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Novel Zaire Ebola Sub-Clade In Guinea and Sierra Leone
Recombinomics Commentary 22:30
July 29, 2014

The Infectious Disease Initiative at the Broad Institute of MIT and Harvard, which is part of the Viral Hemorrhagic Fever Consortium, has released 84 complete or nearly complete Ebola sequences (at Genbank – EBOV_1 – EBOV_84 with accession numbers KM233035KM233118) from Sierra Leone patient collections between June 2 and June 12, 2014.  These sequences follow the release of 14 Sierra Leone sequences by the same group sequencing samples collected on June 1. 

Thus, they have made public 98 sequences from collections in the first 12 days in June, 2014.  They are commended for the rapid release of these important sequences, which are closely related to three full sets of sequences from three Guinea cases collected in March, 2014 from two distinct locations, Gueckedou (Gueckedou-C05 and Gueckedou-C07) and Kissidougou (Kissidougou-C15).

All 101 sequences form a Zaire sub-clade which signals clonal expansion due to human to human transmission following a single introduction.  These 101 sequences are easily distinguished from all other Zaire sub-clades, which have been associated with the largest number of reported Ebola outbreaks, including the previously most deadly outbreak in Yambuku, Zaire in 1976 (280 deaths in 318 cases), which was followed by the second most deadly outbreak, which was 19 years later in Kikwit, Zaire in 1995 (245 deaths in 317cases).  The current outbreak, which is again 19 years later but in Guinea, Sierra Leone, and Liberia, has already produced more reported deaths (672 deaths in 1201 cases) than the two earlier outbreaks combined and comments made in yesterday’s US CDC Ebola telebriefing suggests there is no end in sight.

The CDC telebriefing and Ebola HAN advisory comes after the death of a naturalized American who traveled to Lagos, Nigeria from Monrovia, Liberia and the hospitalization of two American healthcare workers, also in Liberia.  The CDC had noted that Ebola was only one flight away from the United States, and the fatal case had planned on flying to Minnesota in two weeks for his daughter’s birthday.

The June Sierra Leone sequences have evidence of some drift from the March sequences from Guinea.  A prior Zaire sub-clade, which was found in apes and a chimpanzee and was associated with an outbreak in Gabon in 2002 had strong evidence of recombination, which raises concerns of more evolution in the current sub-clade, which has produced a record number of reported Ebola cases and deaths.

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