DRC-2018-Viral Genome Characterization

Dear all,
I am sharing the linked statement on the name of Prof. Steve Ahuka-Mundeke, from INRB on the characterization of the ebolavirus genomes causing the outbreaks in the Democratic Republic of Congo.
Thanks,

-Gustavo Palacios
Director, Center for Genome Sciences, USAMRIID

-Prof. Steve Ahuka-Mundeke ([email protected])
INRB, School of Medicine Kinshasa University

https://drive.google.com/open?id=1Ih02T5z1cpqEgsBUsLtOIQhuEeb2Yh5Y

INRB Statement

From May 8th to July 25th, 2018, the Democratic Republic of the Congo faced its ninth Ebola
outbreak, which affected 54 people, including 33 deaths in the health zones of Bikoro, Iboko and
Wangata, in the Province of Equateur. Institut National de Recherche Biomedicale (INRB), in
collaboration with its partners, deployed 3 mobile laboratories on the 3 affected sites (Mbandaka,
Bikoro and Itipo) to contribute quickly and efficiently to control this epidemic. A total of 432 samples were collected from these 3 laboratories, of which 51 were positive in real-time RT-PCR. These came from the 38 confirmed cases for the whole period of the epidemic (8 May- 25 July 2018). On
July 10th, samples from the mobile laboratories arrived at INRB, and processing of samples and
sequencing began. Thus far 23 samples have been processed yielding 15 coding-complete
genomes that will be released shortly on GenBank as well. Initial phylogenetic analysis indicates
these genomes are closest to the 2014 DRC outbreak (Figure 1, blue labels). Further analysis will
need to be conducted on these preliminary findings as the main focus is to finish processing
available samples from the outbreak, which will be made available as soon as they are generated.
Unfortunately, on August 1st a new cluster of cases was discovered in the region of North
Kivu and confirmed at INRB. Samples were prepared for sequencing at INRB. Two full genome
sequences were obtained (Figure 1, red labels).

Figure 1

The data confirms that the current EVD cases in Nord Kivu (July 30th and ongoing), DRC are caused by a distinct EBOV “strain” than the one causing the outbreak in Equateur province. Based on this findings, although both events are caused by the same ebolavirus species (EBOV), the outbreaks appear not to be connected. On that basis, the available vaccine should work against the new strain.

Partners and collaborators

This work is part of ongoing research collaborations between several partners:
Institut National de Recherche Biomédicale (INRB)
US Army Medical Research Institute of Infectious Diseases (USAMRIID)
Institut Pasteur de Dakar, Dakar, Senegal (IPD)
TransVIHMI (IRD, INSERM, University of Montpellier)

Data availability

Genome sequences for all samples had been shared with all local and international partners working in the DRC. The information reported here is being shared pre-publication to help the research and public health communities respond to the current Ebola virus disease outbreak. Please note though that this data is still based on work in progress and should be considered preliminary. Our analysis of this data is ongoing and a publication communicating our findings is in preparation. INRB will distribute these data to any entity or collaborator that needs it. Please communicate with Drs. Muyembe-Tamfum and Ahuka for further coordination.

Prof. Jean-Jacques Muyembe Tamfum (INRB, School of Medicine Kinshasa University)
Prof. Steve Ahuka-Mundeke (INRB, School of Medicine Kinshasa University)
Dr. Gustavo Palacios (USAMRIID)
Dr. Michael Wiley (USAMRIID)
Dr. Amadou Sall (Institut Pasteur de Dakar, Dakar, Senegal)
Dr. Ousmane Faye (Institut Pasteur de Dakar, Dakar, Senegal)
Prof. Eric Delaporte (TransVIHMI (IRD, INSERM, University of Montpellier)
Dr. Martine Peeters (TransVIHMI (IRD, INSERM, University of Montpellier)

Avenue de la DĂ©mocratie N°5345 – Kin/Gombe – B.P. 1197 – KINSHASA 1 – TĂ©l. 898949 289 – 9913614 - 99 23123 – 081 5144285 E-mail : [email protected], Site web : www.inrb.cd

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Thanks Gus - very helpful and we’re starting to see some interesting clustering of the EBOV tree! Looking forward to seeing the data and manuscripts.

Very interesting to see this. It would certainly seem that there are multiple co-circulating lineages in the non-human hosts. It is interesting that this all goes back to a single clade in 1976-1977. I wonder if perhaps habitat fragmentation of the reservoir has produced divergent lineages?

Yes, reservoir habitat fragmentation - one east, one west, one central

Also evident is the apparently reduced rate of evolution in the lineages leading to the DRC outbreaks in 2014, 2017 and 2018 as first described for the 2014 by Tommy Lam, Eddie Holmes & Yi Guan in http://jvi.asm.org/content/early/2015/07/16/JVI.01226-15 . It would seem now that just two ‘latency’ periods are need parsimoniously, one in the branch leading to the MRCA of Boende-Lokolia/2014 and Bikoro/2018 and another in the branch leading to MRCA of Likati/2017 and Mangina/2018.

Could this be a form of latency in the non-human animal host, related to that seen in survivors in West Africa (i.e., http://advances.sciencemag.org/content/2/4/e1600378, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5189159/)?

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I don’t think this is habitat fragmentation per se, but more loosely connected populations of the host reservoir. We are currently working on some satellite telemetry studies to understand more of the spatial movements of bats in Congo. Rather than habitat fragmentation, it looks like there are more sub populations of hosts (of the same species) and this would drive the evolution of slightly different lineages of EBOV. It would be of interest to see if we can merge some host (and pathogen) ecology with some of the photodynamic analyses.

to an more extreme extend, you see similar dynamics with avian influenza, where separation of the same species on two different continents (mallards) drives the evolution of different lineages of H7 and H7 viruses.

We just released 32 sequences from the Bikoro and Beni outbreak on GenBank that we are calling, Tumba and Ituri, respectively. Publications are hopefully not too far behind. I attached a link to download the sequences as it might take a few days for them to show up on GenBank. Enjoy

Data availability
Genome sequences for all samples are available here: https://drive.google.com/open?id=1_1c3lIukzMFXwiAdVv_nd1_7UGzGzZ9M

Partners and collaborators
This work is part of ongoing research collaborations between several partners:
Prof. Jean-Jacques Muyembe Tamfum (INRB, School of Medicine Kinshasa University)
Prof. Steve Ahuka-Mundeke (INRB, School of Medicine Kinshasa University)
Dr. Gustavo Palacios (USAMRIID)
Dr. Michael Wiley (USAMRIID)
Dr. Amadou Sall (Institut Pasteur de Dakar, Dakar, Senegal)
Dr. Ousmane Faye (Institut Pasteur de Dakar, Dakar, Senegal)
Prof. Eric Delaporte (TransVIHMI (IRD, INSERM, University of Montpellier)
Dr. Martine Peeters (TransVIHMI (IRD, INSERM, University of Montpellier)

Statement on continuing work and analyses prior to publication
These genomes are being shared pre-publication. Please note though that this data is still based on work in progress and should be considered preliminary. Our analyses of this data is ongoing and a publication communicating our findings on these and other published genomes is in preparation. If you intend to use these sequences prior to our publication, please communicate with Drs. Muyembe-Tamfum and Ahuka for coordination.

The Nord-Kivu/Ituri EVD outbreak is continuing in the Democratic Republic of the Congo (DRC). As of 22 January 2019, there have been a total of 713 EVD cases (664 confirmed and 49 probable), including 439 deaths.

Following on from our previous release of 16 EBOV/”Ituri” sequences, we now make available an additional 72 sequences, bringing the total to 88. The sequences are available at the link below, and will shortly be released on GenBank:

https://drive.google.com/open?id=1_1c3lIukzMFXwiAdVv_nd1_7UGzGzZ9M

Please see below for a haplotype network analysis of the sequence data. All data has been shared with the DRC MoH.

Figure 1 . A median-joining haplotype network drawn using POPArt 1,2. Vertices are coloured by health zone as indicated in the key.

haplotype_network.pdf (186.6 KB)

Partners and collaborators
This work is part of ongoing research collaborations between several partners:

Prof. Jean-Jacques Muyembe Tamfum (INRB, School of Medicine Kinshasa University)
Prof. Steve Ahuka-Mundeke (INRB, School of Medicine Kinshasa University)
Dr. Placide Mbala-Kingebeni (INRB, TransVIHMI (IRD, INSERM, University of Montpellier), School of Medicine Kinshasa University)

Dr. Gustavo Palacios (USAMRIID)
Dr. Michael Wiley (USAMRIID, University of Nebraska Medical Center)
Dr. Amadou Sall (Institut Pasteur de Dakar, Dakar, Senegal)
Dr. Ousmane Faye (Institut Pasteur de Dakar, Dakar, Senegal)
Prof. Eric Delaporte (TransVIHMI (IRD, INSERM, University of Montpellier))
Dr. Martine Peeters (TransVIHMI (IRD, INSERM, University of Montpellier))

Statement on continuing work and analyses prior to publication
These genomes are being shared pre-publication. Please note that this data is based on work in progress and should be considered preliminary. Our analyses of this data is ongoing and a publication communicating our findings on these and other published genomes is in preparation. If you intend to use these sequences prior to our publication, please communicate with Drs. Muyembe-Tamfum and Ahuka for coordination.

References

  1. Bandelt, H., Forster, P., & Röhl, A. (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16(1), 37–48.

  2. http://popart.otago.ac.nz

This is interesting but are there any dates for these sequences? The network doesn’t provide a time-line here which makes it hard to interpret. Would it be possible to post a table of sampling dates for these data?

To get an idea of the timescale on this, I crudely highlighted the sequences currently on genbank with their dates (in July & August). By the way, MAN028 (MK007336) seems to be missing from the median-joining tree?

The Nord-Kivu/Ituri EVD outbreak is continuing in the Democratic Republic of the Congo (DRC). As of 1st March 2019, there have been a total of 888 EVD cases (823 confirmed and 65 probable), including 555 deaths.

Following on from our previous release of 88 EBOV/”Ituri” sequences, we now make available an additional 54 sequences, bringing the total to 142. Please see previous posts for information on partners involved in the sequencing effort and data statement. The sequences are available at the link below, and will shortly be released on GenBank:

https://drive.google.com/open?id=1_1c3lIukzMFXwiAdVv_nd1_7UGzGzZ9M

Please see below for a haplotype network analysis of the sequence data. A flipbook separating the network by week, to add a time aspect to the analysis, is available at the above link. All data have been shared with the DRC MoH.

Haplotype_Network_2019-03-01.pdf (74.0 KB)

Figure 1 . A median-joining haplotype network drawn using POPArt. Vertices are coloured by health zone as indicated in the key.

MAN028 was initally left out as there was no epi data available for that sample. Since then we have been including the unknowns. We shall include MAN028 in the next update.

The Nord-Kivu/Ituri EVD outbreak is continuing, with 1,866 cases (1,778 confirmed and 88 probable) as of 22 May 2019. The latest haplotype network is shown below (sequence IDs from samples > 6 months old removed for clarity). The network consists of 223 genome sequences, which are available at the link below.

Haplotype_Network_2019-05-02_LabID-v3.pdf (303.8 KB)

Sequence data:
DRC_outbreak_sequences - Google Drive