NEW YORK (GenomeWeb) – A team from China and the UK analyzed genome sequences for Ebola virus isolates in Sierra Leone in the fall of 2014 to track the virus' diversity and evolution during the latter stages of the Ebola epidemic, which was first recognized last spring.
As they reported online today in Nature, the researchers sequenced nearly 200 EBOV samples collected in five Sierra Leone regions last fall. Their results revealed a rise in EBOV diversity during this stage of the epidemic, manifesting itself in new sub-lineages that were used to trace the virus' movement between individuals in several affected communities.
"The sharp increase in genetic diversity of the 2014 EBOV warrants extensive EBOV surveillance in Sierra Leone, Guinea, and Liberia to better understand the viral evolution and transmission dynamics of the ongoing outbreak," senior author Wu-Chun Cao, a pathogen and biosecurity researcher with China's State Key Laboratory, and co-authors wrote.
The study's authors noted that these and other findings are expected to "facilitate the international efforts to develop [EBOV] vaccines and therapeutics."
Over 26,700 Ebola cases are suspected or have been confirmed in Sierra Leone, Liberia, and Guinea since the start of the West African outbreak, according to the latest reports from the US Centers for Disease Control and Prevention, with more than 11,000 deaths.
In an effort to characterize the source of this outbreak and early EBOV transmission patterns, a Harvard University- and Broad Institute-led team did genome sequencing on isolates from 78 Ebola patients in Sierra Leone — work described in Science last summer.
That analysis suggested the outbreak started from viruses in a natural EBOV reservoir that made the jump to humans in Guinea and was subsequently passed to individuals from Sierra Leone.
Even so, relatively little is known about the trajectory the virus has taken in the months after that analysis.
For the latest analyses, Cao and colleagues started from more than 800 EBOV-positive blood samples collected by the China Mobile Laboratory Testing Team between late September and mid-November of 2014.
From those, the researchers successfully sequenced the genomes of 175 EBOV isolates, representing cases in urban and rural regions of western Sierra Leone, Port Loko, Kambia, and Bombali.
Compared with EBOV isolates from Guinea and Sierra Leone that were sequenced during earlier stages of the outbreak, the team saw signs of enhanced genetic and phylogenetic diversity in the EBOV isolates circulating in Sierra Leone between July and the end of October.
The researchers uncovered sequences consistent with at least seven new EBOV sub-lineages, for example, consistent with mounting variation and diversity in the outbreak-associated isolates. All seven of these sub-lineages seem to have arisen since August of 2014, they noted, mainly around Waterloo, the capital city of Sierra Leone's Western Area Rural District.
A subset of the new lineages also turned up in locations such as the capital city of Freetown and in the Maforki Chiefdom as well, providing insights into EBOV transmission dynamics in the region over different periods of the epidemic.
Meanwhile, the team's peek at substitution rates in the EBOV genomes pointed to viral evolution rates that were on par with those described for the virus during past outbreaks and a population size that continued expanding through October, when it began to plateau.