Description

This track displays variants identified by Gire et al. in 81 isolates from the 2014 strain of Ebola virus (78 from Sierra Leone and 3 from Guinea) that are specific to the 2014 strain, polymorphic in 2014 isolates, and that cause protein-coding changes.

Display Conventions

Items are labeled by gene and amino acid change. The labels of two items also contain "*CONS" to indicate that the changed position is fully conserved across the Ebola genus. Click on an item to view the BLOSUM62 substitution score.

Methods

Blood samples were collected from 78 patients at Kenema Government Hospital in Sierra Leone. For details of RNA preservation, PCR, human RNA depletion, library construction and sequencing, see Supplemental Materials and Methods of Gire et al.

Gire et al. analyzed the 78 Sierra Leone patient sequences together with 3 sequences from the 2014 outbreak in Guinea (Baize et al.; suspected sequencing errors were masked, see Supplemental Materials and Methods of Gire et al.), for a total of 81 sequences from 2014. In addition, some analyses included 20 sequences from past outbreaks of Zaire Ebola virus, 1976-2008, for a total of 101 sequences. Sequence variants were extracted directly from multiple sequence alignments of the group of 101 sequences (1976-2014). A custom release of SnpEff (v4.0, build 2014-07-01, to support ribosomal slippage in transcription of GP gene) was used to predict functional effect of variants on genes (noncoding, synonymous or missense).

References

Baize S, Pannetier D, Oestereich L, Rieger T, Koivogui L, Magassouba N, Soropogui B, Sow MS, Keïta S, De Clerck H et al. Emergence of Zaire Ebola virus disease in Guinea. N Engl J Med. 2014 Oct 9;371(15):1418-25. PMID: 24738640

Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 2014 Sep 12;345(6202):1369-72. PMID: 25214632
Supplemental Materials and Methods