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

IMPACT OF STIGMA, DISCRIMINATION AND SOCIAL SUPPORT ON PSYCHOLOGICAL DISTRESS AMONG AIDS PATIENTS: ROLE OF COGNITIVE BEHAVIOR THERAPY

<p><strong>Abstract</strong></p><p><strong>Objectives: </strong>The HIV (Human Immunodeficiency Virus) is an innovative germ that produced infection of HIV and AIDS. AIDS is a situation in individuals in which immune system is fail to carry its work and increase the infections of cancer and life threating poisons. The main objective of this study was to determine the relationship of stigma, discrimination and social support with psychological distress as symptoms of anxiety, depression, stress and level of stigma among HIV/AIDS patients. Further, the second purpose of the study was to treatment of the AIDS patient's emotional distress through cognitive behavior therapy. <strong>Design/Methods: </strong>Sample of 150 registered patients of AIDS selected trough purposive sampling technique from different Hospitals in district Gujrat, Punjab Pakistan. The age range of the participants were 18-70 years with mean age (36.43). Four scales as "HIV Stigma Scale, Discrimination Scale (subscale of HIV Stigma Scale), Social support Scale and Psychological Distress Scale" were used in the study. After scrutiny twenty (20) patients with high level of psychological distress was registered for intervention. Pearson Correlation, two step cluster and t-test analysis were used.<strong> Results: </strong>Results of study showed that stigma has positive relationship with psychological distress, anxiety, depression and stress (<i>r </i>= .405, <i>p</i> < .01, r= .307,<i> p</i> < .01, <i>r </i>= .467, <i>p</i> < .01, <i>r </i>= .332, <i>p</i> < .01, respectively). Cluster analysis of stigma showed that 33 patients were in low level of stigma, 55 in medium and 62 in high level stigma Discrimination has positive relationship with psychological distress, anxiety, depression and stress (<i>r </i>= .456, <i>p</i> < .01, <i>r </i>= .378, <i>p</i> < .01, <i>r </i>= .434, <i>p</i> < .01, <i>r </i>= .424, <i>p</i> < .01respectively). Social-support has negative relationship with psychological distress, anxiety, depression and stress ((<i>r </i>= -.283, <i>p</i> < .01, <i>r </i>= -.189, <i>p</i> <.05, <i>r </i>=.-.307, <i>p</i> < .01, <i>r </i>= -.275, <i>p</i> < .01 respectively). Results also indicated that Cognitive Behavior Therapy has great effective on Psychological distress as there is significant difference in mean scores of psychological distress of AIDS patients (M= 109.5, M= 94.00). <strong>Conclusion: </strong>The study shows that stigma and discrimination has a significant relationship with psychological distress (anxiety, depression and stress) and most of the patients lie in high level of stigma. Results also showed that social support has inverse relation with psychological distress as symptoms of anxiety, depression and stress. Psychological distress among AIDS patients can be overcome through the intervention as cognitive behavior therapy. </p&gt

Diagnosis of Mediterranean visceral leishmaniasis by detection of Leishmania-related antigen in urine and oral fluid samples

International audienceImplementation of simple diagnostic tests using non-invasive collection of biological specimens is of great importance in the diagnosis of pediatric visceral leishmaniasis caused by Leishmania infantum. Latex agglutination kit (KAtex) is widely used in the diagnosis mainly in L. donovani endemic areas. However its utilization in L. infantum endemic regions remains limited and its use on noninvasive biological specimen apart urine was not reported. In this study, KAtex kit was used to detect Leishmania-related antigen in urine and oral fluid of 35 L. infantum visceral leishmaniasis cases and 62 controls including non-infectious disease and infectious disease controls (34 and 28 respectively). Sensitivity and specificity of urine based KAtex were 51.4% and 98.3% respectively, whereas, sensitivity and specificity of oral-fluid based KAtex were 80% and 88.3% respectively. Although, sensitivity of oral-fluid KAtex (R) was high, its specificity varied significantly according to the presence or the absence of an infectious disease (71.4% versus 97%, p = 0.01)