Evening Ebola Update, Mon, 2/9: What happens to U.S. $2.6 Billion now that EBOV on the run?/PLoS genomic surveillance article   Leave a comment


Dear Colleagues:

l.  FOX News asks tonight what will happen to the $2.6 Billion that the U.S. budget granted to our Department of Defense and USAID for Ebola Response and Prevention now that the caseload in West Africa is dramatically reduced.  The Ebola treatment centers that U.S. troopers built are not being utilized.  I’m hoping that a portion of the $2.6 Billion will go to the WHO/UN to rebuild health care services in West Africa so that the region is ready for the next zoonotic infection outbreak.  See: http://www.foxnews.com/politics/2015/02/09/as-ebola-fades-questions-arise-over-billions-in-us-aid/

2.  PLoS Currents Outbreaks has posted an article by Khiabanian, et. al. from Columbia University re: two techniques to do genomic surveillance on EBOV.  The article is beyond my understanding, so I include the following from the article:

“Gire et al.3 reported sequencing of ebolavirus samples from 78 patients collected during the initial introduction of the virus into Sierra Leone. Their analysis identified three distinct phylogenetic lineages and reported an evolutionary rate of ~2103 per site per year, or roughly one nucleotide change every two weeks. This corresponds to a rate almost twice as high as estimates from previous outbreaks.5 These viral evolutionary dynamics in continuous human-to-human transmission are in agreement with measurements from intra-host evolution of filoviruses in primates.6

Tracking the virus as it evolves during the course of the outbreak is an important goal of genomic surveillance, which has been facilitated with high-throughput genomics techniques. These techniques can rapidly sequence intrahost viral particles to high depth and provide estimates of allele frequencies at each position. Consensus-based approaches, which represent each patient with the majority allele measured at each position, have an inherent resolution of a single nucleotide. When the timescale of the outbreak is shorter than the average evolutionary time, as is the case with the 2014 ebolavirus outbreak, there will be insufficient genetic diversity for consensus approaches to provide good resolution into the evolution of the infectious agent. This suggests additional methods to gain what we term subnucleotide resolution into the evolutionary history of the outbreak.

Here, we incorporate subclonal diversity into a phylogenetic analysis using metrics from population genetics, following suggestions in Spielman et al.7 We identify several variants whose shared presence at subclonal frequencies shed light on interesting phylogenetic relationships not captured by consensus-based analyses. Finally, we introduce an information-theoretic method with which we estimate effective viral population size within a patient and during a transmission. When consensus diversity is limited and the outbreak spread exceeds the evolutionary rate, we show that measurement of subclonal diversity can provide valuable information for genomic surveillance.” 

See the entire article at: http://currents.plos.org/outbreaks/article/obk-14-0092-high-resolution-genomic-surveillance-of-2014-ebolavirus-using-shared-subclonal-variants/



Posted February 10, 2015 by levittrg in Ebola

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