Evening Ebola Update, Tues, 1/13: EBOV Call Centers Work/Training Burial Teams Works/New technique for sequencing EBOV, unknown viruses   Leave a comment

1/13/14

Dear Colleagues:

l.  Becker’s Infection Control and Clinical Quality today has listed the 48 Ebola Treatment Centers now ready for EBOV patients in the U.S.  See the entire list of centers by state at: http://www.beckershospitalreview.com/quality/us-now-has-48-ebola-treatment-centers.html

2.  CDC’s MMWR 13 January has an article by Miller, et. al. of the CDC on the results of Sierra Leone’s 3 day EBOV education project when all citizens were required to remain within their homes while 28,000 volunteers went home to home to find EBOV cases, deaths, and educate citizens.  An EBOV call center was available to citizens during this 3 day period.  The call center was staff by 60 persons working 12 hour shifts.  The call center received 3300 calls over the 3 day period.  One third of the calls reported possible EBOV cases; one third reported deaths; one third asked for EBOV information or for medical advice or about what was going on.  Authors’ conclusion is that call centers for EBOV work.  Sierra Leone has made the call centers permanent and has ramped up the number of workers at the call centers and the response to calls.  See: http://www.cdc.gov/mmwr/preview/mmwrhtml/mm64e0113a2.htm?s_cid=mm64e0113a2_e

3.  CDC MMWR 13 January has an article  by Nielson, et. al. of the CDC on improvement in burial practices and cemetery management in Sierra Leone.  The authors found by observing burial teams and cemeteries that the teams did not handle the bodies safely or with dignity, did not obtain swabs from the bodies, did not spray the home of the deceased persons with bleach, did not remove bedding from the homes, did not bury the bodies deep enough or safely or in accordance with the deceased person’s religion.  As a result, citizens did not report deaths, hid bodies, denied a body had symptoms of EBOV.  The authors trained the burial teams to be able to do all the tasks required to protect the families and themselves.  Handling the pickup of bodies, care of bodies, burial of bodies with respect was a large component of the training.  As a result, more EBOV deaths are now reported in Sierra Leone, villages are sanitized, cemeteries are safe.  See: http://www.cdc.gov/mmwr/preview/mmwrhtml/mm64e0113a1.htm?s_cid=mm64e0113a1_e

4.  Genomic Biology has open-sourced a research article by Matranga, et. al. from the Broad Institute on how to obtain ‘pure’ RNA genomes of EBOV, Lassa virus, and other as yet unknown viruses by removing ribosomal human RNA contaminants (from commercial sequencing ‘kits’) and applying the authors’ primer. The article is beyond my understanding, but here is their Conclusion:

“Our newly developed viral sequencing protocol combines selective depletion of contaminating carrier RNA and host rRNA with unbiased total RNA-seq of randomly-primed cDNA. It thereby improves the quality of raw sequencing data and boosts the fraction of unique informative reads, producing sufficient LASV and EBOV reads for de novo genome assembly and intra-host variant calls in diverse clinical and biological samples. Our RNase H-depletion-RNA-seq method may be more broadly applicable to sequence and assemble the genomes of many RNA viruses, known or unknown. We also developed a hybrid selection method to enrich viral content of libraries prior to sequencing, significantly lowering the cost of sequencing and rescuing RNA-seq libraries with very low coverage. While enrichment by hybrid selection requires prior sequence knowledge, hybrid selection with a complex multi-virus bait may prove to be a broadly applicable, viable and cost-effective approach to sequencing.”

See this article from Sabeti’s lab at: http://genomebiology.com/2014/15/11/519?utm_campaign=BMC12663N&utm_medium=BMCemail&utm_source=Teradata

RGL, MD

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Posted January 14, 2015 by levittrg in Ebola

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