Rapid Genome Analyses of Emergent Human Adenovirus 14a Causing 2006-7 Febrile Respiratory Illness (FRI) Outbreaks in the US via High Throughput 'Next- Generation' Pyrosequencing Technique

摘要

During 2006-7, Ad14a was identified during a series of FRI outbreaks across the US, involving at least ten documented pneumonia fatalities. Leveraging sequence data from the prototype strain Ad14p (GenBank (number sign) AY803294), the full genome sequence of Ad14a was determined using the conventional, and very labor-intensive, Sanger sequencing method. The same genome was analyzed using Pyrosequencing, an emerging alternative genome sequencing technology offering much higher efficiency. This direct shotgun approach relies on random sequencing of small DNA fragments using adaptor sequences, rather than independent amplification of separate fragments using pre-determined pathogen- specific sequences. This new sequencing strategy is therefore ideally suited for the rapid sequencing of hitherto uncharacterized human pathogens. The Roche 454 FLX system was used to sequence and assemble multiple Ad14a viruses from recent US outbreaks, as well as closely related Ad11a isolates causing non-US ARD infections since the 1970s. The US Ad14a strain significantly diverges from the prototypical Eurasian strain, Ad14p, and shares greater than 98% genomic homology with Ad11a. Two genome types of Ad11, Ad11p and Ad11a display different tissue tropisms, causing renal and upper respiratory infections respectively. Ad14a and Ad11a share almost identical Fiber genes, which are known to be responsible for the adenoviruses' organ tropism, and both cause ARD infections. Both also share highly homologous Hexon genes, except for a 400 base pair (bps) region that allows these two viruses to be distinctly differentiated from each other based on serological cross reactivity.