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

Prevalence of Helicobacter Pylori Infection in Yemeni Patients

Background: Helicobacter pylori (Hp), a common bacterial infection linked to disorders of the gastrointestinal tract, are found in half of the world population. In developing countries, Hp infection is a public-health issue (1). It is one of the world’s most common human bacterial infections and associated with chronic gastritis, peptic ulceration and gastric cancer (2). Data on its prevalence in the Middle East is limited (3). There are limited data about H. pylori infection in Yemen.Objective: The objective of this study is to determine the prevalence of H. pylori infection among patients undergoing upper GIT endoscopy with different symptoms at different endoscopic units at Different Hospitals and governorates in Yemen.Subjects and Methods: All patients referred to the endoscopy units at Al-Wehdah Teaching Hospital-Thamar University, Police Model Hospital, Police General Hospital, endoscopic charity camps at Socatra Island, Mukalla, Dowaan and Seiyun Hospitals in Yemen, were enrolled in a prospective study. For each patient clinical and socioeconomic and environmental data were collected. Endoscopy was performed and two gastric biopsies were obtained from antrum and corpus. Helicobacter pylori infection was diagnosed at the time of endoscopy by using the rapid urease test (RUT).Results: A total of 2300 patients ,1300 females (56.522%) with a mean age of 37.395 years (range 16-90 years) and 1000 males (43.478%) with a mean age of 39.168 Years (range 18-75 years) were included in this study. Abdominal pain was the most frequent symptom reported. Gastritis 99% and esophagitis 85% were the most frequent endoscopic findings. Helicobacter pylori were found in 2270 patients (98.7%). Thirty four patients (1.5%) patients were present with gastric cancer, 80 patients with gastric ulcer (3.48%), 1500 (65%) patients with duodenal erosions,150 (6.5%) patients with duodenal ulcer, all patients with duodenal and gastric ulcers have H.pylori positive test, by using rapid urease test (RUT).Conclusions: The prevalence of Helicobacter pylori infection in hospital patients, who undergone upper gastrointestinal endoscopy is very high (98.7%). This study is confirming that Helicobacter pylori are significantly associated with oesophagitis, gastritis and peptic ulcer in Yemen

30-day morbidity and mortality of sleeve gastrectomy, Roux-en-Y gastric bypass and one anastomosis gastric bypass: a propensity score-matched analysis of the GENEVA data

Background: There is a paucity of data comparing 30-day morbidity and mortality of sleeve gastrectomy (SG), Roux-en-Y gastric bypass (RYGB), and one anastomosis gastric bypass (OAGB). This study aimed to compare the 30-day safety of SG, RYGB, and OAGB in propensity score-matched cohorts. Materials and methods: This analysis utilised data collected from the GENEVA study which was a multicentre observational cohort study of bariatric and metabolic surgery (BMS) in 185 centres across 42 countries between 01/05/2022 and 31/10/2020 during the Coronavirus Disease-2019 (COVID-19) pandemic. 30-day complications were categorised according to the Clavien–Dindo classification. Patients receiving SG, RYGB, or OAGB were propensity-matched according to baseline characteristics and 30-day complications were compared between groups. Results: In total, 6770 patients (SG 3983; OAGB 702; RYGB 2085) were included in this analysis. Prior to matching, RYGB was associated with highest 30-day complication rate (SG 5.8%; OAGB 7.5%; RYGB 8.0% (p = 0.006)). On multivariate regression modelling, Insulin-dependent type 2 diabetes mellitus and hypercholesterolaemia were associated with increased 30-day complications. Being a non-smoker was associated with reduced complication rates. When compared to SG as a reference category, RYGB, but not OAGB, was associated with an increased rate of 30-day complications. A total of 702 pairs of SG and OAGB were propensity score-matched. The complication rate in the SG group was 7.3% (n = 51) as compared to 7.5% (n = 53) in the OAGB group (p = 0.68). Similarly, 2085 pairs of SG and RYGB were propensity score-matched. The complication rate in the SG group was 6.1% (n = 127) as compared to 7.9% (n = 166) in the RYGB group (p = 0.09). And, 702 pairs of OAGB and RYGB were matched. The complication rate in both groups was the same at 7.5 % (n = 53; p = 0.07). Conclusions: This global study found no significant difference in the 30-day morbidity and mortality of SG, RYGB, and OAGB in propensity score-matched cohorts. © 2021, The Author(s)