September 2022 Sudan Ebola virus disease outbreak in Uganda

Ebolavirus
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On September 19, 2022 Sudan Ebolavirus was identified in an individual from Mubende District, Uganda by the Viral Hemorrhagic Fever (VHF) Lab at the Uganda Virus Research Institute (UVRI) and on September 20, 2022 the Ministry of Health of Uganda officially declared an outbreak. The virus was sequenced at the VHF lab using unbiased next generation sequencing on an iSeq100. The new Mubende Sudan Ebolavirus genome is 99.6% complete and most closely related to Nakisamata Sudan Ebolavirus strain that emerged in Luwero District, Uganda in May 2011. The new sequence can be accessed here.
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Figure 1: Inferred phylogenetic relatedness of Ebolavirus species, including the new Mubende Sudan Ebolavirus sequence from Uganda 2022. A) Phylogenetic relatedness of Ebolavirus species. The Sudan Ebolavirus species is highlighted grey. B) Expanded Sudan Ebolavirus clade, indicating relatedness of new Mubende Sudan Ebolavirus strain (highlighted red).

DISCLAIMER

The unpublished sequences are shared via the website virological.org under the following conditions: The Ebola virus sequences by the Uganda Ministry of Health support the public health response as well as the development and evaluation of Ebolavirus disease diagnostics and therapeutics. The data may be used and analyzed for these purposes. We are preparing a scientific publication of the data. In the meantime, this post may be cited. If you intend to use the sequences for publication prior to our own publication, please contact us directly.

Dr. Stephen Balinandi

(Principal Research Officer (UVRI), [email protected])

The sequencing work for this project was done in collaboration with the Viral Hemorrhagic Fever laboratory at the Uganda Virus Research Institute and the Viral Special Pathogens Branch at the US Centers for Disease Control and Prevention.

Author list: Stephen Balinandi 1, Shannon Whitmer 2, Sophia Mulei 1, Luke Nyakarahuka 1,3, Alex Tumusiime 1, Jackson Kyondo 1, Jimmy Baluku 1, Jocelyn Kiconco 1, Henry Kyobe 4, Susan Nabadda 4,5, Julius Lutwama 1, Trevor R. Shoemaker 2, Joel Montgomery 2, Pontiano Kaleebu 1,6, John D. Klena 2

1 Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda.

2 Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.

3 School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.

4 Ministry of Health, Kampala, Uganda

5 Uganda National Health Laboratory Services, Kampala, Uganda

6 Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda.

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Thank you for your efforts. I have added the sequence to the tree I built here.

Notably while the sequence is most similar to the Nakisamata strain (outbreak discussed here), taking a wider view it belongs to a larger clade of viruses detected in Southern Uganda (the Luwero, Kibaale and now Mubende outbreaks).

P.S. EboSud-639 / KC589025 sequence shows an unusual pattern of mutations which make me question the sequence assembly. It is retained in the tree for completeness.

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The Uganda Virus Research Institute (UVRI) is providing an update on the status of the Sudan Ebolavirus outbreak in Uganda. Since 17 November, no new confirmed cases have been reported. As of 07 December, a total of 164 cases, representing 142 confirmed and 22 probable cases have occurred. Throughout the outbreak, UVRI has performed NGS of positive and suspect cases. Currently, UVRI has generated 56 genomes with coverage greater than 90%, representing approximately 34% of cases from the outbreak. Sequencing continues at the UVRI lab, and the results of these efforts can be viewed through NextStrain (auspice). A private version is also accessible, where we link lab and epidemiological identifiers together, to conduct molecular epidemiology.

DISCLAIMER

This data is shared under the following conditions: The Ebolavirus sequences by the Uganda Ministry of Health support the public health response as well as the development and evaluation of Ebolavirus disease diagnostics and therapeutics. The data may be used and analyzed for these purposes. We are preparing a scientific publication of the data. In the meantime, this post may be cited. If you intend to use the sequences or data presented here for publication prior to our own publication, please contact us directly.

Dr. Stephen Balinandi

(Principal Research Officer (UVRI), [email protected])

The sequencing work for this project was done in collaboration with the Viral Hemorrhagic Fever laboratory at the Uganda Virus Research Institute and the Viral Special Pathogens Branch at the US Centers for Disease Control and Prevention.

Author list: Stephen Balinandi 1, Shannon Whitmer 2, Sophia Mulei 1, Charity Nassuna 1, Markus Kainulainin 2, Elizabeth Shedroff 2, Inna Krapiunaya 2, Florine Scholte 2, Luke Nyakarahuka 1,3, Alex Tumusiime 1, Jackson Kyondo 1, Jimmy Baluku 1, Jocelyn Kiconco 1, Henry Kyobe 4, Susan Nabadda 4,5, Julius Lutwama 1, Trevor R. Shoemaker 2, Joel Montgomery 2, Pontiano Kaleebu 1,6, John D. Klena 2

1 Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda.

2 Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.

3 School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.

4 Ministry of Health, Kampala, Uganda

5 Uganda National Health Laboratory Services, Kampala, Uganda

6 Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda.

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