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Sequencing of Ebola Samples Finds Cases Transmitted by Sex, Breast Feeding

NEW YORK (GenomeWeb) – Although the Ebola outbreak that began in 2013 in West Africa had largely wound down by mid-2015, there continued to be sporadic recurrences of new cases. To identify the source of transmission of those new cases, researchers led by Ian Goodfellow at the University of Cambridge and Matthew Cotton at the Wellcome Trust Sanger Institute, sequenced the genomes of 554 Ebola isolates from Sierra Leone, finding that many of the new cases had been spread through "unconventional transmission chains" including semen and breast milk, the researchers reported in Virus Evolution this week.

In order to conduct the study, researchers set up a temporary sequencing facility in a tent at the Mateneh Ebola Treatment Center in Makeni, Sierra Leone and sequenced 554 samples from cases diagnosed between December 2014 and September 2015 in Sierra Leone.

The center was set up next to Public Health England's diagnostic facility and included Thermo Fisher Scientific's Ion Torrent PGM for sequencing and the Ion Chef for sample prep. Wellcome Trust funded the research and Thermo Fisher Scientific provided the sequencing equipment. The samples were sequenced at the temporary sequencing facility in Sierra Leone and the data was used to help provide real-time information about the transmission of the virus.  

The sequencing facility has now been moved to the University of Makeni and is part of the new UniMak Infectious Disease Research Laboratory, which is providing training to local students and scientists.

The project showed "how important it is to carry out genome sequencing within the affected countries, and for the data to be shared in a rapid and open way as part of the epidemic response," Jeremy Farrar, director of the Wellcome Trust, said in a statement.

After sequencing and assembly, the researchers compared the genomes to 1,019 previously sequenced Ebola genomes, performing phylogenetic analyses. They found that there were at least nine viral lineages circulating in Sierra Leone, eight of which were derived from one variant that emerged in June 2014 and became the most prevalent lineage. By June 2015, there were three lineages responsible for the reported Ebola cases and most cases were due to two separate outbreaks — 80 of the sequenced genomes were from an outbreak that occurred in the Port Loko and Kambia districts, wile 39 were from an outbreak of a different viral lineage that occurred in an area of Freetown.

The researchers were also able to use the genomic and phylogenetic data to identify unusual modes of transmission as well as to figure out which strain was responsible for specific flare-ups.

For instance, one patient became sick after traveling from Freetown, where Ebola was still active, to Tonoklili, which had been free of the virus for 130 days. The patient's brother and aunt also became ill. Sequencing confirmed that they were all infected with viral strains linked to those circulating in Freetown, and that the cases did not represent a re-emergence of the Ebola strain that had previously been circulating in Tonkolili.

Disturbingly, the researchers also found examples of transmission from individuals who appeared to be free of the virus after having passed the quarantine period without showing symptoms.

In one case, a woman appeared to have transmitted the virus to her baby through breast milk, after having been exposed to the virus from her sister who died from Ebola during childbirth.

In another case, an Ebola sample from a woman who died from the disease in August closely resembled a sample from a male who had recovered from the disease. After the woman died, the male's semen was tested and it was found to still be positive for the virus, suggesting he may have inadvertently passed it on to her.

"Worryingly, evidence is accumulating that [Ebola] survivors may harbor and transmit [the virus] for several months after recovery raising the possibility that transmission through exposure to bodily fluids and/or sexual transmission can occur at times beyond the standard quarantine periods," the authors wrote.