The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Exclosures in people’s mind: perceptions and attitudes in the Tigray Region

The paper examines the perceptions and attitudes of local people living next to nine exclosures in the Tigray RegioninEthiopia.Socialexchangetheorywasusedastheoreticalframeworkanddatawerecollectedfrom446 farminghouseholds.Factoranalysis,multiplelinearregressionandbinarylogisticregressionwereappliedtothe data to identify factors that influenced local household heads’ perceptions of and attitudes towards existing exclosures and further expansion of exclosures. Household heads’ perceptions of exclosures could be grouped undersocial,economicandecologicaldimensions.Somehouseholdheadsexpressedpositiveattitudestowards theexistingexclosures,whilesomewereconcernedaboutthefutureexpansionoftheexclosures.Thefindings alsorevealedthathouseholds’socio-economicprofile,households’knowledgeaboutexclosures,theecological conditionsofexclosures,andthegeographicalattributesofexclosuresallplayedimportantrolesinshapinglocal household heads’ perceptions of exclosures. Moreover, their perceptions of exclosures were significantly correlated with tangible benefits and costs associated with exclosures. Thus, improvement in local communities’ attitudes towards and support for exclosures would follow if exclosures contributed more directly to people’s livelihoods.However,thelevelofsupportforexclosuresisremarkablegiventhefactthattheyhavebeenclosed forgrazingandotheruses.publishedVersio

Exclosures in people’s mind: perceptions and attitudes in the Tigray Region

The paper examines the perceptions and attitudes of local people living next to nine exclosures in the Tigray RegioninEthiopia.Socialexchangetheorywasusedastheoreticalframeworkanddatawerecollectedfrom446 farminghouseholds.Factoranalysis,multiplelinearregressionandbinarylogisticregressionwereappliedtothe data to identify factors that influenced local household heads’ perceptions of and attitudes towards existing exclosures and further expansion of exclosures. Household heads’ perceptions of exclosures could be grouped undersocial,economicandecologicaldimensions.Somehouseholdheadsexpressedpositiveattitudestowards theexistingexclosures,whilesomewereconcernedaboutthefutureexpansionoftheexclosures.Thefindings alsorevealedthathouseholds’socio-economicprofile,households’knowledgeaboutexclosures,theecological conditionsofexclosures,andthegeographicalattributesofexclosuresallplayedimportantrolesinshapinglocal household heads’ perceptions of exclosures. Moreover, their perceptions of exclosures were significantly correlated with tangible benefits and costs associated with exclosures. Thus, improvement in local communities’ attitudes towards and support for exclosures would follow if exclosures contributed more directly to people’s livelihoods.However,thelevelofsupportforexclosuresisremarkablegiventhefactthattheyhavebeenclosed forgrazingandotheruses

Exclosures in people’s mind: Perceptions and attitudes in the Tigray Region

The paper examines the perceptions and attitudes of local people living next to nine exclosures in the Tigray Region in Ethiopia. Social exchange theory was used as theoretical framework and data were collected from 446 farming households. Factor analysis, multiple linear regression and binary logistic regression were applied to the data to identify factors that influenced local household heads’ perceptions of and attitudes towards existing exclosures and further expansion of exclosures. Household heads’ perceptions of exclosures could be grouped under social, economic and ecological dimensions. Some household heads expressed positive attitudes towards the existing exclosures, while some were concerned about the future expansion of the exclosures. The findings also revealed that households’ socio-economic profile, households’ knowledge about exclosures, the ecological conditions of exclosures, and the geographical attributes of exclosures all played important roles in shaping local household heads’ perceptions of exclosures. Moreover, their perceptions of exclosures were significantly correlated with tangible benefits and costs associated with exclosures. Thus, improvement in local communities’ attitudes towards and support for exclosures would follow if exclosures contributed more directly to people’s livelihoods. However, the level of support for exclosures is remarkable given the fact that they have been closed for grazing and other uses

Intimate partner violence during pregnancy and adverse birth outcomes: a case-control study

Abstract Background Intimate partner violence is a common phenomenon in Ethiopia families. About 81% of women believed that a husband is justified in beating his wife. About 30–60% of families were affected by their intimates. Women suffer physical, emotional, sexual and economic violence by their intimate partners. It often remains either for the sake of family secrecy, cultural norms or, due to fear, shame and community’s reluctance on domestic affair and social stigma.The objective of this study is to examine the association between intimate partner violence during pregnancy and adverse birth outcomes. Methods A hospital based unmatched case control study was conducted in four zonal hospitals of Tigray region. A total of 954 study participants (318 cases and 636 controls) were taken. Systematic sampling was used to select the cases and controls. Ethical clearance was obtained throughout the study period. Result Out of 954 interviewed mothers, 389 (40.8%) had experienced intimate partner violence during their index pregnancy period. More than two third (68.6%) of cases had been exposed to intimate partner violence. Multivariable logistic regression analysis showed that, women exposed to intimate partner violence during pregnancy were three times more likely to experience low birth weight (AOR = 3.1; CI 95% [1.470,6.618]) and preterm birth (AOR = 2.5; CI 95% [2.198–2.957]). It was observed that women who had been exposed to physical violence during pregnancy were five times more likely to experience low birth weight (AOR = 4.767; CI 95% [2.515, 9.034]) and preterm birth (AOR = 5.3; CI 95%: 3.95–7.094). Conclusion and recommendation It was found that the risk of preterm birth and low birth weight was increased when the pregnant women were exposed to more than one type of intimate partner violence and physical violence during pregnancy. Therefore, Efforts to address maternal and newborn health need to include issues of violence against women

Commonly missed nursing cares in the obstetrics and gynecologic wards of Tigray general hospitals; Northern Ethiopia.

BackgroundMissed nursing care is considered an error of omission and is defined as any aspect of required patient care that is omitted (either in part or whole) or significantly delayed. Nursing care missed in the perinatal setting can cause negative outcomes and repercussions for the quality and safety of care. This has been reported in multiple settings and countries and is tied to negative maternal outcomes. Preventing missed nursing care requires in-depth research considering the clinical setting.ObjectiveThe main aim of the study was to assess commonly missed nursing care elements, reasons, and factors for the omission in the obstetric and gynecologic units of general hospitals in Tigray 2017/18.Methods and materialsA cross-sectional study was conducted in eight randomly selected general hospitals in Tigray, Ethiopia. A total of 422 nurses and midwives were selected through simple random sampling using the staff list as a sampling frame. To identify the commonly missed nursing care and related factors, the MISSCARE survey tool was used. Descriptive, bivariate, and multivariate logistic regression analysis was performed to assess potential risk factors of nursing cares omission.ResultThe study results showed that 299 (74.6%) participants commonly missed at least one nursing care in the perinatal setting. Labor resources 386(96.3%), teamwork 365(91%), material resources 361 (90%) and communication 342 (85.3%) were the reasons identified for commonly missing care. In the multivariate analyses, sex (p-value ConclusionThe proportion of commonly missed nursing care was high. After adjusting for demographic variables, labor resources, material resources, and communication were reasons for commonly missed nursing care. Increasing male professional proportion, investing in nurses/midwives training, and harmonizing nursing service administration through appropriate working shift arrangement and timely assessment of professionals' stability and satisfaction could minimize frequent omission of nursing care

Seedling survival and plantation success in the drylands of Northern Ethiopia

Abstract We studied tree seedling survival rates and plantation success of the Growth and Transformation Plan I—GTP I (2011–2015) in the drylands of Northern Ethiopia. The study was carried out in six randomly selected districts of Tigrai region that represent three agro-ecological zones: the highland, midland and lowland. A biophysical survey was conducted to assess the survival rates of tree seedlings and the success rate of the plantation interventions. The study employed both primary and secondary data sources. Results revealed that there were variations (P < 0.05) in the survival of planted tree seedlings among plantation sites of the same village, between the villages of the same district and among the districts. The regional mean survival rate of planted tree seedlings was 53%. The planting interventions were not encouraging due to lack of pre- and post-planting management, moisture stress, poor soil and site conditions, planting an unmanageable number of seedlings, weak law enforcement and lack of proper monitoring and evaluation mechanisms. In the study areas, four types of ownership were identified: private, communal, state and youth groups. Among the ownership types, private ownership had the highest rate of success, whereas community ownership had the lowest rate. For sustaining successful plantation development, watering, pre- and post-planting management of planted tree seedlings and permanent employment of guards are important

Virological and immunological failure of HAART and associated risk factors among adults and adolescents in the Tigray region of Northern Ethiopia

<div><p>Background</p><p>Human immunodeficiency virus/Acquired immunodeficiency syndrome associated morbidity and mortality has reduced significantly since the introduction of highly active antiretroviral therapy. As a result of increasing access to highly active antiretroviral therapy, the survival and quality of life of the patients has significantly improved globally. Despite this promising result, regular monitoring of people on antiretroviral therapy is recommended to ensure whether there is an effective treatment response or not. This study was designed to assess virological and immunological failure of highly active antiretroviral therapy users among adults and adolescents in the Tigray region of Northern Ethiopia, where scanty data are available.</p><p>Methods</p><p>A retrospective follow up study was conducted from September 1 to December 30, 2016 to assess the magnitude and factors associated with virological and immunological failure among 260 adults and adolescents highly active antiretroviral therapy users who started first line ART between January 1, 2008 to March 1, 2016. A standardized questionnaire was used to collect socio-demographic and clinical data. SPSS Version21 statistical software was used for analysis. Bivariate and multivariate logistic regression analyses were conducted to identify factors associated to virological and immunological failure. Statistical association was declared significant if p-value was ≤ 0.05.</p><p>Result</p><p>A total of 30 (11.5%) and 17 (6.5%) participants experienced virological and immunological failure respectively in a median time of 36 months of highly active antiretroviral therapy. Virological failure was associated with non-adherence to medications, aged < 40 years old, having CD4⁺ T-cells count < 250 cells/μL and male gender. Similarly, immunological failure was associated with non-adherence, tuberculosis co-infection and Human immunodeficiency virus RNA ≥1000 copies/mL.</p><p>Conclusions</p><p>The current result shows that immunological and virological failure is a problem in a setting where highly active antiretroviral therapy has been largely scale up. The problem is more in patients with poor adherence. This will in turn affect the global targets of 90% viral suppression by 2020. This may indicate the need for more investment and commitment to improving patient adherence in the study area.</p></div

Baseline and follow up characteristics on first line ART from January 1, 2008 to March 1, 2016 at Mekelle hospital and Ayder Comprehensive Specialized Hospital (n = 260).

<p>Baseline and follow up characteristics on first line ART from January 1, 2008 to March 1, 2016 at Mekelle hospital and Ayder Comprehensive Specialized Hospital (n = 260).</p

Immunological failure and associated risk factors among HIV infected individuals on ART from January 2008 to March 2016 at Mekelle hospital and Ayder Comprehensive Specialized Hospital(n = 17).

<p>Immunological failure and associated risk factors among HIV infected individuals on ART from January 2008 to March 2016 at Mekelle hospital and Ayder Comprehensive Specialized Hospital(n = 17).</p