Molecular Characterization of HIV-1 And Drug Resistance Among HIV-1 Infected Patients Attending Kayanza District Hospital, Burundi

This study was funded by the East Africa Public health Laboratory Network Project (EAPHLNP)/Burundi. Abstract Virological failure in management of HIV-1 infection has been reported to be between 11 to 24% after 12 months of treatment. Out of these, acquired or transmitted drug resistance mutations have been reported at 71% to 90% in Sub-Sahara Africa. In this cross-sectional study we aimed to determine virological failure and drug resistance mutations in HIV-1 infected patients on ART attending Kayanza district hospital, Burundi. Patients were recruited using a purposive sampling technique. After informed consent, 4mL of venous blood was collected from each patient. The blood was separated into plasma and cells for various laboratory assays. Plasma viral loads were quantified using the Abbott m2000rt system. Polymerase chain reaction using gene specific primers was done after extraction of nucleic acids from plasma with >1000 copies/ mL, followed by sequencing of all amplified samples. Drug resistance was determined using the IAS and Stanford University database, with phylogenetic analyses done using the neighbor joining method.Two hundred patients were recruited; 13% of the respondents had virological failure associated with multiple sex partners (adjusted odds ratio (aOR, 0.154 , p =0.016) and irregularity in taking medications (aOR: 0.4 , p=0.014). Fifteen samples were successfully sequenced; 80% (12/15) were HIV-1 subtype C, 7% (1/15) subtype A, and 13% (2/15) were HIV-1 subtype A1. Of these, 87.5% had at least one mutation (NRTI or NNRTI), while 12.5 % did not carry any Drug Resistance Mutations. The most common drug resistance mutations were M183V, T215V M41L, E44D, L74I, L210W and K65R, K103N, Y188H. The prevalence of virological failure was established at 13%.Our findings showed possible gaps in the last 90% of the 90-90-90 WHO target by 2020. The results highlight the need for intense viral load and resistance testing for patients to improve overall treatment outcome. Some strategies are needed to improve adherence counselling and drug resistance mutation testing should be implemented to monitor HIV-1 patients on ART in Burundi. Keywords: HIV-1, antiretroviral therapy, Virological failure, DRMs, Burundi. DOI: 10.7176/JBAH/9-10-05 Publication date:May 31st 201

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

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

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

Clinical and Epidemiology Characteristics of COVID-19 Cases Detected During Mass Screening Campaign from July to October 2020 in Bujumbura, Burundi

Background: Coronavirus disease of 2019 (COVID-19) is an infectious disease caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2 Virus). It was reported for the first time in Wuhan city, Hubei province of China. The first cases of COVID-19 in Burundi were identified on 31st March 2020. Several signs and symptoms, including mainly; fever, dry cough, fatigue, myalgia, and dyspnea are the most prominent characteristics of the disease. The aim of this study was to provide description of the clinical and epidemiological characteristics of COVID-19 cases identified during the mass screening campaign conducted between July and October, 2020 in Burundi. Methods: We conducted a retrospective secondary analysis of data of clients to the mass screening campaign in Bujumbura city that was run between July and October 2020. Clients with complete data and tested for COVID-19 with Reverse Transcription Polymerase Chain Reaction (RT-PCR) were included in the study. Epi-Info 7.2.2.6 was used to perform descriptive and analytical statistics and Quantum Geographic Information System (QGIS) was used for cases mapping.Association between positive cases and independent variables such as sex, history of contact with confirmed COVID-19 case was measured using X2 statistical test at a p-value of .05. Results: The study included 20,114 participants. 243 (1.2%) were tested positive for COVID-19. The mean age for confirmed cases was 33 (±15) years. The majority of cases (72.8%) were between 20 and 59 years of age and they were predominantly males (67.9%). 164 (67.5%) were symptomatic and cough was the most frequent symptom observed 109 (66.5%), followed by rhinorrhea 69 (42.1%). Fever was present in only 18 (11.0%) of symptomatic patients. Participants with a history of contact with a COVID-19 confirmed case (aOR=2.2; 95%CI [1.6-3.0]; p-value &lt;.001), were more likely to be positive for COVID-19. Also, those who were coughing (aOR=1.47; 95%CI [1.06-2.05]; p-value=.023) and having sore throat (aOR=2.4; 95%CI [1.1-4.9]; p-value=.02) were more likely to test positive for COVID-19. Conclusion: This study revealed that a significant proportion (32.5%) of COVID-19 patients were silent carriers of the virus. Data highlighted that high proportion of cases were among the active age group and contacts with confirmed cases, and noted high proportion of asymptomatic cases at diagnosis. Measures including routine testing of asymptomatic contacts of confirmed cases could contribute to tackling corona virus in Burundi.</jats:p

Outcomes and Their State-level Variation in Patients Undergoing Surgery With Perioperative SARS-CoV-2 Infection in the USA. A Prospective Multicenter Study

Objective: To report the 30-day outcomes of patients with perioperative SARS-CoV-2 infection undergoing surgery in the USA. Background: Uncertainty regarding the postoperative risks of patients with SARS-CoV-2 exists. Methods: As part of the COVIDSurg multicenter study, all patients aged ≥17 years undergoing surgery between January 1 and June 30, 2020 with perioperative SARS-CoV-2 infection in 70 hospitals across 27 states were included. The primary outcomes were 30-day mortality and pulmonary complications. Multivariable analyses (adjusting for demographics, comorbidities, and procedure characteristics) were performed to identify predictors of mortality. Results: A total of 1581 patients were included; more than half of them were males (n = 822, 52.0%) and older than 50 years (n = 835, 52.8%). Most procedures (n = 1261, 79.8%) were emergent, and laparotomies (n = 538, 34.1%). The mortality and pulmonary complication rates were 11.0 and 39.5%, respectively. Independent predictors of mortality included age ≥70 years (odds ratio 2.46, 95% confidence interval [1.65-3.69]), male sex (2.26 [1.53-3.35]), ASA grades 3-5 (3.08 [1.60-5.95]), emergent surgery (2.44 [1.31-4.54]), malignancy (2.97 [1.58-5.57]), respiratory comorbidities (2.08 [1.30-3.32]), and higher Revised Cardiac Risk Index (1.20 [1.02-1.41]). While statewide elective cancelation orders were not associated with a lower mortality, a sub-analysis showed it to be associated with lower mortality in those who underwent elective surgery (0.14 [0.03-0.61]). Conclusions: Patients with perioperative SARS-CoV-2 infection have a significantly high risk for postoperative complications, especially elderly males. Postponing elective surgery and adopting non-operative management, when reasonable, should be considered in the USA during the pandemic peaks