Dataset Information

Integration of SARS-CoV-2 testing and genomic sequencing into influenza sentinel surveillance in Uganda, January to December 2022.

ABSTRACT:

Importance

Respiratory pathogens cause high rates of morbidity and mortality globally and have high pandemic potential. During the SARS-CoV-2 pandemic, influenza surveillance was significantly interrupted because of resources being diverted to SARS-CoV-2 testing and sequencing. Based on recommendations from the World Health Organization, the Uganda Virus Research Institute, National Influenza Center laboratory integrated SARS-CoV-2 testing and genomic sequencing into the influenza surveillance program. We describe the results of influenza and SARS-CoV-2 testing of samples collected from 16 sentinel surveillance sites located throughout Uganda as well as SARS-CoV-2 testing and sequencing in other health centers. The surveillance system showed that both SARS-CoV-2 and influenza can be monitored in communities at the national level. The integration of SARS-CoV-2 detection and genomic surveillance into the influenza surveillance program will help facilitate the timely release of SARS-CoV-2 information for COVID-19 pandemic mitigation and provide important information regarding the persistent threat of influenza.

SUBMITTER: Kayiwa JT

PROVIDER: S-EPMC10715035 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature

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Publications

Integration of SARS-CoV-2 testing and genomic sequencing into influenza sentinel surveillance in Uganda, January to December 2022.

Kayiwa John T JT Nassuna Charity C Mulei Sophia S Kiggundu Gladys G Nakaseegu Joweria J Nabbuto Maria M Amwine Esther E Nakamoga Bridget B Nankinga Sarah S Atuhaire Phiona P Nabiryo Pheobe P Alunzi Pixy P Mbaziira Tony T Isabirye Paul P Ayuro Noel N Owor Nicholas N Kiconco Jocelyn J Bakamutumaho Barnabas B Middlebrook Earl Austin EA Kaleebu Pontiano P Lutwama Julius J JJ Bartlow Andrew William AW

Microbiology spectrum 20231009 6

<h4>Importance</h4>Respiratory pathogens cause high rates of morbidity and mortality globally and have high pandemic potential. During the SARS-CoV-2 pandemic, influenza surveillance was significantly interrupted because of resources being diverted to SARS-CoV-2 testing and sequencing. Based on recommendations from the World Health Organization, the Uganda Virus Research Institute, National Influenza Center laboratory integrated SARS-CoV-2 testing and genomic sequencing into the influenza survei ...[more]

PMID: 37811997

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Project description:BackgroundThe World Health Organization (WHO) recommends periodic evaluations of influenza surveillance systems to identify areas for improvement and provide evidence of data reliability for policymaking. However, data on the performance of established influenza surveillance systems are limited in Africa, including Tanzania. We aimed to assess the usefulness of the Influenza surveillance system in Tanzania and to ascertain if the system meets its objectives, including; estimating the burden of disease caused by the Influenza virus in Tanzania and identifying any circulating viral strains with pandemic potential.MethodologyFrom March to April 2021, we collected retrospective data through a review of the Tanzania National Influenza Surveillance System electronic forms for 2019. Furthermore, we interviewed the surveillance personnel about the system's description and operating procedures. Case definition (ILI-Influenza Like Illness and SARI-Severe Acute Respiratory Illness), results, and demographic characteristics of each patient were obtained from the Laboratory Information System (Disa*Lab) at Tanzania National Influenza Center. The United States Centers for disease control and prevention updated guidelines for evaluating public health surveillance systems were used to evaluate the system's attributes. Additionally, the system's performance indicators (including turnaround time) were obtained by evaluating Surveillance system attributes, each being scored on a scale of 1 to 5 (very poor to excellent performance).ResultsA total of 1731 nasopharyngeal and oropharyngeal samples were collected from each suspected influenza case in 2019 from fourteen (14/14) sentinel sites of the influenza surveillance system in Tanzania. Laboratory-confirmed cases were 21.5% (373/1731) with a predictive value positive of 21.7%. The majority of patients (76.1%) tested positive for Influenza A. Thirty-seven percent of patients' results met the required turnaround time, and 40% of case-based forms were incompletely filled. Although the accuracy of the data was good (100%), the consistency of the data was below (77%) the established target of ≥ 95%.ConclusionThe overall system performance was satisfactory in conforming with its objectives and generating accurate data, with an average performance of 100%. The system's complexity contributed to the reduced consistency of data from sentinel sites to the National Public Health Laboratory of Tanzania. Improvement in the use of the available data could be made to inform and promote preventive measures, especially among the most vulnerable population. Increasing sentinel sites would increase population coverage and the level of system representativeness.

Project description:BackgroundThe emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants have challenged the control of the COVID-19 pandemic globally. Burundi was not spared by that pandemic, but the genetic diversity, evolution, and epidemiology of those variants in the country remained poorly understood. The present study sought to investigate the role of different SARS-COV-2 variants in the successive COVID-19 waves experienced in Burundi and the impact of their evolution on the course of that pandemic. We conducted a cross-sectional descriptive study using positive SARS-COV-2 samples for genomic sequencing. Subsequently, we performed statistical and bioinformatics analyses of the genome sequences in light of available metadata.ResultsIn total, we documented 27 PANGO lineages of which BA.1, B.1.617.2, AY.46, AY.122, and BA.1.1, all VOCs, accounted for 83.15% of all the genomes isolated in Burundi from May 2021 to January 2022. Delta (B.1.617.2) and its descendants predominated the peak observed in July-October 2021. It replaced the previously predominant B.1.351 lineage. It was itself subsequently replaced by Omicron (B.1.1.529, BA.1, and BA.1.1). Furthermore, we identified amino acid mutations including E484K, D614G, and L452R known to increase infectivity and immune escape in the spike proteins of Delta and Omicron variants isolated in Burundi. The SARS-COV-2 genomes from imported and community-detected cases were genetically closely related.ConclusionThe global emergence of SARS-COV-2 VOCs and their subsequent introductions in Burundi was accompanied by new peaks (waves) of COVID-19. The relaxation of travel restrictions and the mutations occurring in the virus genome played an important role in the introduction and the spread of new SARS-COV-2 variants in the country. It is of utmost importance to strengthen the genomic surveillance of SARS-COV-2, enhance the protection by increasing the SARS-COV-2 vaccine coverage, and adjust the public health and social measures ahead of the emergence or introduction of new SARS-COV-2 VOCs in the country.

Project description:Mass gatherings frequently include close, prolonged interactions between people, which presents opportunities for infectious disease transmission. Over 20,000 pilgrims gathered at Namugongo Catholic and Protestant shrines to commemorate 2022 Uganda Martyr's Day. We described syndromes suggestive of key priority diseases particularly COVID-19 and viral hemorrhagic fever (VHF) among visiting pilgrims during May 25-June 5, 2022. We conducted a survey among pilgrims at the catholic and protestant shrines based on signs and symptoms for key priority diseases: COVID-19 and VHF. A suspected COVID-19 case was defined as acute respiratory illness (temperature greater 37.5°C and at least one sign/symptom of respiratory infection such as cough or shortness of breath) whereas a suspected VHF case was defined as fever >37.5°C and unexplained bleeding among pilgrims who visited Namugongo Catholic and Protestant shrines from May 25 to June 5, 2022. Pilgrims were sampled systematically at entrances and demarcated zonal areas to participate in the survey. Additionally, we extracted secondary data on pilgrims who sought emergency medical services from Health Management Information System registers. Descriptive analysis was conducted to identify syndromes suggestive of key priority diseases. Among 1,350 pilgrims interviewed, 767 (57%) were female. The mean age was 37.9 (±17.9) years. Nearly all pilgrims 1,331 (98.6%) were Ugandans. A total of 236 (18%) reported ≥1 case definition symptom and 42 (3%) reported ≥2 symptoms. Thirty-nine (2.9%) were suspected COVID-19 cases and three (0.2%) were suspected VHF cases from different regions of Uganda. Among 5,582 pilgrims who sought medical care from tents, 628 (11.3%) had suspected COVID-19 and one had suspected VHF. Almost one in fifty pilgrims at the 2022 Uganda Martyrs' commemoration had at least one symptom of COVID-19 or VHF. Intensified syndromic surveillance and planned laboratory testing capacity at mass gatherings is important for early detection of public health emergencies that could stem from such events.

Dataset Information

Integration of SARS-CoV-2 testing and genomic sequencing into influenza sentinel surveillance in Uganda, January to December 2022.

Importance

Publications

Integration of SARS-CoV-2 testing and genomic sequencing into influenza sentinel surveillance in Uganda, January to December 2022.

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