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

Cancer truth disclosure by Lebanese doctors

Truthful disclosure of cancer diagnosis is still uncommon in some cultures. In Lebanon, legislation is permissive of non-disclosure. Physicians choose the recourse most agreeable to them. This study's goal was to determine the proportion of Lebanese physicians who choose truthful diagnosis disclosure to cancer patients and to identify factors affecting their choice. A survey of a random sample of Lebanese physicians was conducted to determine the proportion of those who prefer truthful diagnosis disclosure to cancer patients and to identify factors affecting that choice. The survey involved 268 participants representing 10% of all physicians practicing in specialties with potential contact with cancer cases in the Greater Beirut area. It was completed by 212 (79%), of whom 47% would usually tell the patient about cancer. Disclosure preference was not associated with gender, location of medical training, rate of patient contact or teaching activities. It was associated with longer clinical practice and with specialties outside primary care. Most participants were open to changing their policies and considered the patient's desire to know, compliance with treatment and the patient's profession as a physician as most influencing in their choice of disclosure. Exploring the Lebanese public predicament regarding disclosure seems necessary.patient-doctor communication Lebanon cancer disclosure

Thalassemia Screening by Sentiment Analysis on Social Media Platform Twitter

Thalassemia syndrome is a genetic blood disorder induced by the reduction of normal hemoglobin production, resulting in a drop in the size of red blood cells. In severe forms, it can lead to death. This genetic disorder has posed a major burden on public health wherein patients with severe thalassemia need periodic therapy of iron chelation and blood transfusion for survival. Therefore, controlling thalassemia is extremely important and is made by promoting screening to the general population, particularly among thalassemia carriers. Today Twitter is one of the most influential social media platforms for sharing opinions and discussing different topics like people’s health conditions and major public health affairs. Exploring individuals’ sentiments in these tweets helps the research centers to formulate strategies to promote thalassemia screening to the public. An effective Lexiconbased approach has been introduced in this study by highlighting a classifier called valence aware dictionary for sentiment reasoning (VADER). In this study applied twitter intelligence tool (TWINT), Natural Language Toolkit (NLTK), and VADER constitute the three main tools. VADER represents a gold-standard sentiment lexicon, which is basically tailored to attitudes that are communicated by using social media. The contribution of this study is to introduce an effective Lexicon-based approach by highlighting a classifier called VADER to analyze the sentiment of the general population, particularly among thalassemia carriers on the social media platform Twitter. In this study, the results showed that the proposed approach achieved 0.829, 0.816, and 0.818 regarding precision, recall, together with F-score, respectively. The tweets were crawled using the search keywords, “thalassemia screening,” thalassemia test, “and thalassemia diagnosis”. Finally, results showed that India and Pakistan ranked the highest in mentions in tweets by the public’s conversations on thalassemia screening with 181 and 164 tweets, respectivel