From ancient tomb to animal viruses: mobile suitcase lab for nanopore sequencing at field setting

Next to speak in the Field sequencing breakout, Dr. Ahmed Abd El Wahed from the University of Göttingen gave an entertaining overview of his work characterising microbes in a variety of field settings — including an ancient Egyptian tomb. First Ahmed described the constituents of the solar-powered mobile laboratory that he and the team at Göttingen developed, which comprised one suitcase for sample preparation and another for library preparation and sequencing. Unlike other mobile nanopore sequencing approaches, Ahmed’s kit is all anchored into the suitcase and surrounded by an easy to clean PVC layer. This allows the experiments to be performed in the actual suitcase, with no need to unpack the equipment. Ahmed also stated that the incorporated battery pack can run the mobile lab for two days from just 12 hours of charge from the integrated solar panel.

Ahmed discussed the application of this mobile sequencing lab to the analysis of foot and mouth disease viruse (FMDV) and capripoxviruses. The former is a highly infectious 8 kb RNA virus that affects cloven-hoofed (two-toed) mammals – causing blisters in the mouth and on the feet, abortion and, in some young animals, death. Capripoxviruses (150 kb DNA virus) are among the most serious of all animal poxviruses, with three host-specific strains affecting sheep, goats, and cattle. These viruses damage the hides of animals and prevent their import and export, resulting in significant economic consequences.

Sequencing is the only method for serotyping of FMDV and differentiation of capripoxviruses. Ahmed presented his novel nanopore sequencing protocol, which allowed reliable characterisation of FMD and capripoxviruses within just 5 hours and 2 hours, respectively. This time frame included sample extraction, barcoding, sequencing, and analysis. In order to perform in-field data analysis, Ahmed and his team used GENEIOUS, a user-friendly offline BLAST database that could be interrogated without the need for internet access or bioinformatics training.

Closing this part of his presentation, Ahmed expressed his thoughts that, even though viruses such as FMD rarely cause human disease, they can have devastating socio-economic consequences for resource-limited regions. As such, he believes they deserve much greater focus.

Next, Ahmed spoke about his work analysing the microbiome of an ancient Egyptian tomb. There was some decay on the surface, which was speculated to be fungal; however, to confirm this, the team in charge of opening the tomb wanted to perform metagenomic analysis. Swabs taken from different areas inside the tomb were analysed using the MinION. The results revealed a predominance of bacterial families that are adapted to survive in harsh environments, including Neisseriaceae. In addition, they found Bacillaceae which can cause severe respiratory illness in immune suppressed individual. Such findings may have potential implications when opening long closed tombs to the public. The team also found microorganisms that may provide evidence of the tomb’s former use as a byre (cowshed).

Authors: Ahmed Abd El Wahed