescent individuals in Southern Nigeria throughout the three waves of the COVID-19 pandemic in Nigeria. We also examined the pre-existing immune responses to SARS-CoV-2 from samples collected prior to the COVID-19 pandemic. Methods: We used spike RBD and N- IgG antibody ELISA to measure binding antibody responses, SARS-CoV-2 pseudotype assay protocol expressing the spike protein of different variants (D614G, Delta, Beta, Omicron BA1) to measure neutralizing antibody responses and nucleoprotein (N) and spike (S1, S2) direct ex vivo interferon gamma (IFNγ) T cell ELISpot to measure T cell responses. Result: Our study demonstrated a similar magnitude of both binding (N-IgG (74% and 62%), S-RBD IgG (70% and 53%) and neutralizing (D614G (49% and 29%), Delta (56% and 47%), Beta (48% and 24%), Omicron BA1 (41% and 21%)) antibody responses from symptomatic and asymptomatic survivors in Nigeria. A similar magnitude was also seen among vaccinated participants. Interestingly, we revealed the presence of preexisting binding antibodies (N-IgG (60%) and S-RBD IgG (44%)) but no neutralizing antibodies from samples collected prior to the pandemic. Discussion: These findings revealed that both vaccinated, non-vaccinated and convalescent individuals in Southern Nigeria make similar magnitude of both binding and cross-reactive neutralizing antibody responses. It supported the presence of preexisting binding antibody responses among some Nigerians prior to the COVID-19 pandemic. Lastly, hybrid immunity and heterologous vaccine boosting induced the strongest binding and broadly neutralizing antibody responses compared to vaccine or infection-acquired immunity alone.

Genomic analyses in African populations identify novel risk loci for cleft palate.

Orofacial clefts are common developmental disorders that pose significant clinical, economical and psychological problems. We conducted genome-wide association analyses for cleft palate only (CPO) and cleft lip with or without palate (CL/P) with ~17 million markers in sub-Saharan Africans. After replication and combined analyses, we identified novel loci for CPO at or near genome-wide significance on chromosomes 2 (near CTNNA2) and 19 (near SULT2A1). In situ hybridization of Sult2a1 in mice showed expression of SULT2A1 in mesenchymal cells in palate, palatal rugae and palatal epithelium in the fused palate. The previously reported 8q24 was the most significant locus for CL/P in our study, and we replicated several previously reported loci including PAX7 and VAX1.

Identification of paternal uniparental disomy on chromosome 22 and a de novo deletion on chromosome 18 in individuals with orofacial clefts.

BACKGROUND: Orofacial clefts are the most common malformations of the head and neck region. Genetic and environmental factors have been implicated in the etiology of these traits. METHODS: We recently conducted genotyping of individuals from the African population using the multiethnic genotyping array (MEGA) to identify common genetic variation associated with nonsyndromic orofacial clefts. The data cleaning of this dataset allowed for screening of annotated sex versus genetic sex, confirmation of identify by descent and identification of large chromosomal anomalies. RESULTS: We identified the first reported orofacial cleft case associated with paternal uniparental disomy (patUPD) on chromosome 22. We also identified a de novo deletion on chromosome 18. In addition to chromosomal anomalies, we identified cases with molecular karyotypes suggesting Klinefelter syndrome, Turner syndrome and Triple X syndrome. CONCLUSION: Observations from our study support the need for genetic testing when clinically indicated in order to exclude chromosomal anomalies associated with clefting. The identification of these chromosomal anomalies and sex aneuploidies is important in genetic counseling for families that are at risk. Clinicians should share any identified genetic findings and place them in context for the families during routine clinical visits and evaluations.

Novel GREM1 Variations in Sub-Saharan African Patients With Cleft Lip and/or Cleft Palate.

OBJECTIVE: Cleft lip and/or cleft palate (CL/P) are congenital anomalies of the face and have multifactorial etiology, with both environmental and genetic risk factors playing crucial roles. Though at least 40 loci have attained genomewide significant association with nonsyndromic CL/P, these loci largely reside in noncoding regions of the human genome, and subsequent resequencing studies of neighboring candidate genes have revealed only a limited number of etiologic coding variants. The present study was conducted to identify etiologic coding variants in GREM1, a locus that has been shown to be largely associated with cleft of both lip and soft palate. PATIENTS AND METHOD: We resequenced DNA from 397 sub-Saharan Africans with CL/P and 192 controls using Sanger sequencing. Following analyses of the sequence data, we observed 2 novel coding variants in GREM1. These variants were not found in the 192 African controls and have never been previously reported in any public genetic variant database that includes more than 5000 combined African and African American controls or from the CL/P literature. RESULTS: The novel variants include p.Pro164Ser in an individual with soft palate cleft only and p.Gly61Asp in an individual with bilateral cleft lip and palate. The proband with the p.Gly61Asp GREM1 variant is a van der Woude (VWS) case who also has an etiologic variant in IRF6 gene. CONCLUSION: Our study demonstrated that there is low number of etiologic coding variants in GREM1, confirming earlier suggestions that variants in regulatory elements may largely account for the association between this locus and CL/P.

Identification of ASAH1 as a susceptibility gene for familial keloids.

Keloids result from abnormal proliferative scar formation with scar tissue expanding beyond the margin of the original wound and are mostly found in individuals of sub-Saharan African descent. The etiology of keloids has not been resolved but previous studies suggest that keloids are a genetically heterogeneous disorder. Although possible candidate genes have been suggested by genome-wide association studies using common variants, by upregulation in keloids or their involvement in syndromes that include keloid formation, rare coding variants that contribute to susceptibility in non-syndromic keloid formation have not been previously identified. Through analysis of whole-genome data we mapped a locus to chromosome 8p23.3-p21.3 with a statistically significant maximum multipoint LOD score of 4.48. This finding was followed up using exome sequencing and led to the identification of a c.1202T>C (p.(Leu401Pro)) variant in the N-acylsphingosine amidohydrolase (ASAH1) gene that co-segregates with the keloid phenotype in a large Yoruba family. ASAH1 is an acid ceramidase known to be involved in tumor formation by controlling the ratio of ceramide and sphingosine. ASAH1 is also involved in cell proliferation and inflammation, and may affect the development of keloids via multiple mechanisms. Functional studies need to clarify the role of the ASAH1 variant in wound healing.

Multidisciplinary approach to genomics research in Africa: the AfriCRAN model.

This article is an outcome of the African Craniofacial Anomalies Research Network (AfriCRAN) Human Hereditary and Health (H3A) grant planning meeting in 2012 in Lagos, Nigeria. It describes the strengths of a multidisciplinary team approach to solving complex genetic traits in the craniofacial region. It also highlights the different components and argues for the composition of similar teams to fast track the discovery of disease genes, diagnostic tools, improved clinical treatment and ultimately prevention of diseases.

Malignant skin lesions in Oshogbo, Nigeria.

INTRODUCTION: The aim of this study is to retrospectively assess the prevalence of some of skin malignancies in our environment and to provide a data base for creating awareness for prevention and early detection of the diseases in order to reduce morbidity and mortality associated with these skin lesions in our environment. METHODS: This is a retrospective study of all histologically diagnosed malignant skin lesions which presented at Ladoke Akintola University of Technology Teaching Hospital Osogbo Osun State between January 2006 and December 2010. RESULTS: Ninety- eight patients presented with skin cancers out of which 60 (61.2%)were males and 38 (38.8%) were females. Malignant melanoma ranked highest followed by squamous cell carcinoma, dermatofibrosarcoma and basal cell carcinoma in that order. Malignant melanoma affects male more than female and it commonly affects lower limbs. CONCLUSION: Skin malignancies pose a burden to the economy of the country. Efforts should be directed toward prevention, early diagnosis and management in order to abolish or reduce morbidity, as well as mortality associated with late presentation of people in the developing countries.

Awareness and attitude of healthcare workers to cosmetic surgery in osogbo, Nigeria.

This study aimed at understanding the level of awareness and elucidates the attitude and disposition of healthcare workers to cosmetic surgery in Osogbo, Nigeria. A questionnaire-based survey was done at LAUTECH Teaching Hospital, Osogbo, in 2012. Questionnaires were administered to 213 workers and students in the hospital. These were then analysed using SPSS version 16.0 with frequencies, means, and so forth. Respondents were 33 doctors, 32 nurses, 79 medical students, 60 nursing students, 4 administrative staff, 1 pharmacist, and 4 ward maids. There is fair awareness about cosmetic surgery generally with 94.5% and its availability in Nigeria with 67.0%. A fewer proportion of the respondents (44.5%) were aware of the facility for cosmetic surgery in their locality. A large percentage (86.5%) favorably considers facilities outside Nigeria when making choice of facility to have cosmetic surgery done. 85.5% considered the information about cosmetic surgery reliable while 19.0% objected going for cosmetic surgery of their choice even if done free. Only 34.0% consider cosmetic surgery socially acceptable. Although the awareness of health workers about cosmetic surgery is high, their disposition to it is low. There is a need to increase the awareness in order to increase cosmetic surgery practice in Nigeria.

Quality of life of Nigerians living with human immunodeficiency virus.

INTRODUCTION: Few reports from Nigeria have examined the quality of life (QOL) of people living with HIV/AIDS (PLWHA) despite the fact that Nigeria has the second largest number of PLWHA in the world. This study evaluated the QOL of Nigerians living with HIV/AIDS using the World Health Organization Quality of Life Questionnaire for HIV-Brief Version (WHOQOL-BREF) instrument and assessed the impact of demographic, laboratory and disease-related variables on QOL. METHODS: This cross-sectional study involved 491 consecutive PLWHA aged ≥ 18 years attending the dedicated clinic to PLWHA in South-west Nigeria. RESULTS: The lowest mean QOL scores were recorded in the environment and social domains. Participants aged ≥ 40 years had better QOL in the environment (p = 0.039) and spirituality (p = 0.033) domains and those in relationships had better QOL in the social relationship domain (p = 0.002). Subjects with no or primary education and those who rated their health status as good gave significantly higher ratings in all QOL domains. Participants with AIDS had significant lower QOL in the level of independence domain (p = 0.018) and those with CD4 count ≥ 350 cells /mm3 had better QOL scores in the physical, psychological and level of independence domains. Subjects without tuberculosis co-infection and those on antiretroviral therapy (ART) reported significantly better QOL in the physical, psychological, level of independence and spirituality domains. CONCLUSION: Marital relationship, absence of tuberculosis, CD4 count ≥ 350 cells /mm3 and use of ART positively impacted QOL of our patients.

Recruitment of Yoruba families from Nigeria for genetic research: experience from a multisite keloid study.

BACKGROUND: More involvement of sub-Saharan African countries in biomedical studies, specifically in genetic research, is needed to advance individualized medicine that will benefit non-European populations. Missing infrastructure, cultural and religious beliefs as well as lack of understanding of research benefits can pose a challenge to recruitment. Here we describe recruitment efforts for a large genetic study requiring three-generation pedigrees within the Yoruba homelands of Nigeria. The aim of the study was to identify genes responsible for keloids, a wound healing disorder. We also discuss ethical and logistical considerations that we encountered in preparation for this research endeavor. METHODS: Protocols for this bi-national intercultural study were approved by the Institutional Review Board (IRB) in the US and the ethics committees of the Nigerian institutions for consideration of cultural differences. Principles of community based participatory research were employed throughout the recruitment process. Keloid patients (patient advisors), community leaders, kings/chiefs and medical directors were engaged to assist the research teams with recruitment strategies. Community meetings, church forums, and media outlets (study flyers, radio and TV announcements) were utilized to promote the study in Nigeria. Recruitment of research participants was conducted by trained staff from the local communities. Pedigree structures were re-analyzed on a regular basis as new family members were recruited and recruitment challenges were documented. RESULTS: Total recruitment surpassed 4200 study participants over a 7-year period including 79 families with complete three-generation pedigrees. In 9 families more than 20 family members participated, however, in 5 of these families, we encountered issues with pedigree structure as members from different branches presented inconsistent family histories. These issues were due to the traditional open family structure amongst the Yoruba and by beliefs in voodoo or in juju. In addition, family members living in other parts of the country or abroad complicated timely and complete family recruitment. CONCLUSIONS: Organizational, logistics and ethics challenges can be overcome by additional administrative efforts, good communication, community involvement and education of staff members. However, recruitment challenges due to infrastructural shortcomings or cultural and religious beliefs can lead to significant delays, which may negatively affect study time lines and expectations of funding agencies.