Description
This track displays protein changing variants identified in 81 samples from the Zaire clade of Ebola viruses found by Gire et al., 2014.
Display Conventions
In "dense" mode, a vertical line is drawn at the position of each variant.
In "full" mode, in addition to the vertical line, a label to
the left shows the reference allele first and variant alleles below
(A = red, C = blue,
G = green, T = magenta,
Indels = black).
Hovering the pointer over any variant will prompt the display of the occurrences numbers for each
allele in Gire et al., 2014. Clicking on any variant will result in
full details of that variant being displayed.
By default, in "pack" mode, the
display shows a clustering of haplotypes in the viewed range, sorted
by similarity of alleles weighted by proximity to a central variant.
The clustering view can highlight local patterns of linkage.
Each variant is a vertical bar with white (invisible) representing the reference allele
and black representing the non-reference allele(s).
Tick marks are drawn at the top and bottom of each variant's vertical bar
to make the bar more visible when most alleles are reference alleles.
The vertical bar for the central variant used in clustering is outlined in purple.
In order to avoid long compute times, the range of alleles used in clustering
may be limited; alleles used in clustering have purple tick marks at the
top and bottom.
The clustering tree is displayed to the left of the main image.
It does not represent relatedness of individuals; it simply shows the arrangement
of local haplotypes by similarity. When a rightmost branch is purple, it means
that all haplotypes in that branch are identical, at least within the range of
variants used in clustering.
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
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