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23Apr22

Ebola virus disease case in Equateur Province, DRC, represents a new spillover event

On 23 Apr 2022, the Minister of Public Health, Hygiene, and Prevention announced a new case of Ebola virus disease (EVD) occurring in Mbandaka health zone in Equateur Province, Democratic Republic of the Congo (DRC). EVD outbreaks occurred previously in Equateur Province in 2018 and 2020

The 31-year-old male, a student from Boende in Tshuapa Province, returned to Mbandaka, Equateur Province on 25 Feb 2022. He was vaccinated against Ebola virus in 2020 and is not known to be an EVD survivor. Symptom onset occurred on 5 Apr 2022 with fever and headache, which were treated at home. He was admitted to the Bongisa Libota Health Center in Mbandaka on 16 Apr 2022, where he was hospitalized for 3 days, before being transferred on 19 Apr 2022 to the Wangata General Reference Hospital in Mbandaka. On 21 Apr 2022, signs of haemorrhagic fever appeared, and the patient was placed in isolation at the Wangata Ebola treatment center as a suspected EVD patient but died the same day.

Blood and swab samples were taken, which tested positive for Ebola virus at the Mbandaka provincial laboratory on 21 Apr 2022. The 2 samples were sent to the Institut National Recherche Biomedicale (INRB) in Kinshasa where Ebola virus was confirmed by GeneXpert on 23 Apr 2022.

Sequencing

The blood and oral swab samples were sequenced at the Pathogen Genomics Laboratory at INRB-Kinshasa on an Oxford Nanopore Technologies GridION. Sequencing libraries were prepared using an amplicon sequencing approach (Mbala-Kingebeni, 2021; Grubaugh et al., 2019; Quick et al. 2017), generating identical genomes with 98.3% and 96.7% genome coverage.

The 2 genomes were identical and the genome with highest coverage (22MBK0001) was aligned with genomes from prior sequenced Ebola virus disease outbreaks using MAFFT (Katoh, 2013). A phylogenetic tree was inferred using RAxML (Stamatakis, 2014; Figure 1 [available at the source URL above]: Maximum likelihood phylogenetic tree of all EVD outbreaks, midpoint rooted, including genome sequences from the Equateur 2018 (blue), Equateur 2020 (green), and new Equateur 2022 (red) outbreaks). The new genome was most closely related to the Equateur 2020 outbreak but fell outside the outbreak clade, indicating that this case represents a new spillover event from the host reservoir and is not directly linked to the Equateur 2018 or Equateur 2020 EVD outbreaks. Further epidemiologic investigations are ongoing.

[Source: By Kristian Andersen, Scripps Research, California via Promed, Minn., 23Apr22]
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