Application of Genomic Medicine in Africa: 14th Conference of the African Society of Human Genetics and the 2nd International Congress of the Moroccan Society of Genomics and Human Genetics, Rabat, Morocco 2022

The 14th African Society of Human Genetics (AfSHG) Morocco Meeting and 2nd International Congress of the Moroccan Society of Genomics and Human Genetics (SM2GH), held in Rabat, Morocco, from December 12 through 17, 2022, brought together 298 attendees from 23 countries, organized by the AfSHG in collaboration with the SM2GH. The conference's overarching theme was "Applications of Genomics Medicine in Africa," covering a wide range of topics, including population genetics, genetics of infectious diseases, hereditary disorders, cancer genetics, and translational genetics. The conference aimed to address the lag in the field of genetics in Africa and highlight the potential for genetic research and personalized medicine on the continent. The goal was to improve the health of African populations and global communities while nurturing the careers of young African scientists in the field. Distinguished scientists from around the world shared their recent findings in genetics, immunogenetics, genomics, genome editing, immunotherapy, and ethics genomics. Precongress activities included a 2-day bioinformatics workshop, "NGS Analysis for Monogenic Disease in African Populations," and a Young Investigators Forum, providing opportunities for young African researchers to showcase their work. The vast genetic diversity of the African continent poses a significant challenge in investigating and characterizing public health issues at the genetic and functional levels. Training, research, and the development of expertise in genetics, immunology, genomics, and bioinformatics are vital for addressing these challenges and advancing genetics in Africa. The AfSHG is committed to leading efforts to enhance genetic research, coordinate training, and foster research collaborations on the continent.

Incidence, Clearance and Persistence of Penile High-Risk Human Papillomavirus among Rwandan Men who have Sex with Men

BACKGROUND

Little is known about penile high-risk HPV among MSM in low-and-middle income countries. We aimed to determine the incidence, clearance and persistence of penile hrHPV among Rwandan MSM.

METHODS

We enrolled 350 MSM (345 with valid HPV results), aged ≥18 years, at each visit (6-12 months apart), we collected penile PreservCyt specimens and blood for HPV and HIV testing, socio-demographic and behavioral variables. HPV testing was performed using the Ampfire assay. Penile hrHPV incidence and clearance/1,000 person-months of follow-up (PMF), prevalent- and incident-persistence were computed and compared by HIV status.

RESULTS

The mean age was 27.7 ± 6.7 years and 19.4% were living with HIV. Penile hrHPV incidence was 34.8 (95% CI: 29.1, 41.8)/1,000 PMF. HPV16 (11.7, CI 9.26, 14.9) and HPV59 (6.1, CI 4.52, 8.39) had the highest incidence rates. Prevalent- and incident-persistence were 47.5% and 46.6%, respectively. HPV66 (33.3%), HPV52 (30.8%) and HPV16 (29.2%) had the highest prevalent-persistence and HPV33 (53.8%), HPV31 (46.7%) and HPV16 (42.6%) the highest incident-persistence. No differences were found by HIV status except for HPV45 (higher in MSM with HIV).

CONCLUSION

We found high incidence and prevalent/incident-persistence of penile hrHPV among Rwandan MSM. This highlights the importance of preventive strategies for HPV-associated anogenital cancers.

Awareness and willingness to use pre-exposure prophylaxis for HIV prevention among men who have sex with men in Rwanda: findings from a web-based survey

Introduction

Pre-exposure Prophylaxis (PrEP) is a daily pill aimed at reducing HIV transmission risk when taken as prescribed. It's highly recommended for high-risk Men who have sex with Men (MSM). This study aimed to assess PrEP awareness and willingness to use it among Rwandan MSM, a critical aspect given PrEP's proven effectiveness. The findings are expected to inform policy decisions and further advance the implementation of PrEP strategies.

Methods

This is a cross-sectional study design that utilized a web-based survey conducted between April and June 2019 to assess awareness and willingness to use PrEP among sexually active MSM in Rwanda. A snowball sampling technique was used to recruit participants via social media such as WhatsApp and e-mail. Eligibility criteria included being sexually active, aged ≥18 years, self-identifying as MSM, residing in Rwanda, self-reported engagement in receptive or insertive anal sex in the last 12 months, and self-reported HIV-negative serostatus. We assessed two primary outcomes: PrEP awareness (having ever heard of PrEP) and willingness to use PrEP within one month of completing the survey. Multivariable logistic regression was performed to identify participant characteristics associated with PrEP awareness and willingness to use it.

Results

Out of 521 participants, the majority (73%) demonstrated awareness of PrEP. Factors linked to PrEP awareness included residing outside the capital, Kigali, being in the 18-29 age group, having higher education levels, perceiving a benefit from PrEP, and engaging in vaginal sex with a woman while using a condom in the last year. Additionally, 96% of participants expressed a strong willingness to use PrEP.

Conclusion

Rwandan MSM exhibits a high level of PrEP awareness, notably associated with factors like location, age, education, perceived benefits, and condom use. The study also revealed a strong willingness to use PrEP, indicating promising prospects for its adoption among this group. These findings highlight the need for targeted awareness campaigns, personalized interventions, and comprehensive sexual health education to promote PrEP adoption and strengthen HIV prevention efforts among Rwandan MSM.

An Assessment of the Knowledge and Perceptions of Precision Medicine (PM) in the Rwandan Healthcare Setting

INTRODUCTION

Precision medicine (PM) or personalized medicine is an innovative approach that aims to tailor disease prevention and treatment to consider the differences in people's genes, environments, and lifestyles. Although many efforts have been made to accelerate the universal adoption of PM, several challenges need to be addressed in order to advance PM in Africa. Therefore, our study aimed to establish baseline data on the knowledge and perceptions of the implementation of PM in the Rwandan healthcare setting.

METHOD

A descriptive qualitative study was conducted in five hospitals offering diagnostics and oncology services to cancer patients in Rwanda. To understand the existing policies regarding PM implementation in the country, two additional institutions were surveyed: the Ministry of Health (MOH), which creates and sets policies for the overall vision of the health sector, and the Rwanda Biomedical Center (RBC), which coordinates the implementation of health sector policies in the country. The researchers conducted 32 key informant interviews and assessed the functionality of available PM equipment in the 5 selected health facilities. The data were thematically categorized and analyzed.

RESULTS

The study revealed that PM is perceived as a complex and expensive program by most health managers and health providers. The most cited challenges to implementing PM included the following: the lack of policies and guidelines; the lack of supportive infrastructures and limited suppliers of required equipment and laboratory consumables; financial constraints; cultural, behavioral, and religious beliefs; and limited trained, motivated, and specialized healthcare providers. Regarding access to health services for cancer treatment, patients with health insurance pay 10% of their medical costs, which is still too expensive for Rwandans.

CONCLUSION

The study participants highlighted the importance of PM to enhance healthcare delivery if the identified barriers are addressed. For instance, Rwandan health sector leadership might consider the creation of specialized oncology centers in all or some referral hospitals with all the necessary genomic equipment and trained staff to serve the needs of the country and implement a PM program.

Genomic Analysis of Rwandan G9P[8] Rotavirus Strains Pre- and Post-RotaTeq® Vaccine Reveals Significant Distinct Sub-Clustering in a Post-Vaccination Cohort

Although the introduction of rotavirus vaccines has substantially contributed to the reduction in rotavirus morbidity and mortality, concerns persist about the re-emergence of variant strains that might alter vaccine effectiveness in the long term. The G9 strains re-emerged in Africa during the mid-1990s and have more recently become predominant in some countries, such as Ghana and Zambia. In Rwanda, during the 2011 to 2015 routine surveillance period, G9P[8] persisted during both the pre- and post-vaccine periods. The pre-vaccination cohort was based on the surveillance period of 2011 to 2012, and the post-vaccination cohort was based on the period of 2013 to 2015, excluding 2014. The RotaTeq® vaccine that was first introduced in Rwanda in 2012 is genotypically heterologous to Viral Protein 7 (VP7) G9. This study elucidated the whole genome of Rwandan G9P[8] rotavirus strains pre- and post-RotaTeq® vaccine introduction. Fecal samples from Rwandan children under the age of five years (pre-vaccine n = 23; post-vaccine n = 7), conventionally genotyped and identified as G9P[8], were included. Whole-genome sequencing was then performed using the Illumina® MiSeq platform. Phylogenetic analysis and pair-wise sequence analysis were performed using MEGA6 software. Distinct clustering of three post-vaccination study strains was observed in all 11 gene segments, compared to the other Rwandan G9P[8] study strains. Specific amino acid differences were identified across the gene segments of these three 2015 post-vaccine strains. Important amino acid differences were identified at position N242S in the VP7 genome segment of the three post-vaccine G9 strains compared to the other G9 strains. This substitution occurs at a neutralization epitope site and may slightly affect protein interaction at that position. These findings indicate that the Rwandan G9P[8] strains revealed a distinct sub-clustering pattern among post-vaccination study strains circulating in Rwanda, with changes at neutralization epitopes, which may play a role in neutralization escape from vaccine candidates. This emphasizes the need for continuous whole-genome surveillance to better understand the evolution and epidemiology of the G9P[8] strains post-vaccination.

Awareness and Willingness to Use HIV Infection Pre-Exposure Prophylaxis among Rwandan Men Who Have Sex with Men: Findings from a Web-based Survey

Introduction

Pre-exposure Prophylaxis (PrEP) is a daily pill intended to reduce the risk of acquiring Human Immunodeficiency Virus (HIV) when taken as prescribed. It is strongly recommended for Men who have sex with Men (MSM) at high risk of HIV transmission to minimize infection risk. Despite its proven effectiveness, there is a lack of information about awareness and willingness to use PrEP among Rwandan MSM. In the context of HIV acquisition, the purpose of this study was to ascertain the awareness and willingness to use PrEP among high-risk Rwandan MSM. The findings of this research will provide valuable perspectives to mold policy and direct the effective execution of PrEP within the country.

Method

This is a cross-sectional study design that utilized a web-based survey conducted between April and June 2019 to assess awareness and willingness to use PrEP among sexually active MSM in Rwanda. A snowball sampling technique was used to recruit participants who were contacted via social medial such as WhatsApp and e-mail. To be eligible, participants were supposed to be sexually active, aged ≥18 years, self-identify as MSM, residence in Rwanda, self-reported engagement in receptive or insertive anal sex in the last 12 months, and self-reported HIV-negative sero-status. We assessed two primary outcomes: PrEP awareness (having ever heard of PrEP) and willingness to use PrEP within one month of completing the survey. Multivariable logistic regression was performed to identify participant characteristics associated with PrEP awareness and willingness to use it.

Results

Among the 521 participants included in the analysis, 63% were aged below 24 years. The majority (73%) demonstrated awareness of PrEP. Factors associated with PrEP awareness included residing outside of the capital, Kigali, as opposed to living in Kigali (adjusted odds ratio [aOR] 2.35, 95% confidence interval [CI] 1.40-3.97), being in the age groups 18-24 years (aOR 2.28, 95% CI: 1.03-5.01) or 25-29 years (aOR 3.06, 95% CI 1.35-6.93) compared to those aged 30 or older, having higher education levels, such as completing secondary education (aOR 1.76, 95% CI 1.01-3.06) or university education (aOR 2.65, 95% CI 1.18-5.96) in contrast to having no education. Lastly, perceiving a benefit from PrEP (aOR 9.52, 95% CI 4.27-21.22), and engaging in vaginal sex with a woman using a condom in the last 12 months (aOR 1.82, 95% CI 1.14-2.91) versus not. Impressively, 96% of participants expressed a strong willingness to use PrEP.

Conclusion

Among Rwandan MSM, there is a high level of awareness of PrEP, notably associated with factors such as residing outside Kigali, younger age, higher education, perceived benefits of PrEP and condom use during vaginal sex in the past year. Furthermore, a significant portion of participants demonstrated an intense desire to use PrEP, suggesting promising possibilities for its extensive implementation among this group of people. The findings from this study emphasize the importance of implementing highly focused awareness campaigns, personalized intervention, and comprehensive sexual health education programs in order to enhance the adoption of PrEP and bolster HIV prevention initiatives among the Rwandan population of MSM.

A Mendelian randomization study of genetic liability to post-traumatic stress disorder and risk of ischemic stroke

Observational studies have shown an association between post-traumatic stress disorder (PTSD) and ischemic stroke (IS) but given the susceptibility to confounding it is unclear if these associations represent causal effects. Mendelian randomization (MR) facilitates causal inference that is robust to the influence of confounding. Using two sample MR, we investigated the causal effect of genetic liability to PTSD on IS risk. Ancestry-specific genetic instruments of PTSD and four quantitative sub-phenotypes of PTSD, including hyperarousal, avoidance, re-experiencing, and total symptom severity score (PCL-Total) were obtained from the Million Veteran Programme (MVP) using a threshold P value (P) of <5 × 10-7, clumping distance of 1000 kilobase (Mb) and r2 < 0.01. Genetic association estimates for IS were obtained from the MEGASTROKE consortium (Ncases = 34,217, Ncontrols = 406,111) for European ancestry individuals and from the Consortium of Minority Population Genome-Wide Association Studies of Stroke (COMPASS) (Ncases = 3734, Ncontrols = 18,317) for African ancestry individuals. We used the inverse-variance weighted (IVW) approach as the main analysis and performed MR-Egger and the weighted median methods as pleiotropy-robust sensitivity analyses. In European ancestry individuals, we found evidence of an association between genetic liability to PTSD avoidance, and PCL-Total and increased IS risk (odds ratio (OR)1.04, 95% Confidence Interval (CI) 1.007-1.077, P = 0.017 for avoidance and (OR 1.02, 95% CI 1.010-1.040, P = 7.6 × 10-4 for PCL total). In African ancestry individuals, we found evidence of an association between genetically liability to PCL-Total and reduced IS risk (OR 0.95 (95% CI 0.923-0.991, P = 0.01) and hyperarousal (OR 0.83 (95% CI 0.691-0.991, P = 0.039) but no association was observed for PTSD case-control, avoidance, or re-experiencing. Similar estimates were obtained with MR sensitivity analyses. Our findings suggest that specific sub-phenotypes of PTSD, such as hyperarousal, avoidance, PCL total, may have a causal effect on people of European and African ancestry's risk of IS. This shows that the molecular mechanisms behind the relationship between IS and PTSD may be connected to symptoms of hyperarousal and avoidance. To clarify the precise biological mechanisms involved and how they may vary between populations, more research is required.

Advancing detection and response capacities for emerging and re-emerging pathogens in Africa

Recurrent disease outbreaks caused by a range of emerging and resurging pathogens over the past decade reveal major gaps in public health preparedness, detection, and response systems in Africa. Underlying causes of recurrent disease outbreaks include inadequacies in the detection of new infectious disease outbreaks in the community, in rapid pathogen identification, and in proactive surveillance systems. In sub-Saharan Africa, where 70% of zoonotic outbreaks occur, there remains the perennial risk of outbreaks of new or re-emerging pathogens for which no vaccines or treatments are available. As the Ebola virus disease, COVID-19, and mpox (formerly known as monkeypox) outbreaks highlight, a major paradigm shift is required to establish an effective infrastructure and common frameworks for preparedness and to prompt national and regional public health responses to mitigate the effects of future pandemics in Africa.

Comparison of AmpFire and MY09/11 assays for HPV genotyping in anogenital specimen of Rwandan men who have sex with men

Introduction

The AmpFire HPV genotyping Assay (Atila Biosystems, Mountain View, CA, USA) is a new test for which there are few data regarding its analytic performance and reliability. Using anal and penile swab specimens from a cohort study of men who have sex with men (MSM) in Rwanda, we compared high-risk HPV (hrHPV) detection by AmpFire done at two laboratories, one at University of California San Francisco (UCSF) and the other Rwanda Military Hospital, and well-validated MY09/11-based assay done at UCSF.

Methods

Anal and penile specimens collected from 338 MSM from March 2016 to September 2016 were tested for high-risk HPV genotypes (hrHPV) by MY09/11, AmpFire UCSF and AmpFire RMH. Cohen's kappa coefficient was used to test for reproducibility.

Results

The hrHPV positivity by MY09/11 and AmpFire UCSF was 13% and 20.7% (k = 0.73) for anal specimens and was 26.3% and 32.6% (k = 0.67) for penile specimens. Specifically, good reproducibility was for types 16 and 18 (k = 0.69 and k = 0.71) for anal specimens and (k = 0.50 and k = 0.72) for penile specimens. The hrHPV positivity by AmpFire at UCSF and RMH was 20.7% for both laboratories (k = 0.87) for anal specimens and was 34.9% and 31.9% (k = 0.89) for penile specimens. Specifically, excellent reproducibility was for types 16 and 18 for anal specimens (k = 0.80 and k = 1.00) and penile specimens (k = 0.85 and k = 0.91).

Conclusion

Results show that MY09/11 and AmpFire assays have good reproducibility while the AmpFire UCSF and RMH assays have excellent reproducibility. These results show that AmpFire is a promising HPV genotyping test.

The Evolution of Post-Vaccine G8P[4] Group a Rotavirus Strains in Rwanda; Notable Variance at the Neutralization Epitope Sites

Africa has a high level of genetic diversity of rotavirus strains, which is suggested to be a possible reason contributing to the suboptimal effectiveness of rotavirus vaccines in this region. One strain that contributes to this rotavirus diversity in Africa is the G8P[4]. This study aimed to elucidate the entire genome and evolution of Rwandan G8P[4] strains. Illumina sequencing was performed for twenty-one Rwandan G8P[4] rotavirus strains. Twenty of the Rwandan G8P[4] strains had a pure DS-1-like genotype constellation, and one strain had a reassortant genotype constellation. Notable radical amino acid differences were observed at the neutralization sites when compared with cognate regions in vaccine strains potentially playing a role in neutralization escape. Phylogenetic analysis revealed that the closest relationship was with East African human group A rotavirus (RVA) strains for five of the genome segments. Two genome sequences of the NSP4 genome segment were closely related to bovine members of the DS-1-like family. Fourteen VP1 and eleven VP3 sequences had the closest relationships with the RotaTeq™ vaccine WC3 bovine genes. These findings suggest that the evolution of VP1 and VP3 might have resulted from reassortment events with RotaTeq™ vaccine WC3 bovine genes. The close phylogenetic relationship with East African G8P[4] strains from Kenya and Uganda suggests co-circulation in these countries. These findings highlight the need for continued whole-genomic surveillance to elucidate the evolution of G8P[4] strains, especially after the introduction of rotavirus vaccination.

Neurofibromatosis type 1 – A clinical case report and management review

INTRODUCTION: Neurofibromatosis Type 1 (NF1) or Von Recklinghausen’s disease, is a rare genetic disease characterized by multiple benign tumors of nerves and skin (neurofibromas), and skin decorations. However, it is multisystem and can affect each organ in the body, leading to debilitating effects.CLINICAL CASE: We present a case of an 18-year-old girl with NF1. The disease onset started in childhood at the age of 3 years with the appearance of hyperpigmented skin macules. Her mother also presented with multiple nodules on the face and trunk, and her little brother was reported to have disseminated macules. She had poor performance at school and delayed menses. The diagnosis of NF-1 was made, and a multidisciplinary team was involved in management of the patientCONCLUSION: Although genetic testing and confirmation are available, NF1 remains a clinical diagnosis and requires management by multidisciplinary team

Diagnosis of Treacher-Collins Syndrome: The role of the multidisciplinary team in patient management and family genetic counseling

INTRODUCTION: Although Treacher-Collins syndrome has to be considered a differential diagnosis in congenital craniofacial abnormalities, the clinical diagnosis and research related to it still present a gap, especially in African regions. Thus, this work aims at highlighting this syndrome's clinical features for raising medical awareness. CLINICAL CASE: We reviewed a 1-year-old patient referred to our clinical genetic unit at Rwanda military hospital, Kigali, Rwanda. Physical examinations indicated severe craniofacial abnormalities, including downward-sloping eyes, slight notching of the lower lids, small and underdeveloped eyebrow bones, vision problems, small outer ears, small and underdeveloped cheekbones, and jaw. Within the limits of the techniques used in our laboratory, the cytogenetic analysis revealed a normal karyotype, 46, XY. CONCLUSION: The patient was diagnosed with Treacher-Collins syndrome based on clinical manifestations of craniofacial features. Nevertheless, laboratory tests performed were limited to karyotyping and should not detect any gene defect. Long-term follow-up of the patient and his family was recommended. Further molecular analyses should be performed to identify causing genetic mutation mainly in the TCOF1, POLR1C, or POLR1D genes.

Use of trained scent dogs for detection of COVID-19 and evidence of cost-saving

Background

One of the lessons learned from the coronavirus disease 2019 (COVID-19) pandemic is the importance of early, flexible, and rapidly deployable disease detection methods. Currently, diagnosis of COVID-19 requires the collection of oro/nasopharyngal swabs, nasal turbinate, anterior nares and saliva but as the pandemic continues, disease detection methods that can identify infected individuals earlier and more quickly will be crucial for slowing the spread of the virus. Previous studies have indicated that dogs can be trained to identify volatile organic compounds (VOCs) produced during respiratory infections. We sought to determine whether this approach could be applied for detection of COVID-19 in Rwanda and measured its cost-saving.

Methods

Over a period of 5 months, four dogs were trained to detect VOCs in sweat samples collected from human subjects confirmed positive or negative for COVID-19 by reverse transcription polymerase chain reaction (RT-PCR) testing. Dogs were trained using a detection dog training system (DDTS) and in vivo diagnosis. Samples were collected from 5,253 participants using a cotton pad swiped in the underarm to collect sweat samples. Statistical analysis was conducted using R statistical software.

Findings

From August to September 2021 during the Delta wave, the sensitivity of the dogs' COVID-19 detection ranged from 75.0 to 89.9% for the lowest- and highest-performing dogs, respectively. Specificity ranged from 96.1 to 98.4%, respectively. In the second phase coinciding with the Omicron wave (January-March 2022), the sensitivity decreased substantially from 36.6 to 41.5%, while specificity remained above 95% for all four dogs. The sensitivity and specificity by any positive sample detected by at least one dog was 83.9, 95% CI: 75.8-90.2 and 94.9%; 95% CI: 93.9-95.8, respectively. The use of scent detection dogs was also found to be cost-saving compared to antigen rapid diagnostic tests, based on a marginal cost of approximately $14,000 USD for testing of the 5,253 samples which makes 2.67 USD per sample. Testing turnaround time was also faster with the scent detection dogs, at 3 h compared to 11 h with routine diagnostic testing.

Conclusion

The findings from this study indicate that trained dogs can accurately identify respiratory secretion samples from asymptomatic and symptomatic COVID-19 patients timely and cost-effectively. Our findings recommend further uptake of this approach for COVID-19 detection.

The right of access to healthcare: an analysis of how legal and institutional frameworks constrain or facilitate access to healthcare for residents in border areas in the East African Community

Background

Despite many countries working hard to attain Universal Health Coverage (UHC) and the Health-related Sustainable Development Goals, access to healthcare services has remained a challenge for communities residing along national borders in the East Africa Community (EAC). Unlike the communities in the interior, those along national borders are more likely to face access barriers and exclusion due to low health investments and inter-state rules for non-citizens. This study explored the legal and institutional frameworks that facilitate or constrain access to healthcare services for communities residing along the national borders in EAC.

Methods

This study is part of a broader research implemented in East Africa (2018–2020), employing mixed methods. For this paper, we report data from a literature review, key informant interviews and sub-national dialogues with officials involved in planning and implementing health and migration services in EAC. The documents reviewed included regional and national treaties, conventions, policies and access rules, regulations and guidelines that affect border crossing and access to healthcare services. These were retrieved from official online and physical libraries and archives.

Results

Overall, the existing laws, policies and guidelines at all levels do not explicitly deal with cross border healthcare access especially for border residents, but address citizen rights and entitlements including health within national frameworks. There is no clarity on whether these rights can be enjoyed beyond one’s country of citizenship. The review found examples of investments in shared health infrastructure to benefit all EAC member countries – a signal of closer cooperation for specialized health care, this had not been accompanied by access rule for citizens outside the host country. The focus on specialized care is unlikely to contribute to the every-day health care needs of border resident communities in remote areas of EAC. Nevertheless, the establishment of the EAC entail opportunities for increased collaboration and integration beyond the trade and customs union to included health care and other social services. The study established active cooperation aimed at disease surveillance and epidemic control among sub-national officials responsible for health and migration services across borders. Health insurance cards, national identification cards and official travel documents were found to constrain access to health services across the borders in EAC.

Conclusion

In the era of UHC, there is need to take advantage of the EAC integration to revise legal and policy frameworks to leverage existing investments and facilitate cross-border access to healthcare services for communities residing along EAC borders.

Agreement between Xpert and AmpFire tests for high-risk human papillomavirus among HIV-positive women in Rwanda

BACKGROUND

High-risk human papillomavirus (hrHPV) may cause more than 99% of cervical cancers worldwide. Little is known about performance differences in tests for hrHPV.

OBJECTIVE

This study analysed agreement for detection of hrHPV between the established, clinically validated Xpert HPV assay and the novel isothermal amplification-based AmpFire HPV genotyping assay.

METHODS

This study was nested in a larger project on cervical cancer screening among approximately 5000 women living with HIV in Kigali, Rwanda. This sub-study included 298 participants who underwent initial screening for cervical cancer using the Xpert HPV assay and visual inspection with acetic acid in 2017 and tested positive by either or both. Participants were rescreened using colposcopy, and cervical samples were collected between June 2018 and June 2019. Samples were then tested for HPV using the Xpert HPV assay and AmpFire HPV genotyping assay. Agreement between results from both tests was analysed using an exact version of McNemar test and chi-square test.

RESULTS

Overall agreement and kappa value for detection of hrHPV by Xpert and AmpFire were 89% and 0.77 (95% confidence interval: 0.70-0.85). AmpFire was marginally more likely to diagnose hrHPV-positive than Xpert (p = 0.05), due primarily to the extra positivity for HPV16 (p < 0.001).

CONCLUSION

Overall, there was good to excellent agreement between the Xpert and AmpFire when testing hrHPV types among women living with HIV. AmpFire was more likely to test extra cases of HPV16, the most carcinogenic HPV type, but the clinical meaning of detecting additional HPV16 infections remains unknown.

Management challenges of disorders of sex development- Case Series

INTRODUCTION: Disorders of sex development (DSDs) are genetic abnormalities characterized by discordance between phenotypic, gonadal, and genetic sex. They are grouped into two categories based on karyotype: 46, XX DSD and 46, XY DSD.CASES: We reviewed two patients referred to the Rwanda Military Hospital genetic unit. The first patient was a 3-year-old toddler who was referred for confusing sex organs. Physical examination showed ambiguous genital organs with hypospadias and micropenis. Pelvic examination showed a swelling solid mass hat leading to a suspicion of ovary or undescended testes or combined ovary and testes (ovotestes). The second patient was a 17 years old teenager who presented with primary amenorrhea and lack of female secondary sexual characteristics at her age. The karyotype test was performed to investigate the genotypic sex of the patients and results revealed the karyotype formula of 46, XX/XY indicating the presence of two cell lines in the patient for the toddler and 46XYinv9 (p11q13) indicating the mismatch between the genotype and phenotype of the patients for the teenager. CONCLUSION: Patients were diagnosed with Disorder of Sex Development with 46, XX/XY and 46, XY genotypes respectively. A multidisciplinary team of a geneticist, urologist, endocrinologist and a psychologist reviewed the patient for the effective management.

Community engagement in epigenomic and neurocognitive research on post-traumatic stress disorder in Rwandans exposed to the 1994 genocide against the Tutsi: lessons learned

Epigenomic and neurocognitive studies have provided new perspectives on post-traumatic stress disorder and its intergenerational transmission. This article outlines the lessons learned from community engagement (CE) in such research on Rwandan genocide survivors. A strong trauma-related response was observed within the research project-targeted community (genocide survivors) during explanation of the project. CE also revealed privacy concerns, as community members worried that any leakage of genetic/(epi)genomic data could affect not only themselves but also their close relatives. Adopting a culture of CE in the process of research implementation enables the prioritization of targeted community needs and interests. Furthermore, CE has stimulated the development of mental healthcare interventions, which married couples can apply to protect their offspring and thus truly break the cycle of inherited vulnerability.

"Black Lives Matter and Black Research Matters": the African Society of Human Genetics' call to halt racism in science

The African Society of Human Genetics (AfSHG) was formed to provide a forum for human genetics and genomics scientists in Africa to interact, network, and collaborate. This is critical to facilitate development of solutions to the public health burden of many rare and common diseases across the continent. AfSHG fully supports the Black Lives Matter movement, which is dedicated to fighting racism and ensuring that society values the lives and humanity of Black people. The AfSHG would like to add its "voice" to the public outcry against racism sparked by George Floyd's death and to declare its commitment to ensuring that injustice and systematic racism, as well as abuse and exploitation of Africans and their biological material, are no longer tolerated. This is particularly relevant now as African genomic variation is poised to make significant contributions across several disciplines including ancestry, personalized medicine, and novel drug discovery. "Black Lives Matter and Black Research Matters" is AfSHG's call for the global community to support halting, and reversing, the perpetuation of exploitation of African people through neocolonial malpractices in genomic research. We also propose five key ways to curb racism in science, so that we can move forward together, with a common humanity, collectively embracing scientific endeavors.

Electroencephalography and psychological assessment datasets to determine the efficacy of a low-cost, wearable neurotechnology intervention for reducing Post-Traumatic Stress Disorder symptom severity

The datasets described here comprise electroencephalography (EEG) data and psychometric data freely available on data.mendeley.com. The EEG data is available in .mat formatted files containing the EEG signal values structured in two-dimensional (2D) matrices, with channel data and trigger information in rows, and samples in columns (having a sampling rate of 250Hz). Twenty-nine female survivors of the 1994 genocide against the Tutsi in Rwanda, underwent a psychological assessment before and after an intervention aimed at reducing Post-Traumatic Stress Disorder (PTSD) symptom severity. Three measures of trauma and four measures of wellbeing were assessed using empirically validated standardised assessments. The pre- and post- intervention psychometric data were analysed using non-parametric statistical methods and the post-intervention data were further evaluated according to diagnostic assessment rules to determine clinically relevant improvements for each group. The participants were assigned to a control group (CG, n = 9), a motor-imagery group (MI, n = 10), and a neurofeedback group (NF, n = 10). Participants in the latter two groups received Brain-Computer Interface (BCI) based training as a treatment intervention over a sixteen-day period, between the pre- and post- clinical interviews. The training involved presenting feedback visually via a videogame, based on real-time analysis of the EEG recorded data during the BCI-based treatment session. Participants were asked to regulate (NF) or intentionally modulate (MI) brain activity to affect/control the game.

A handmade trap for malaria mosquito surveillance by citizens in Rwanda

For effective sampling of mosquitoes in malaria surveillance programmes, it is essential to include attractive cues in traps. With the aim of implementing a citizen science project on malaria vectors in rural Rwanda, a handmade plastic bottle trap was designed and tested in the field to determine its effectiveness in capturing adult Anopheles gambiae sensu lato, the main malaria vector, and other mosquito species. Carbon dioxide (CO2) and light were used as attractive cues. CO2 was produced by inoculating sugar with yeast and water. Light was emitted from a torch by light-emitting diodes (LEDs). Under field conditions in rural Rwanda, three handmade trap designs were compared to Centers for Disease Control and Prevention miniature light traps (CDC-LT) in houses. The trap baited with yeast produced CO2 and light caught the highest number of mosquitoes compared to the traps baited with light alone or CO2 alone. The number of An. gambiae s.l. in the handmade trap with light and CO2 was approximately 9–10% of the number caught with a CDC light trap. This suggests that about 10 volunteers with a handmade trap could capture a similar-sized sample of An. gambiae as one CDC-LT would collect. Based on these findings, the handmade plastic bottle trap baited with sugar fermenting yeast and light represents an option for inclusion in mosquito surveillance activities in a citizen science context.

Leukocyte methylomic imprints of exposure to the genocide against the Tutsi in Rwanda: a pilot epigenome-wide analysis

Aim & methods: We conducted a pilot epigenome-wide association study of women from Tutsi ethnicity exposed to the genocide while pregnant and their resulting offspring, and a comparison group of women who were pregnant at the time of the genocide but living outside of Rwanda.Results: Fifty-nine leukocyte-derived DNA samples survived quality control: 33 mothers (20 exposed, 13 unexposed) and 26 offspring (16 exposed, 10 unexposed). Twenty-four significant differentially methylated regions (DMRs) were identified in mothers and 16 in children. Conclusions:In utero genocide exposure was associated with CpGs in three of the 24 DMRs: BCOR, PRDM8 and VWDE, with higher DNA methylation in exposed versus unexposed offspring. Of note, BCOR and VWDE show significant correlation between brain and blood DNA methylation within individuals, suggesting these peripherally derived signals of genocide exposure may have relevance to the brain.

Experiences of seeking healthcare across the border: lessons to inform upstream policies and system developments on cross-border health in East Africa

OBJECTIVES

This study explored the experiences of accessing care across the border in East Africa.

PARTICIPANTS

From February to June 2018, a cross-sectional study using qualitative and quantitative methods was conducted among 279 household adults residing along selected national border sites of Uganda, Kenya and Rwanda and had accessed care from the opposite side of the border 5 years prior to this study.

SETTING

Access to HIV treatment, maternal delivery and childhood immunisation services was explored. We applied the health access framework and an appreciative inquiry approach to identify factors that enabled access to the services.

MEASURES

Exploratory factor analysis and linear regression were used for quantitative data, while deductive content analysis was done for the qualitative data on respondent's experiences navigating health access barriers.

RESULTS

The majority of respondents (83.9%; 234/279) had accessed care from public health facilities. Nearly one-third (77/279) had sought care across the border more than a year ago and 22.9% (64/279) less than a month ago. From the linear regression, the main predictor for ease of access for healthcare were ''ease of border crossing' (regression coefficient (RegCoef) 0.381); 'services being free' (RegCoef 0.478); 'services and medicines availability' (RegCoef 0.274) and 'acceptable quality of services' (RegCoef 0.364). The key facilitators for successful navigation of access barriers were related to the presence of informal routes, speaking a similar language and the ability to pay for the services.

CONCLUSION

Communities resident near national borders were able to cross borders to seek healthcare. There is need for a policy environment to enable East Africa invest better and realise synergies for these communities. This will advance Universal Health Coverage goals for communities along the border who represent the far fang areas of the health system with multiple barriers to healthcare access.

Neurofeedback with low-cost, wearable electroencephalography (EEG) reduces symptoms in chronic Post-Traumatic Stress Disorder

BACKGROUND

The study examines the effectiveness of both neurofeedback and motor-imagery brain-computer interface (BCI) training, which promotes self-regulation of brain activity, using low-cost electroencephalography (EEG)-based wearable neurotechnology outside a clinical setting, as a potential treatment for post-traumatic stress disorder (PTSD) in Rwanda.

METHODS

Participants received training/treatment sessions along with a pre- and post- intervention clinical assessment, (N = 29; control n = 9, neurofeedback (NF, 7 sessions) n = 10, and motor-imagery (MI, 6 sessions) n = 10). Feedback was presented visually via a videogame. Participants were asked to regulate (NF) or intentionally modulate (MI) brain activity to affect/control the game.

RESULTS

The NF group demonstrated an increase in resting-state alpha 8-12 Hz bandpower following individual training sessions, termed alpha 'rebound' (Pz channel, p = 0.025, all channels, p = 0.024), consistent with previous research findings. This alpha 'rebound', unobserved in the MI group, produced a clinically relevant reduction in symptom severity in NF group, as revealed in three of seven clinical outcome measures: PCL-5 (p = 0.005), PTSD screen (p = 0.005), and HTQ (p = 0.005).

LIMITATIONS

Data collection took place in environments that posed difficulties in controlling environmental factors. Nevertheless, this limitation improves ecological validity, as neurotechnology treatments must be deployable outside controlled environments, to be a feasible technological treatment.

CONCLUSIONS

The study produced the first evidence to support a low-cost, neurotechnological solution for neurofeedback as an effective treatment of PTSD for victims of acute trauma in conflict zones in a developing country.

Willingness to Contribute to Bio-Larviciding in the Fight against Malaria: A Contingent Valuation Study among Rice Farmers in Rwanda

There is broad consensus that successful and sustained larval source management (LSM) interventions, including bio-larviciding campaigns, require embeddedness in local community institutions. Ideally, these community structures should also be capable of mobilizing local resources to (co-)finance interventions. To date, farmer cooperatives, especially cooperatives of rice growers whose economic activity facilitates mosquito breeding, have remained under the radar in designing community-based bio-larviciding campaigns. This study explores the potential of rice farmer cooperatives in Bugesera district, Rwanda, to take up the aforementioned roles. To this purpose, we surveyed 320 randomly selected rice farmers who belonged to one of four rice cooperatives in the area and elicited their willingness-to-pay (WTP) for application of Bti, a popular bio-larvicide, in their rice paddies. Results from a (non-incentivized) bidding game procedure, which tested two alternative contribution schemes showed that financial contributions would be significantly different from zero and sufficient to carry a co-financing share of 15-25 per cent. A strong heterogeneity in mean WTP is revealed across cooperatives, in addition to variation among individual farmers, which needs to be anticipated when engaging farmer cooperatives in LSM.

Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity

COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the B.1.1.7 and B.1.351 variants of concern among incoming travelers tested at Kigali International Airport. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences were available. Our results highlight the importance of systematic genomic surveillance and regional collaborations for a durable response towards combating COVID-19.

Vitamin D Levels in Mother-Baby Pairs: A Cross-Sectional Prospective Study in a Rwandan Tertiary Hospital

BACKGROUND

Exposure to the sunlight contributes largely to the production of vitamin D. However, vitamin D deficiency is a reality in tropical countries, despite enjoying enough sunlight, especially bearing women in their last trimester whose foetuses exclusively depend on their reserves. This work aimed at demonstrating the state of vitamin D in mother-baby pairs and associated factors in one of the University Hospitals in Rwanda.

METHODS

This cross-sectional prospective study was performed on mother-baby pairs at Kigali University Hospital. Mother's serum 25-hydroxyvitamin D levels were considered as outcomes compared with demographic, clinical and biological markers. Correlation analysis was conducted in order to assess the association between serum 25-hydroxyvitamin D levels for the couple mothers-babies.

RESULTS

Approximately 38% of women and 65% of neonates had deficiency in 25-hydroxyvitamin D (<20 ng/ml). The use of a vitamin D rich diet within 24 h recall (p < 0.01) or 1 week recall (p < 0.001) before delivery was associated with appropriate vitamin D levels in mothers. Interestingly, a strong positive correlation was found between maternal and neonatal serum 25-hydroxyvitamin D levels (r = 0.760).

CONCLUSIONS

There was a high rate of vitamin D deficiency in mothers and their babies. Babies born from women with deficiency were likely to develop low levels of vitamin D. This stresses on the need to strengthen the interventions for preventing vitamin D deficiency in the couple mothers-babies such as supplement in vitamin D before and after delivery, improving the quality of meals and regular contact with sunlight.

Intergenerational trauma transmission is associated with brain metabotranscriptome remodeling and mitochondrial dysfunction

Intergenerational trauma increases lifetime susceptibility to depression and other psychiatric disorders. Whether intergenerational trauma transmission is a consequence of in-utero neurodevelopmental disruptions versus early-life mother–infant interaction is unknown. Here, we demonstrate that trauma exposure during pregnancy induces in mouse offspring social deficits and depressive-like behavior. Normal pups raised by traumatized mothers exhibited similar behavioral deficits to those induced in pups raised by their biological traumatized mothers. Good caregiving by normal mothers did not reverse prenatal trauma-induced behaviors, indicating a two-hit stress mechanism comprising both in-utero abnormalities and early-life poor parenting. The behavioral deficits were associated with profound changes in the brain metabotranscriptome. Striking increases in the mitochondrial hypoxia marker and epigenetic modifier 2-hydroxyglutaric acid in the brains of neonates and adults exposed prenatally to trauma indicated mitochondrial dysfunction and epigenetic mechanisms. Bioinformatic analyses revealed stress- and hypoxia-response metabolic pathways in the neonates, which produced long-lasting alterations in mitochondrial energy metabolism and epigenetic processes (DNA and chromatin modifications). Most strikingly, early pharmacological interventions with acetyl-L-carnitine (ALCAR) supplementation produced long-lasting protection against intergenerational trauma-induced depression.

Sammy Alhassen, Siwei Chen, et al. use mouse models to examine the effects of prenatal and postnatal stress on metabolomic and transcriptomic pathways in the brain. Their results suggest that altered mitochondrial metabolism may underlie trauma-induced behavioral deficits, and that correcting metabolism with ALCAR supplementation may protect against intergenerational transmission of traumatic stress.

Association of Plasmodium falciparum kelch13 R561H genotypes with delayed parasite clearance in Rwanda: an open-label, single-arm, multicentre, therapeutic efficacy study

BACKGROUND

Partial artemisinin resistance is suspected if delayed parasite clearance (ie, persistence of parasitaemia on day 3 after treatment initiation) is observed. Validated markers of artemisinin partial resistance in southeast Asia, Plasmodium falciparum kelch13 (Pfkelch13) R561H and P574L, have been reported in Rwanda but no association with parasite clearance has been observed. We aimed to establish the efficacy of artemether-lumefantrine and genetic characterisation of Pfkelch13 alleles and their association with treatment outcomes.

METHODS

This open-label, single-arm, multicentre, therapeutic efficacy study was done in 2018 in three Rwandan sites: Masaka, Rukara, and Bugarama. Children aged 6-59 months with P falciparum monoinfection and fever were eligible and treated with a 3-day course of artemether-lumefantrine. Treatment response was monitored for 28 days using weekly microscopy screenings of blood samples for P falciparum. Mutations in Pfkelch13 and P falciparum multidrug resistance-1 (Pfmdr1) genes were characterised in parasites collected from enrolled participants. Analysis of flanking microsatellites surrounding Pfkelch13 was done to define the origins of the R561H mutations. The primary endpoint was PCR-corrected parasitological cure on day 28, as per WHO protocol.

FINDINGS

228 participants were enrolled and 224 (98·2%) reached the study endpoint. PCR-corrected efficacies were 97·0% (95% CI 88-100) in Masaka, 93·8% (85-98) in Rukara, and 97·2% (91-100) in Bugarama. Pfkelch13 R561H mutations were present in 28 (13%) of 218 pre-treatment samples and P574L mutations were present in two (1%) pre-treatment samples. 217 (90%) of the 240 Pfmdr1 haplotypes observed in the pretreatment samples, had either the NFD (N86Y, Y184F, D1246Y) or NYD haplotype. Eight (16%) of 51 participants in Masaka and 12 (15%) of 82 participants in Rukara were microscopically positive 3 days after treatment initiation, which was associated with pre-treatment presence of Pfkelch13 R561H in Masaka (p=0·0005). Genetic analysis of Pfkelch13 R561H mutations suggest their common ancestry and local origin in Rwanda.

INTERPRETATION

We confirm evidence of emerging artemisinin partial resistance in Rwanda. Although artemether-lumefantrine remains efficacious, vigilance for decreasing efficacy, further characterisation of artemisinin partial resistance, and evaluation of additional antimalarials in Rwanda should be considered.

FUNDING

The US President's Malaria Initiative.

TRANSLATION

For the French translation of the abstract see Supplementary Materials section.

Twelve-Year Trend in the Prevalence of High-Risk Human Papillomavirus Infection Among Rwandan Women Living With HIV

BACKGROUND

We examined the trend in prevalence of high-risk human papillomavirus (hrHPV) cervical infection among Rwandan women living with HIV (WLWH) over 12 years.

METHODS

Prevalence of cervical hrHPV DNA was measured in 3 studies at 3 different time periods in 3 different groups of WLWH using 3 different but comparable hrHPV tests: a MY09/MY11 PCR test in 2005 (RWISA; n = 497), careHPV in 2009-2010 (HPV Demonstration; n = 1242), and Xpert HPV test in 2016-2018 (U54; n = 4734). Prevalences were adjusted for age and CD4 cell count.

RESULTS

HrHPV prevalence decreased over time from 42.5% to 32.2% to 26.5% (P < .001). CD4 cell counts improved over time (Ptrend <.001) so that the percentage of WLWH with CD4 counts of ≥500 cells/μL increased from 7.7% in 2005 to 42.2% in 2009-2010 and 61.1% in 2016-2018. Thus, after adjustment for differences in CD4 counts and age, hrHPV prevalences were more similar over time: 32.6% for RWISA, 30.6% for HPV Demonstration, and 27.1% for U54 (P = .007).

CONCLUSIONS

Prevalence of hrHPV among WLWH has decreased over the past decade, most likely the result of improved immune reconstitution due to better HIV care and management in Rwanda.

One hundred thirty-three observed COVID-19 deaths in 10 months: unpacking lower than predicted mortality in Rwanda

The African region was predicted to have worse COVID-19 infection and death rates due to challenging health systems and social determinants of health. However, in the 10 months after its first case, Rwanda recorded 10316 cases and 133 COVID-19-related deaths translating to a case fatality rate (CFR) of 1.3%, which raised the question: why does Rwanda have a low COVID-19 CFR? Here we analysed COVID-19 data and explored possible explanations to better understand the disease burden in the context of Rwanda's infection control strategies.We investigated whether the age distribution plays a role in the observed low CFR in Rwanda by comparing the expected number of deaths for 10-year age bands based on the CFR reported in other countries with the observed number of deaths for each age group. We found that the age-specific CFRs in Rwanda are similar to or, in some older age groups, slightly higher than those in other countries, suggesting that the lower population level CFR reflects the younger age structure in Rwanda, rather than a lower risk of death conditional on age. We also accounted for Rwanda's comprehensive SARS-CoV-2 testing strategies and reliable documentation of COVID-19-related deaths and deduced that these measures may have allowed them to likely identify more asymptomatic or mild cases than other countries and reduced their reported CFR.Overall, the observed low COVID-19 deaths in Rwanda is likely influenced by the combination of effective infection control strategies, reliable identification of cases and reporting of deaths, and the population's young age structure.

Whole-Genome Analyses Identifies Multiple Reassortant Rotavirus Strains in Rwanda Post-Vaccine Introduction

Children in low-and middle-income countries, including Rwanda, experience a greater burden of rotavirus disease relative to developed countries. Evolutionary mechanisms leading to multiple reassortant rotavirus strains have been documented over time which influence the diversity and evolutionary dynamics of novel rotaviruses. Comprehensive rotavirus whole-genome analysis was conducted on 158 rotavirus group A (RVA) samples collected pre- and post-vaccine introduction in children less than five years in Rwanda. Of these RVA positive samples, five strains with the genotype constellations G4P[4]-I1-R2-C2-M2-A2-N2-T1-E1-H2 (n = 1), G9P[4]-I1-R2-C2-M2-A1-N1-T1-E1-H1 (n = 1), G12P[8]-I1-R2-C2-M1-A1-N2-T1-E2-H3 (n = 2) and G12P[8]-I1-R1-C1-M1-A2-N2-T2-E1-H1 (n = 1), with double and triple gene reassortant rotavirus strains were identified. Phylogenetic analysis revealed a close relationship between the Rwandan strains and cognate human RVA strains as well as the RotaTeq^® vaccine strains in the VP1, VP2, NSP2, NSP4 and NSP5 gene segments. Pairwise analyses revealed multiple differences in amino acid residues of the VP7 and VP4 antigenic regions of the RotaTeq^® vaccine strain and representative Rwandan study strains. Although the impact of such amino acid changes on the effectiveness of rotavirus vaccines has not been fully explored, this analysis underlines the potential of rotavirus whole-genome analysis by enhancing knowledge and understanding of intergenogroup reassortant strains circulating in Rwanda post vaccine introduction.

Monitoring mosquito nuisance for the development of a citizen science approach for malaria vector surveillance in Rwanda

BACKGROUND

Many countries, including Rwanda, have mosquito monitoring programmes in place to support decision making in the fight against malaria. However, these programmes can be costly, and require technical (entomological) expertise. Involving citizens in data collection can greatly support such activities, but this has not yet been thoroughly investigated in a rural African context.

METHODS

Prior to the implementation of such a citizen-science approach, a household entomological survey was conducted in October-November 2017 and repeated one year later in Busoro and Ruhuha sectors, in southern and eastern province of Rwanda, respectively. The goal was to evaluate the perception of mosquito nuisance reported by citizens as a potential indicator for malaria vector hotspots. Firstly, mosquito abundance and species composition were determined using Centers for Disease Control and Prevention (CDC) light traps inside the houses. Secondly, household members were interviewed about malaria risk factors and their perceived level of mosquito nuisance.

RESULTS

Tiled roofs, walls made of mud and wood, as well as the number of occupants in the house were predictors for the number of mosquitoes (Culicidae) in the houses, while the presence of eaves plus walls made of mud and wood were predictors for malaria vector abundance. Perception of mosquito nuisance reported indoors tended to be significantly correlated with the number of Anopheles gambiae sensu lato (s.l.) and Culicidae collected indoors, but this varied across years and sectors. At the village level, nuisance also significantly correlated with An. gambiae s.l. and total mosquito density, but only in 2018 while not in 2017.

CONCLUSIONS

Perception of mosquito nuisance denoted in a questionnaire survey could be used as a global indicator of malaria vector hotspots. Hence, involving citizens in such activities can complement malaria vector surveillance and control.

A pooled testing strategy for identifying SARS-CoV-2 at low prevalence

Suppressing infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will probably require the rapid identification and isolation of individuals infected with the virus on an ongoing basis. Reverse-transcription polymerase chain reaction (RT-PCR) tests are accurate but costly, which makes the regular testing of every individual expensive. These costs are a challenge for all countries around the world, but particularly for low-to-middle-income countries. Cost reductions can be achieved by pooling (or combining) subsamples and testing them in groups^1-7. A balance must be struck between increasing the group size and retaining test sensitivity, as sample dilution increases the likelihood of false-negative test results for individuals with a low viral load in the sampled region at the time of the test⁸. Similarly, minimizing the number of tests to reduce costs must be balanced against minimizing the time that testing takes, to reduce the spread of the infection. Here we propose an algorithm for pooling subsamples based on the geometry of a hypercube that, at low prevalence, accurately identifies individuals infected with SARS-CoV-2 in a small number of tests and few rounds of testing. We discuss the optimal group size and explain why, given the highly infectious nature of the disease, largely parallel searches are preferred. We report proof-of-concept experiments in which a positive subsample was detected even when diluted 100-fold with negative subsamples (compared with 30-48-fold dilutions described in previous studies^9-11). We quantify the loss of sensitivity due to dilution and discuss how it may be mitigated by the frequent re-testing of groups, for example. With the use of these methods, the cost of mass testing could be reduced by a large factor. At low prevalence, the costs decrease in rough proportion to the prevalence. Field trials of our approach are under way in Rwanda and South Africa. The use of group testing on a massive scale to monitor infection rates closely and continually in a population, along with the rapid and effective isolation of people with SARS-CoV-2 infections, provides a promising pathway towards the long-term control of coronavirus disease 2019 (COVID-19).

Antenatal Care Visits and Adverse Pregnancy Outcomes at a Hospital in Rural Western Province, Rwanda

In many economically developing countries, and especially in the rural regions of sub-Saharan African coun-tries, there have been only limited investigations into the association between antenatal care (ANC) and adverse pregnancy outcomes. We obtained information on ANC and pregnancy outcomes between 2011 and 2016 from hospital files of pregnant women (n = 4,960) served at a rural hospital in Rwanda, and we examined the associa-tions between their ANC visits and the adverse pregnancy and neonatal outcomes by using univariate and mul-tivariate logistic regression models to estimate the odds ratios (ORs) and 95% confidence intervals (CIs). Most of the pregnant women had ≥ 4 ANC visits, but 39% (n = 1,911) did not have ≥ 3 visits before delivery. The prev-alence of low birth weight (LBW) and that of preterm birth (PTB) were 12% and 9.9%, respectively. Compared to the women who attended only one ANC visit, those who attended ≥ 4 ANC visits had lower risks of LBW (OR 0.20; 95%CI: 0.11-0.36) and PTB (OR 0.28; 95%CI: 0.11-0.76). Frequent ANC visits were also associ-ated with better postnatal outcomes of the newborns. Encouraging women to attend ANC visits before delivery can markedly reduce PTB-related and LBW-related complications, especially in resource-limited settings.

Burden of post-traumatic stress disorder in postgenocide Rwandan population following exposure to 1994 genocide against the Tutsi: A meta-analysis

BACKGROUND

The 1994 genocide against Tutsi resulted in a massive death toll that reached one million people. Despite the tremendous efforts made to mitigate the adverse effects of the genocide, a substantial burden of mental health disorders still exists including the notably high prevalence of post-traumatic stress disorder (PTSD) among genocide survivors. However, a synthesized model of PTSD vulnerability in this population is currently lacking.

METHODS

A meta-analysis of 19 original research studies that reported PTSD prevalence (n = 12,610). Medline-PubMed and Science.gov were key search engines. Random-Effects Model (k = 19; tau^2 estimator: DL) was applied. Data extraction, synthesis, and meta-analysis were carried out using R.

RESULTS

The total of 2957 out of 11,746 individuals suffered from PTSD. The summary proportion is 25% (95% CI=0.16,0.36). The tau^2 is 0.06 (95% CI=0.03,0.14) in the absence of subgroups, and the Q-statistic is 2827.65 (p<0.0001), all of which suggests high heterogeneity in the effect sizes. Year of data collection and Year of publication were significant moderators. PTSD pooled prevalence in the genocide survivor category was estimated at 37% (95% CI=0.21,0.56).

CONCLUSION

The PTSD prevalence among genocide survivors is considerably higher compared to the general Rwandan population. The burden of PTSD in the general Rwandan population declined significantly over time, likely due to treatment of symptoms through strong national mental health programs, peace building and resolution of symptoms over time. To the best of our knowledge little evidence has reported the burden of PTSD prevalence in African post conflict zones particularly in Rwanda.

LIMITATION

Limitations of our review include the use of retrospective studies and studies with very small sample sizes, as well as language criterion.

Rubinstein-Taybi syndrome in diverse populations

Rubinstein-Taybi syndrome (RSTS) is an autosomal dominant disorder, caused by loss-of-function variants in CREBBP or EP300. Affected individuals present with distinctive craniofacial features, broad thumbs and/or halluces, and intellectual disability. RSTS phenotype has been well characterized in individuals of European descent but not in other populations. In this study, individuals from diverse populations with RSTS were assessed by clinical examination and facial analysis technology. Clinical data of 38 individuals from 14 different countries were analyzed. The median age was 7 years (age range: 7 months to 47 years), and 63% were females. The most common phenotypic features in all population groups included broad thumbs and/or halluces in 97%, convex nasal ridge in 94%, and arched eyebrows in 92%. Face images of 87 individuals with RSTS (age range: 2 months to 47 years) were collected for evaluation using facial analysis technology. We compared images from 82 individuals with RSTS against 82 age- and sex-matched controls and obtained an area under the receiver operating characteristic curve (AUC) of 0.99 (p < .001), demonstrating excellent discrimination efficacy. The discrimination was, however, poor in the African group (AUC: 0.79; p = .145). Individuals with EP300 variants were more effectively discriminated (AUC: 0.95) compared with those with CREBBP variants (AUC: 0.93). This study shows that clinical examination combined with facial analysis technology may enable earlier and improved diagnosis of RSTS in diverse populations.

Screening of germline mutations in young Rwandan patients with breast cancers

Background

In Sub‐Saharan Africa breast cancer is commonly detected at younger age and the profile is more aggressive with a high mortality rate compared to the European countries. It is suggested that African‐specific genetic background plays a key role in this matter. The present study aimed at understanding the role of genetic factors in breast cancer development in young Rwandan.

Methods

We performed a massive parallel sequencing on Illumina MiSeq NGS system for the screening of 26 genes associated with hereditary breast cancer from 40 patients under 35 years old from two University Teaching Hospitals in Kigali, Rwanda. Sanger sequencing was used to confirm pathogenic and likely pathogenic mutations.

Results

Five patients out of 40 (12.5%) presented with pathogenic mutations including four patients (10%) carrying BRCA1 or BRCA2 pathogenic variants. One patient showed a missense likely pathogenic TP53 variant. We have also detected additional missense, intronic, and 3’UTR variants of unknown significance in all study participants.

Conclusion

This preliminary study suggests that the frequency of germline mutations in young Rwandan patients with breast cancer is similar to the observations made in Caucasians. However, further large studies including patients and controls are needed to better understand the impact of genetic factors as well as the environmental risk factors in the development of breast cancer in young Rwandans.

Screening of germline mutations in Rwandan young patients with breast cancer. The next generation sequencing detected pathogenic BRCA 1 and 2 mutations in 6 patients. We have also detected additional missense, intronic, and 3’UTR variants of unknown significance in all study participants.

Building Skills and Resources for Genomics, Epigenetics, and Bioinformatics Research for Africa: Report of the Joint 11th Conference of the African Society of Human Genetics and 12th H3Africa Consortium, 2018

The 11th Congress of the African Society of Human Genetics (AfSHG) was held from September 16, 2018 to September 21, 2018, in conjunction with the 12th Human Heredity and Health in Africa (H3Africa) Consortium meeting in Kigali, Rwanda. The event was organized by the AfSHG in partnership with the Rwanda Society of Human Genetics and the University of Rwanda. A 2-day workshop on the application of next-generation sequencing technologies for analyzing monogenic disease in African populations was organized as part of the conference (September 22, 2018−September 23, 2018, Kigali, Rwanda). The theme of the conference was “Building skills and resources for genomics, epigenetics and bioinformatics research for Africa.” The conference served as a platform to bring together members from country-specific Societies of Human Genetics, including Rwanda, Cameroon, Democratic Republic of Congo, Egypt, Mali, Senegal, and South Africa, and included 435 delegates from 38 countries, including 29 African countries that attended the conference. A major topic of discussion was how to bridge the gap between the emerging knowledge on genomics and Omics in African populations. The importance of understanding the role of genetic variation in disease causation and susceptibility among Africans was a constant theme during the meeting, as was the need to develop research infrastructure and resources to enhance healthcare systems, so that they are not left behind in the genomic revolution. It was concluded that there is a need to inspire more African scientists to train and work as investigators, clinicians, and genetic counselors in the field of human genetics in Africa. Local investments, and South–South and South–North collaboration were identified as the key drivers for the successful implementation of research and development on the continent.

What do people benefit from a citizen science programme? Evidence from a Rwandan citizen science programme on malaria control

Background

Malaria control remains a challenge globally and in malaria-endemic countries in particular. In Rwanda, a citizen science programme has been set up to improve malaria control. Citizens are involved in collecting mosquito species and reporting mosquito nuisance. This study assessed what people benefit from such a citizen science programme. The analysis was conducted on how the citizen science programme influenced perceptions and behaviour related to malaria control.

Methods

This study employed a mixed-methods approach using dissemination workshops, a survey, and village meetings as the main data collection methods. Dissemination workshops and village meetings involved 112 volunteers of the citizen science programme and were conducted to explore: (1) the benefits of being involved in the programme and (2) different ways used to share malaria-related information to non-volunteers. The survey involved 328 people (110 volunteers and 218 non-volunteers) and was used to compare differences in malaria-related perceptions and behaviour over time (between 2017 and 2019), as well as between volunteers and non-volunteers.

Results

Malaria-related perceptions and behaviour changed significantly over time (between 2017 and 2019) and became favourable to malaria control. When the findings were compared between volunteers and non-volunteers, for perceptions, only perceived self-efficacy showed a significant difference between these two groups. However, volunteers showed significantly more social interaction, participation in malaria-related activities at the community level, and indoor residual spraying (IRS) acceptance. In addition, both volunteers and non-volunteers reported to have gained knowledge and skills about the use of malaria control measures in general, and mosquito species in particular among volunteers.

Conclusion

The reported knowledge and skills gained among non-volunteers indicate a diffusion of the citizen science programme-related information in the community. Thus, the citizen science programme has the potential to provide individual and collective benefits to volunteers and society at large.

Transgenerational effects of the genocide against the Tutsi in Rwanda: A post-traumatic stress disorder symptom domain analysis

Background: A number of studies have investigated transgenerational effects of parental post-traumatic stress disorder (PTSD) and its repercussions for offspring. Few studies however, have looked at this issue in the African context. Methods: The present study addresses this gap by utilizing a Pearson correlation matrix to investigate symptom severity within the three Diagnostic and Statistical Manual of Mental Disorders IV (DSM-IV) PTSD symptom domains in mothers exposed to the genocide against the Tutsi in Rwanda (n=25) and offspring (n=25), and an ethnically matched set of controls (n=50) who were outside of Rwanda during the 1994 genocide. All mothers were pregnant with the offspring included in the study during the time of the genocide. Results: Total PTS score was significantly (p<0.01) correlated with each of the three symptom domains at various strengths in both cases and controls. No significant differences in association of total PTS score and PTSD symptom domains were observed between exposed mothers and offspring, suggesting that each symptom domain contributed equivalently to both exposed mothers and offspring distress. In contrast, the re-experiencing symptom domain showed a significant difference in correlation to overall PTS score in non-exposed mothers compared to their offspring (p<0.05), with mothers showing a significantly higher correlation. Furthermore, the correlation between avoidance/numbing symptoms to overall PTS was significantly different (p≤0.01) across exposed and non-exposed mothers. As a secondary analysis, we explored the relationship between DNA methylation in the glucocorticoid receptor (NR3C1) locus, an important stress modulating gene, and PTSD symptom domains, finding an association between DNA methylation and re-experiencing among genocide-exposed mothers that exceeded any other observed associations by approximately two-fold.  Conclusions: This is the first report, to our knowledge, of a symptom-based analysis of transgenerational transmission of PTSD in sub-Saharan Africa. These findings can be leveraged to inform further mechanistic and treatment research for PTSD.

CD4+ regulatory T cells and CD4+ activated T cells in new active and relapse tuberculosis

The aim of the present study was to examine characteristics of tuberculosis (TB) patients with different clinical forms and to study the frequency of Regulatory T cells (Treg cells) and Activated T cells in patients with new active and relapse TB. Forty-five pulmonary TB patients and a control group of 15 healthy individuals were enrolled in this study. Of the 45 TB patients, 15 were new cases with drug-susceptible active TB and 30 were relapsed cases (15 drug-susceptible and 15 multidrug resistant-TB). The age of study participants ranged from 21 to 68 years old. According to sex presentation, males were appreciably highly affected than females with a sex ratio of 2. The patients reported a mean recent weight loss of 8.9 kg. The Erythrocyte Sedimentation Rate was high in TB group, far exceeding the normal value. The results revealed that the number of CD3+ CD4+ T-cells significantly decreased whereas the level of blood Treg cells and expression of activation markers CD38 and HLA-DR on CD4+ T-cells significantly increased in TB group compared with the control group (p&lt;0.05). The frequency of Treg cells was significantly higher in the TB group than the control group. Both the patients with new active TB and relapse TB demonstrated significantly higher levels of CD4+FoxP3+ Treg compared to healthy subjects (p&lt;0.05). A high and significant percentage of Treg cells were found in patients with DS active TB than patients with MDR relapse TB. Interestingly, the frequency of CD4+FoxP3+ cells also differs according to the sputum smear microscopy status. The presence of high numbers of Treg cells and corresponding high immune activation may be an unfavourable factor that can predispose individuals to different clinical forms of TB, including relapse TB.

Role of individual perceptions in the consistent use of malaria preventive measures: mixed methods evidence from rural Rwanda

Background

Malaria preventive measures, including long-lasting insecticide-treated bet nets (LLINs), indoor residual spraying (IRS), and controlling mosquito breeding sites, are key measures to achieve malaria elimination. Still, compliance with these recommended measures remains a major challenge. By applying a novel and comprehensive model for determinants of malaria prevention behaviour, this study tests how individual perceptions influence the intentions to use malaria preventive measures and explores strategies that stimulate their consistent use.

Methods

The study was carried out in the sectors of Ruhuha and Busoro, Rwanda during October and November 2017, and these were conducted into two phases. Phase one involved a questionnaire survey (N = 742), whereas Phase two employed a qualitative approach that included nine focus group discussions, seven key informant interviews, and three in-depth interviews.

Results

The findings of the quantitative study showed that participants very often use LLINs (66.6%), accept IRS (73.9%), and drain stagnant water in case of presence (62%). The intentions to use malaria preventive measures were consistently driven by perceived severity, perceived self-efficacy, perceived response efficacy, and subjective norms, and hindered by perceived barriers. The intentions were also positively associated with the actual use of LLINs, acceptance of IRS, and drainage of stagnant water. There is no evidence that either not having enough LLINs (ownership of at least one bed net in the household, here referred to as availability) or having sufficient LLINs (having one LLIN per two people in the household, here referred to as accessibility) moderated the relationship between behavioural intentions and actual use of LLINs. The qualitative study indicated that participants believed malaria risk to be high and perceived a high mosquito density. They also believed that repetitive malaria episodes are caused by the perceived low effectiveness of anti-malaria medications. Lack of LLINs increased the perceived added value of LLINs, and together with the increased malaria burden increased the perceived response efficacy. Participants highlighted the need to continuously mobilize and engage community members especially those who do not use LLINs when having one, and those who do not accept the spraying activities.

Conclusion

Malaria prevention interventions should target individual perceptions to enhance consistent use of malaria preventive measures. Three strategies to improve consistent use and acceptance of these measures are highlighted: (1) ensure access to LLINs and regular spraying activities, (2) community mobilization and (3) citizen engagement in malaria prevention activities.

Identification and characterization of the Onchocerca volvulus Excretory Secretory Product Ov28CRP, a putative GM2 activator protein

Onchocerca volvulus is the nematode pathogen responsible for human onchocerciasis also known as "River blindness", a neglected tropical disease that affects up to 18 million people worldwide. Helminths Excretory Secretory Products (ESPs) constitute a rich repertoire of molecules that can be exploited for host-parasite relationship, diagnosis and vaccine studies. Here, we report, using a range of molecular techniques including PCR, western blot, recombinant DNA technology, ELISA, high performance thin-layer chromatography and mass spectrometry that the 28 KDa cysteine-rich protein (Ov28CRP) is a reliable component of the O. volvulus ESPs to address the biology of this parasite. We showed that (1) Ov28CRP is a putative ganglioside GM2 Activator Protein (GM2AP) conserved in nematode; (2) OvGM2AP gene is transcriptionally activated in all investigated stages of the parasitic life cycle, including larval and adult stages; (3) The full-length OvGM2AP was detected in in-vitro O. volvulus ESPs of adult and larval stages; (4) the mass expressed and purified recombinant OvGM2AP purified from insect cell culture medium was found to be glycosylated at asparagine 173 and lacked N-terminal signal peptide sequence; (5) the recombinant OvGM2AP discriminated serum samples of infected and uninfected individuals; (6) OvGM2AP competitively inhibits MUG degradation by recombinant β-hexosaminidase A but not MUGS, and could not hydrolyze the GM2 to GM3; (7) humoral immune responses to the recombinant OvGM2AP revealed a negative correlation with ivermectin treatment. Altogether, our findings suggest for the first time that OvGM2AP is an antigenic molecule whose biochemical and immunological features are important to gain more insight into our understanding of host-parasite relationship, as well as its function in parasite development at large.

VPS51 biallelic variants cause microcephaly with brain malformations: A confirmatory report

Whole exome sequencing undertaken in two siblings with delayed psychomotor development, absent speech, severe intellectual disability and postnatal microcephaly, with brain malformations consisting of cerebellar atrophy in the eldest affected and hypoplastic corpus callosum in the younger sister; revealed a homozygous intragenic deletion in VPS51, which encodes the vacuolar protein sorting-associated protein, one the four subunits of the Golgi-associated retrograde protein (GARP) and endosome-associated recycling protein (EARP) complexes that promotes the fusion of endosome-derived vesicles with the trans-Golgi network (GARP) and recycling endosomes (EARP). This observation supports a pathogenic effect of VPS51 variants, which has only been reported previously once, in a single child with microcephaly. It confirms the key role of membrane trafficking in normal brain development and homeostasis.

Social contexts as mediator of risk behaviors in Rwandan men who have sex with men (MSM): Implications for HIV and STI transmission

INTRODUCTION

Men who have sex with men (MSM) are disproportionately impacted by HIV/AIDS resulting from risky sexual behaviors. Social and contextual factors are known to mediate risk behaviors, but there is limited information about the prevalence of risky sexual practices of Rwandan MSM and the concomitant socio-contextual determinants making it difficult to assess implications for preventing HIV/STI transmission in this key population.

METHODS

Using exploratory qualitative design, we obtained socio-contextual information regarding prevalence of risky sexual behavior and assessed implications for HIV/ STIs transmission and preventive measures taken by MSM to improve sexual health and wellbeing. Thirty MSM were recruited to participate in in-depth interviews using respondent-driven sampling from LGBT associations in Kigali. Data were analyzed using standard qualitative data analysis procedures.

RESULTS

Respondents' were between 18-40 years old; all completed primary education and are mostly low-socioeconomic status. Risky sexual practices were common, but differed by peculiar individual and contextual factors. Older MSM often reported occasional sexual relations with women to avoid suspicion and social stigma. Younger MSM's risky sexual practices are mostly transactional and mediated by the need for social acceptance and support. Knowledge of STIs was poor, but prevalence, especially of HPV was high. The options for improving sexual wellbeing are limited and mostly clandestine.

CONCLUSION

Risky sexual behavior of Rwandan MSM has major implications for HIV/STI transmission. An environment of intense social stigma and social isolation makes it difficult to obtain information or services to improve sexual health. Effective interventions that address individual and contextual determinants of risk and access to health services are urgently needed to limit the consequence of MSM as a bridge for HIV transmission to the general population.

Cornelia de Lange syndrome in diverse populations

Cornelia de Lange syndrome (CdLS) is a dominant multisystemic malformation syndrome due to mutations in five genes-NIPBL, SMC1A, HDAC8, SMC3, and RAD21. The characteristic facial dysmorphisms include microcephaly, arched eyebrows, synophrys, short nose with depressed bridge and anteverted nares, long philtrum, thin lips, micrognathia, and hypertrichosis. Most affected individuals have intellectual disability, growth deficiency, and upper limb anomalies. This study looked at individuals from diverse populations with both clinical and molecularly confirmed diagnoses of CdLS by facial analysis technology. Clinical data and images from 246 individuals with CdLS were obtained from 15 countries. This cohort included 49% female patients and ages ranged from infancy to 37 years. Individuals were grouped into ancestry categories of African descent, Asian, Latin American, Middle Eastern, and Caucasian. Across these populations, 14 features showed a statistically significant difference. The most common facial features found in all ancestry groups included synophrys, short nose with anteverted nares, and a long philtrum with thin vermillion of the upper lip. Using facial analysis technology we compared 246 individuals with CdLS to 246 gender/age matched controls and found that sensitivity was equal or greater than 95% for all groups. Specificity was equal or greater than 91%. In conclusion, we present consistent clinical findings from global populations with CdLS while demonstrating how facial analysis technology can be a tool to support accurate diagnoses in the clinical setting. This work, along with prior studies in this arena, will assist in earlier detection, recognition, and treatment of CdLS worldwide.