Ahmed Abd El Wahed
From ancient tomb to animal viruses: mobile suitcase lab for nanopore sequencing at field setting
About Ahmed Abd El Wahed
Dr Abd El Wahed studied veterinary medicine at Mansoura University in Egypt, and received his PhD in biology from Göttingen University, Germany in 2011. He has participated in the development of 30 point-of-care assays for the detection of infectious agents, and In 2013, he was awarded the Young Investigator award from the ASTMH on the establishment of a mobile laboratory for rapid detection of haemorrhagic fever viruses at low resource settings. Recently, he established a mobile suitcase laboratory for rapid detection of viruses, bacteria and parasites. The mobile setup was in field trials in Guinea, Sri Lanka, Nepal, Senegal, Egypt, Bangladesh and Brazil.
Nanopore sequencing technology can be applied to identify the pathogen responsible for an outbreak through sequencing all nucleic acids existing in the collected sample in a single run. In addition, it gives insight about the origin and variant of the causative agent. We have established a novel sequencing protocol relying on nanopore sequencing and offline BLAST search beside a microbiome screening of an ancient tomb. The whole procedure was conducted in a solar powered mobile suitcase laboratory, which is easy to use at the point of need. The procedure was completed in 5 hours including extraction, barcoding, sequencing and data analysis, which did not require a bioinformatician. Our protocol enables rapid and reliable foot and mouth disease virus serotyping and the differentiation of the Capri poxviruses (Sheep poxvirus, Goat poxvirus and Lumpy Skin Disease virus). The microbiome composition of the ancient tomb revealed potential threat of respiratory illness due to bacteria from family of Bacillaceae. Furthermore, bacteria from family of Pseudomonadaceae gave hints to the former use of the tomb as a byre.
Ahmed Abd El Wahed