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

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.

Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains.

Genetic characterisation of circulating influenza viruses directs annual vaccine strain selection and mitigation of infection spread. We used next-generation sequencing to locally generate whole genomes from 116 A(H1N1)pdm09 and 118 A(H3N2) positive patient swabs collected across Uganda between 2010 and 2018. We recovered sequences from 92% (215/234) of the swabs, 90% (193/215) of which were whole genomes. The newly-generated sequences were genetically and phylogenetically compared to the WHO-recommended vaccines and other Africa strains sampled since 1994. Uganda strain hemagglutinin (n = 206), neuraminidase (n = 207), and matrix protein (MP, n = 213) sequences had 95.23-99.65%, 95.31-99.79%, and 95.46-100% amino acid similarity to the 2010-2020 season vaccines, respectively, with several mutated hemagglutinin antigenic, receptor binding, and N-linked glycosylation sites. Uganda influenza type-A virus strains sequenced before 2016 clustered uniquely while later strains mixed with other Africa and global strains. We are the first to report novel A(H1N1)pdm09 subclades 6B.1A.3, 6B.1A.5(a,b), and 6B.1A.6 (± T120A) that circulated in Eastern, Western, and Southern Africa in 2017-2019. Africa forms part of the global influenza ecology with high viral genetic diversity, progressive antigenic drift, and local transmissions. For a continent with inadequate health resources and where social distancing is unsustainable, vaccination is the best option. Hence, African stakeholders should prioritise routine genome sequencing and analysis to direct vaccine selection and virus control.

Arbovirus circulation, epidemiology and spatiotemporal distribution in Uganda.

Background: Arboviruses are endemic in Uganda; however, little is known about their epidemiology, seasonality and spatiotemporal distribution. Our study sought to provide information on arbovirus outbreaks from acute clinical presentations. Methods: Immunoglobulin M (IgM) and confirmatory Plaque Reduction Neutralisation Test (PRNT) results for arbovirus diagnosis of samples collected from patients attending sentinel sites from 2016-19 were analysed retrospectively. Demographic data were analysed with SaTScan and SPSS software to determine the epidemiology and spatiotemporal distribution of arboviruses. Results: Arbovirus activity peaked consistently during March-May rainy seasons. Overall, arbovirus seroprevalence was 9.5%. Of 137 IgM positives, 52.6% were confirmed by PRNT, of which 73.6% cases were observed in central Uganda with Yellow Fever Virus had the highest prevalence (27.8%). The 5-14 age group were four times more likely to be infected with an arbovirus p=0.003, 4.1 (95% CI 1.3-12.3). Significant arboviral activity was observed among outdoor workers(p=0.05) . Spatiotemporal analysis indicated arboviral activity in 23 of the 85 districts analysed.. Interpretation: Our study shows that arbovirus activity peaks during the March-May rainy season and highlights the need for YFV mass vaccination to reduce the clinical burden of arboviruses transmitted within the region.

Phylogenetic Analysis of Wesselsbron Virus Isolated from Field-Captured Mosquitoes during a Rift Valley Fever Outbreak in Kabale District, Uganda-2016.

After confirmation of two human cases of Rift Valley fever (RVF) in March 2016 in the Kabale district of Uganda, an entomological investigation was conducted with a focus on mosquito species composition and abundance of known and potential mosquito vector species, and virus testing to identify species most likely involved in Rift Valley fever virus transmission. This information could be used to forecast risk and facilitate improvement of prevention and response tools for use in preventing or controlling future outbreaks. From these collections, two virus isolates were obtained, one each from a pool of Aedes tricholabis and Ae. gibbinsi. Next-generation sequencing identified both isolates as Wesselsbron virus, family Flaviviridae, a neglected arbovirus of economic importance. These are the first reported Wesselsbron virus isolates from Uganda since 1966.

Complete Genome Sequence of O'nyong Nyong Virus Isolated from a Febrile Patient in 2017 in Uganda.

Despite causing numerous large outbreaks in the 20th century, few isolates of o'nyong nyong virus (ONNV) have been fully sequenced. Here, we report the complete genome sequence of an isolate of ONNV obtained from a febrile patient in northwest Uganda in 2017, designated ONNV UVRI0804.

Early cases of SARS-CoV-2 infection in Uganda: epidemiology and lessons learned from risk-based testing approaches - March-April 2020.

BACKGROUND: On March 13, 2020, Uganda instituted COVID-19 symptom screening at its international airport, isolation and SARS-CoV-2 testing for symptomatic persons, and mandatory 14-day quarantine and testing of persons traveling through or from high-risk countries. On March 21, 2020, Uganda reported its first SARS-CoV-2 infection in a symptomatic traveler from Dubai. By April 12, 2020, 54 cases and 1257 contacts were identified. We describe the epidemiological, clinical, and transmission characteristics of these cases. METHODS: A confirmed case was laboratory-confirmed SARS-CoV-2 infection during March 21-April 12, 2020 in a resident of or traveler to Uganda. We reviewed case-person files and interviewed case-persons at isolation centers. We identified infected contacts from contact tracing records. RESULTS: Mean case-person age was 35 (±16) years; 34 (63%) were male. Forty-five (83%) had recently traveled internationally ('imported cases'), five (9.3%) were known contacts of travelers, and four (7.4%) were community cases. Of the 45 imported cases, only one (2.2%) was symptomatic at entry. Among all case-persons, 29 (54%) were symptomatic at testing and five (9.3%) were pre-symptomatic. Among the 34 (63%) case-persons who were ever symptomatic, all had mild disease: 16 (47%) had fever, 13 (38%) reported headache, and 10 (29%) reported cough. Fifteen (28%) case-persons had underlying conditions, including three persons with HIV. An average of 31 contacts (range, 4-130) were identified per case-person. Five (10%) case-persons, all symptomatic, infected one contact each. CONCLUSION: The first 54 case-persons with SARS-CoV-2 infection in Uganda primarily comprised incoming air travelers with asymptomatic or mild disease. Disease would likely not have been detected in these persons without the targeted testing interventions implemented in Uganda. Transmission was low among symptomatic persons and nonexistent from asymptomatic persons. Routine, systematic screening of travelers and at-risk persons, and thorough contact tracing will be needed for Uganda to maintain epidemic control.

Dengue fever and chikungunya virus infections: identification in travelers in Uganda - 2017.

Arboviruses are (re-) emerging viruses that cause significant morbidity globally. Clinical manifestations usually consist of a non-specific febrile illness that may be accompanied by rash, arthralgia and arthritis and/or with neurological or hemorrhagic syndromes. The broad range of differential diagnoses of other infectious and non-infectious etiologies presents a challenge for clinicians. While knowledge of the geographic distribution of pathogens and the current epidemiological situation, incubation periods, exposure risk factors and vaccination history can help guide the diagnostic approach, the non-specific and variable clinical presentation can delay final diagnosis. This case report summarizes the laboratory-based findings of three travel-related cases of arbovirus infections in Uganda. These include a patient from Bangladesh with chikungunya virus infection and two cases of dengue fever from Ethiopia. Early detection of travel-imported cases by public health laboratories is important to reduce the risk of localized outbreaks of arboviruses such as dengue virus and chikungunya virus. Because of the global public health importance and the continued risk of (re-) emerging arbovirus infections, specific recommendations following diagnosis by clinicians should include obtaining travel histories from persons with arbovirus-compatible illness and include differential diagnoses when appropriate.

Influenza-associated pneumonia hospitalizations in Uganda, 2013-2016.

BACKGROUND: Influenza is an important contributor to acute respiratory illness, including pneumonia, and results in substantial morbidity and mortality globally. Understanding the local burden of influenza-associated severe disease can inform decisions on allocation of resources toward influenza control programs. Currently, there is no national influenza vaccination program in Uganda. METHODS: In this study, we used data on pneumonia hospitalizations that were collected and reported through the Health Management Information System (HMIS) of the Ministry of Health, Uganda, and the laboratory-confirmed influenza positivity data from severe acute respiratory illness (SARI) surveillance in three districts (Wakiso, Mbarara, and Tororo) to estimate the age-specific incidence of influenza-associated pneumonia hospitalizations from January 2013 through December 2016. RESULTS: The overall estimated mean annual rate of pneumonia hospitalizations in the three districts was 371 (95% confidence interval [CI] 323-434) per 100,000 persons, and was highest among children aged <5 years (1,524 [95% CI 1,286-1,849]) compared to persons aged ≥5 years (123 [95% CI 105-144]) per 100,000 persons. The estimated mean annual rate of influenza-associated pneumonia hospitalization was 34 (95% CI 23-48) per 100,000 persons (116 [95% CI 78-165] and 16 [95% CI 6-28] per 100,000 persons among children aged <5 years and those ≥5 years, respectively). Among children aged <5 years, the rate of hospitalized influenza-associated pneumonia was highest among those who were <2 years old (178 [95% CI 109-265] per 100,000 persons). Over the period of analysis, the estimated mean annual number of hospitalized influenza-associated pneumonia cases in the three districts ranged between 672 and 1,436, of which over 70% represent children aged <5 years. CONCLUSIONS: The burden of influenza-associated pneumonia hospitalizations was substantial in Uganda, and was highest among young children aged <5 years. Influenza vaccination may be considered, especially for very young children.

Outbreak of yellow fever in central and southwestern Uganda, February-may 2016.

BACKGROUND: On 28 March, 2016, the Ministry of Health received a report on three deaths from an unknown disease characterized by fever, jaundice, and hemorrhage which occurred within a one-month period in the same family in central Uganda. We started an investigation to determine its nature and scope, identify risk factors, and to recommend eventually control measures for future prevention. METHODS: We defined a probable case as onset of unexplained fever plus ≥1 of the following unexplained symptoms: jaundice, unexplained bleeding, or liver function abnormalities. A confirmed case was a probable case with IgM or PCR positivity for yellow fever. We reviewed medical records and conducted active community case-finding. In a case-control study, we compared risk factors between case-patients and asymptomatic control-persons, frequency-matched by age, sex, and village. We used multivariate conditional logistic regression to evaluate risk factors. We also conducted entomological studies and environmental assessments. RESULTS: From February to May, we identified 42 case-persons (35 probable and seven confirmed), of whom 14 (33%) died. The attack rate (AR) was 2.6/100,000 for all affected districts, and highest in Masaka District (AR = 6.0/100,000). Men (AR = 4.0/100,000) were more affected than women (AR = 1.1/100,000) (p = 0.00016). Persons aged 30-39 years (AR = 14/100,000) were the most affected. Only 32 case-patients and 128 controls were used in the case control study. Twenty three case-persons (72%) and 32 control-persons (25%) farmed in swampy areas (ORadj = 7.5; 95%CI = 2.3-24); 20 case-patients (63%) and 32 control-persons (25%) who farmed reported presence of monkeys in agriculture fields (ORadj = 3.1, 95%CI = 1.1-8.6); and 20 case-patients (63%) and 35 control-persons (27%) farmed in forest areas (ORadj = 3.2; 95%CI = 0.93-11). No study participants reported yellow fever vaccination. Sylvatic monkeys and Aedes mosquitoes were identified in the nearby forest areas. CONCLUSION: This yellow fever outbreak was likely sylvatic and transmitted to a susceptible population probably by mosquito bites during farming in forest and swampy areas. A reactive vaccination campaign was conducted in the affected districts after the outbreak. We recommended introduction of yellow fever vaccine into the routine Uganda National Expanded Program on Immunization and enhanced yellow fever surveillance.

The viral aetiology of influenza-like illnesses in Kampala and Entebbe, Uganda, 2008.

BACKGROUND: As the threat of zoonoses and the emergence of pandemic-prone respiratory viruses increases, there is a need to establish baseline information on the incidence of endemic pathogens in countries worldwide. OBJECTIVES: To investigate the presence of viruses associated with influenza-like illnesses (ILI) in Uganda. METHODS: A cross-sectional study was conducted in which nasopharyngeal swab specimens were collected from patients diagnosed with ILI in Kampala and Entebbe between 14 August 2008 - 15 December 2008. A multiplex polymerase chain reaction assay for detecting 12 respiratory viruses was used. RESULTS: A total of 369 patients (52.3% females) was enrolled; the median age was 6 years (range 1-70). One or more respiratory viruses were detected in 172 (46.6%) cases and their prevalence were influenza A virus (19.2%), adenovirus (8.7%), human rhinovirus A (7.9%), coronavirus OC43 (4.3%), parainfluenza virus 1 (2.7%), parainfluenza virus 3 (2.7%), influenza B virus (2.2%), respiratory syncytial virus B (2.2%), human metapneumovirus (1.4%), respiratory syncytial virus A (1.1%), parainfluenza virus 2 (0.5%) and coronavirus 229E (0.5%). There were 24 (14.0%) mixed infections. CONCLUSIONS: This study identified some of the respiratory viruses associated with ILI in Uganda. The circulation of some of the viruses was previously unknown in the study population. These results are useful in order to guide future surveillance and case management strategies involving respiratory illnesses in Uganda.

Clinic- and hospital-based sentinel influenza surveillance, Uganda 2007-2010.

BACKGROUND: To assess the epidemiology and seasonality of influenza in Uganda, we established a sentinel surveillance system for influenza in 5 hospitals and 5 outpatient clinics in 4 geographically distinct regions, using standard case definitions for influenzalike illness (ILI) and severe acute respiratory illness (SARI). METHODS: Nasopharyngeal and oropharyngeal specimens were collected from April 2007 through September 2010 from patients with ILI and SARI aged ≥ 2 months, tested for influenza A and B with real-time reverse-transcription polymerase chain reaction, and subtyped for seasonal A/H1, A/H3, A/H5, and 2009 pandemic influenza A (pH1N1). RESULTS: Among the 2758 patients sampled, 2656 (96%) enrolled with ILI and 101 (4%) with SARI. Specimens from 359 (13.0%) were positive for influenza; 267 (74.4%) were influenza A, and 92 (25.6%) were influenza B. The median age of both patients with ILI and patients with SARI was 4 years (range, 2 months to 67 years); patients aged 5-14 years had the highest influenza-positive percentage (19.6%), and patients aged 0-4 years had the lowest percentage (9.1%). Influenza circulated throughout the year, but the percentage of influenza-positive specimens peaked during June-November, coinciding with the second rainy season. CONCLUSIONS: Continued and increased surveillance is needed to better understand the morbidity and mortality of influenza in Uganda.

Isolation of genetically diverse Marburg viruses from Egyptian fruit bats.

In July and September 2007, miners working in Kitaka Cave, Uganda, were diagnosed with Marburg hemorrhagic fever. The likely source of infection in the cave was Egyptian fruit bats (Rousettus aegyptiacus) based on detection of Marburg virus RNA in 31/611 (5.1%) bats, virus-specific antibody in bat sera, and isolation of genetically diverse virus from bat tissues. The virus isolates were collected nine months apart, demonstrating long-term virus circulation. The bat colony was estimated to be over 100,000 animals using mark and re-capture methods, predicting the presence of over 5,000 virus-infected bats. The genetically diverse virus genome sequences from bats and miners closely matched. These data indicate common Egyptian fruit bats can represent a major natural reservoir and source of Marburg virus with potential for spillover into humans.