A paper published this month in BMC Genomics discusses findings from a collaborative project to sequence cholera samples linked to the 2010 outbreak in Haiti — and we’re pleased to report that the Pippin platform from Sage Science was used in the work.
Lead author Rachel Sealfon and senior author Pardis Sabeti, along with a team of scientists hailing from MIT, Harvard, the Broad Institute, and other organizations, sequenced seven isolates of Vibrio cholera, including four collected recently in Haiti and the Dominican Republic.
The paper, entitled “High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic,” concludes that the outbreak strain found in Haiti and the isolate found in the Dominican Republic most closely match strains found in South Asia, confirming publications released last year that suggested the epidemic came from a South Asian strain of cholera brought to Haiti through human activity.
The scientists also note that part of their goal was to assess coverage needed for sequencing, particularly for this type of effort — that is, sequencing closely related isolates and identifying the variants distinguishing them. “We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads,” the authors write.