Biology subjects

Lutwama, J.

Publications and source records attributed to Lutwama, J..

4 recordsLinked to original sources

bioRxiv2026

Detection of diverse coronaviruses, paramyxoviruses, and rhabdoviruses from cave-dwelling bats in Eastern Uganda

Bats harbor a diversity of viruses, some of which have the potential to impact human and livestock health. Caves in Eastern Uganda are commonly inhabited by bats in the genera Rhinolophus, Hipposideros, Myonycteris, and others. Human encroachment into these caves for shelter, hunting, mineral harvesting, and tourism poses a risk of exposure to infectious agents these bats may carry, yet little is known about the viruses present in these bats. From 2021 - 2023, 635 unique bats were captured in caves by mist net, with 69 bats resampled over the study for a total of 706 sampling instances. A total of 1,394 oral and rectal swabs were collected non-destructively and screened using molecular techniques for coronaviruses, paramyxoviruses, rhabdoviruses, flaviviruses, and filoviruses. Of these samples, 399 (56.5%) were collected during the rainy season and 307 (43.5%) during the dry season. Coronavirus RNA was detected in 59/706 (8.36%) of samples from Rhinolophus spp. (n = 35), Hipposideros caffer (n = 12), Myonycteris angolensis (n = 6), and Miniopterus spp. (n = 6). Six bats (0.85%) were positive for paramyxoviruses. Finally, (3 H. caffer, 1 M. angolensis, 1 Rhinolophus spp. and 1 Nycteris thebaica) 3 Rhinolophus bats were positive for rhabdoviruses (0.42%, all Rhinolophus spp.). No samples were positive for filovirus or flavivirus RNA. This project has generated novel data on the association of bat species and different viral strains present in these bats, advancing our knowledge of viral ecology and spillover risk at the human/bat interface.

genomics↗

bioRxiv2023

Mosquito virus diversity in Western and North-western Uganda

IntroductionSurveillance for mosquito borne arboviruses in Sub Saharan Africa has largely focussed on known viruses including Yellow fever virus (YFV), Rift Valley fever virus (RVFV), Chikungunya virus (CHIKV), West Nile virus (WNV) and Dengue viruses (DENV). Routine surveillance and outbreak investigations traditionally rely on serology, PCR and cell culture. Although such methods are useful, they are do not detect novel or unexpected viruses. MethodsThis study employed unbiased metagenomic next generation sequencing (MNGS) to characterise viruses circulating in mosquitoes of Arua and Kasese districts of Uganda collected systematically as part the ArboViral Infection (AVI) study. Adult mosquito sampling was carried out from multiple sites using light traps baited with solid carbon dioxide (indoors) and pyrethrum spray (outdoors). 10,026 mosquitoes were identified using appropriate morphological identification keys and separated into 96 pools by species and location of collection. Viral RNA extracted from homogenised mosquitoes was reverse transcribed to complimentary DNA and sequenced on the flow cell of an Illumina NextSeq platform. Bioinformatic analysis was performed using a customized in-house metagenomics pipeline. Downstream analyses were carried out in R version 4.2.1. Results97 viruses from 24 families and 31 genera were detected in 96 mosquito pools from Arua and Kasese districts. The abundance of viruses in different families was in the order Rhabdoviridae (33), Flaviviridae (28), Orthomyxoviridae (13), Mesoniviridae (9), Piconarviridae (9), Peribunyaviridae (9), Phasmaviridae (9), Iflaviridae (8), Phenuiviridae (7), Nodaviridae (5), Xinmoviridae (4), Reoviridae (4), Virusidae (2), Nairoviridae (2), Qinviridae (2), Togaviridae (2), Alphatetraviridae (2), Picornaviralesidae (2), Iridoviridae, (1), Nudiviridae (1), Parvoviridae (1), Permutetraviridae (1) and 22 viruses from different families remain unclassified. The Flaviviridae, Togaviridae, Rhabdoviridae, Peribunyaviridae, Phenuiviridae, Nairoviridae, Nodaviridae and Orthomyxoviridae harbor viruses that cause disease in humans and other mammals. Viruses from insect-specific virus families that were detected included the Chuviridae, Iflaviridae, Phasmaviridae and Alphatetraviridae. 92/173 (53%) of the viral genomes had full opening reading frames (ORFs) and diverged by >30% nucleotide pairwise distance from the nearest reference genome. ConclusionThe majority of viruses detected were novel species described for the first time with unknown potential to cause disease. The diversity of virus species in mosquitoes from Uganda, a hotspot for emerging arboviruses has been only partially characterized. This study, carried out in Western and North West Uganda illustrates the scale of richness and virus diversity in the region and the need to further characterise the virome in mosquitoes, especially those with a propensity to feed from human and animal hosts.

genomics↗

bioRxiv2022

Identification and molecular characterization of novel viruses in Ugandan cattle

The risk for the emergence of novel viral zoonotic diseases in animals and humans in Uganda is high given its geographical location with high biodiversity. We aimed to identify and characterize viruses in 175 blood samples from cattle selected in Uganda using molecular approaches. We identified 8 viral species belonging to 4 families (Flaviviridae, Peribunyaviridae, Reoviridae and Rhabdoviridae) and 6 genera (Hepacivirus, Pestivirus, Orthobunyavirus, Coltivirus, Dinovernavirus and Ephemerovirus). Four viruses were novel and tetantively named as Zikole virus (Family: Flaviviridae), Zeboroti virus (Family: Reoviridae), Zebtine virus (Family: Rhabdoviridae) and Kokolu virus (Family: Rhabdoviridae). In addition, Bovine hepacivirus, Obodhiang virus, Aedes pseudoscutellaris reovirus and Schmallenberg virus were identified for the first time in Ugandan cattle. We report a broad range of viruses including novel ones in the blood of cattle likely as reservoir hosts for emergence of novel viruses with serious public health implications. HighlightsO_LIPan PCR and High Throughput Sequencing Approaches reveal novel viruses in the blood of cattle. C_LIO_LIIdentified 8 viral species belonging to 4 families: Flaviviridae, Peribunyaviridae, Reoviridae and Rhabdoviridae C_LIO_LI60% of the identified viruses were found in the Ankole cattle breed C_LI

microbiology↗

bioRxiv2019

Co-circulation of Dengue Virus Serotypes 1 and 3 during the 2019 epidemic in Dar es Salaam, Tanzania

BackgroundDengue is an important mosquito-borne viral disease in tropical and sub-tropical countries. In this study molecular characterization was carried out to determine dengue viruses circulating among patients at health facilities during 2019 epidemic in Dar es Salaam, Tanzania.\n\nMethodsThe study involved outpatients seeking care for febrile illness at four health facilities in Kinondoni and Ilala Districts of Dar es Salaam City in Tanzania. A total of 45 sera from the outpatients were confirmed dengue-positive for dengue virus (DENV) non-structural protein 1 (NS1) antigen and/or NS1-IgG/IgM antibodies using on-site rapid test. The presence of the virus was detected by reverse-transcription polymerase chain reaction (RT-PCR) method. Of the 45 sera, 20 samples were selected randomly for identification of specific dengue virus serotypes using RT-PCR followed by evaluation of resulting amplicons on agarose gel electrophoresis.\n\nFindings and significanceBoth Dengue virus serotypes 1 (DENV-1) and 3 (DENV-3) were detected in the samples tested with the former being dominant. We present the first evidence of dengue virus co-infection of DENV-1 and DENV-3 serotypes in Tanzania. The emergence of DENV-1 indicates the possibility of importation of the virus to Tanzania from endemic countries. Due to DENV serotype co-circulation, there is an increased risk of severe dengue in future epidemics. Our findings advocate the importance of genomic-based surveillance to provide rapid evidence of dengue virus emergence/re-emergence and spread.\n\nAuthor SummaryDengue viruses are the most important mosquito-borne pathogens that pose a serious global health threat. Tanzania has reported several dengue virus epidemics since 2010 with the majority of the epidemics occurring in Dar-es-Salaam city. Until August 2019, a total of 6,859 dengue cases have been confirmed in the country. We performed molecular characterization of dengue viruses (DENV) circulating during the 2019 epidemic phase. It was found that DENV-1 serotype was dominant during the epidemic and two samples of the tested sera were co-infected by DENV-1 and DENV-3 serotypes. These findings emphasize the importance of genomic-based surveillance of dengue viruses in Tanzania to guide strategies for appropriate interventions.

genomics↗