Next Generation Sequencing

Next Generation Sequencing (NGS) is a novel method, in which the entirety of DNA and RNA present in a sample is sequenced. In the wake of decreasing sequencing costs, NGS is becoming progressively exploitable in the veterinary diagnostic field. Classical methods such as enzyme-linked immunosorbent assay (ELISA) or polymerase chain reaction (PCR) are limited to circumscribed groups of known pathogens, require careful selection and a targeted approach. Using NGS technology, identification and discovery of viruses is possible without prior sequence knowledge – all viruses present in a sample are sequenced. NGS is therefore ideal to study the so-called virome, the entirety of viruses present in a specific environment. For example in 2011, Schmallenberg virus was identified as an emerging pathogen in ruminants thanks to NGS. In the course of a veterinary dissertation project (Dr. Jakub Kubacki), an NGS protocol for virus detection has been established at our institute (Implementation (PDF, 835 KB)). In the meantime, our scientists gained a lot of experience with the new approach. As a result, we are the first Swiss veterinary diagnostic laboratory to offers NGS for diagnostic purposes, under the name “ViroScreen” (PDF, 376 KB) NGS Research (PDF, 2 MB)

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Application field of ViroScreen:
• Single animal diagnostics
• Herd diagnostics
• Herd screening and monitoring
• Unknown cause of disease
• High mortality

Previous results from our NGS studies:
• Detection of Hepatitis E virus (HEV) in a human stool sample, raw pork sausage and liver of fattening pigs
• Detection of specific papillomaviruses from skin lesions of Boa (Boa constrictor) and Okapi (Okapia johnstoni)
• Detection of tick-borne encephalitis virus (TBEV) in a European hedgehog (Erinaceus europaeus)
• Sequencing of the complete genome of a Bovine Viral Diarrhea Virus (BVDV) Subgenotype 1e field strain
• First detection of porcine kobuvirus and porcine rotavirus H in fecal samples of pigs in Switzerland
• First detection of porcine circovirus type 3 in wild boar livers
• First detection of a novel gemicircularvirus in Swiss water buffalos

Current NGS research projects:
• Investigation of the virome of Swiss bats
• Viral population diversity of endemic and invasive arthropod vectors
• The dynamics of the bovine microbiome
• Investigation of potential commensal viruses in Swiss pigs
• Prevalence of Hepatitis E virus (HEV) in boar, deer, domestic pigs and processed meat products
• Characterization of Influenza viruses in nasal swabs of Swiss pigs
• Viral diversity in waste water

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