Filovirus and HFV Sequence Alignments
- For filoviruses, we offer three types of manually-curated sequence alignments:
- For other HFV, only Genus references are currently available. These references are organized by genus and by segment. They can be used as a "background set" for trees and other classification tools. These alignments also form the basis for the Hidden Markov Models that create on-the-fly alignments in the HFV search interface.
* Year indicates when the alignments were made.
Ebola/Marburg naming conventions: Ebola Coordinates and Naming.
Filovirus Alignment Types
For filoviruses, (ebolavirus, marburgvirus, cuevavirus), three options are offered for manually-curated alignments.
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Whole set: these alignments contain all complete genome sequences available at the time of the most recent update. The smaller region alignments also include some partial genome sequences.
- Genus references: 8 filovirus reference sequences are provided, as defined by Kuhn et al., 2014.
One sequence per outbreak: contains one sequence per disease outbreak.
Outbreaks were defined based on CDC tables of Ebola and Marburg outbreaks.
From the set of all complete genome sequences, we selected one sequence per group of sequences derived from each human outbreak. Sequences from viruses passaged in non-human cells were chosen in some cases where human-derived sequences were not available. For example, from the 1967 Marburg outbreak, no sequence from a direct human source is available. For Reston viruses, there are several strains sequenced from the USA and from separate isolations in the Philippines, but only one was chosen because these viruses have not caused human outbreaks. For Lloviu virus, only one isolate, from a bat, has been sequenced to date, and no human cases are known.