Harmless or Threatening? Interpreting the Results of Molecular Diagnosis in the Context of Virus-Host Relationships

Molecular methods, established in the 1980s, expanded and delivered tools for the detection of vestigial quantities of nucleic acids in biological samples. Nucleotide sequencing of these molecules reveals the identity of the organism it belongs to. However, the implications of such detection are often misinterpreted as pathogenic, even in the absence of corroborating clinical evidence. This is particularly significant in the field of virology where the concepts of commensalism, and other benign or neutral relationships, are still very new. In this manuscript, we review some fundamental microbiological concepts including commensalism, mutualism, pathogenicity, and infection, giving special emphasis to their application in virology, in order to clarify the difference between detection and infection. We also propose a system for the correct attribution of terminology in this context.info:eu-repo/semantics/publishedVersio

Leporids’ Emerging Diseases as a Threat to Biodiversity

Wild leporids have been gaining interest and prominence in the scientific and social community worldwide. While endangered of extinction in its native territory, the Iberian Peninsula, where it has a key role in the Mediterranean ecosystems, the European rabbit (Oryctolagus cuniculus) is considered a plague in Australia, due to the great economic and ecological consequences of its presence in the territories. The impact of viral diseases on the Leporidae family’ members, namely on the European rabbit, has been largely recognized worldwide since the early 50s, due to the emergence of myxomatosis and, from the mid-80s onwards, due to the emergence of rabbit haemorrhagic disease virus 1 and 2. More recently, in 2018, a recombinant myxoma virus emerged with the ability to infect and cause severe disease in the Iberian hare (Lepus ganatensis). Also, a new gammaherpesvirus was described in Iberian hares, associated with myxoma virus infections. In this chapter, we revise the main viral infectious treats to the native leporids of the Iberian Peninsula. The recovery of the European rabbit populations, as well as of other leporid species around the world, is currently a major challenge for the scientific and social communities and policy-makers. If we fail, the ripple effects on the trophic web will be so dramatic that are likely to be unrecoverable

A Quadruplex qPCR for Detection and Differentiation of Classic and Natural Recombinant Myxoma Virus Strains of Leporids

A natural recombinant myxoma virus (referred to as ha-MYXV or MYXV-Tol08/18) emerged in the Iberian hare (Lepus granatensis) and the European rabbit (Oryctolagus cuniculus) in late 2018 and mid-2020, respectively. This new virus is genetically distinct from classic myxoma virus (MYXV) strains that caused myxomatosis in rabbits until then, by acquiring an additional 2.8 Kbp insert within the m009L gene that disrupted it into ORFs m009L-a and m009L-b. To distinguish ha-MYXV from classic MYXV strains, we developed a robust qPCR multiplex technique that combines the amplification of the m000.5L/R duplicated gene, conserved in all myxoma virus strains including ha-MYXV, with the amplification of two other genes targeted by the real-time PCR systems designed during this study, specific either for classic MYXV or ha-MYXV strains. The first system targets the boundaries between ORFs m009L-a and m009L-b, only contiguous in classic strains, while the second amplifies a fragment within gene m060L, only present in recombinant MYXV strains. All amplification reactions were validated and normalized by a fourth PCR system directed to a housekeeping gene (18S rRNA) conserved in eukaryotic organisms, including hares and rabbits. The multiplex PCR (mPCR) technique described here was optimized for Taqman® and Evagreen® systems allowing the detection of as few as nine copies of viral DNA in the sample with an efficiency > 93%. This real-time multiplex is the first fast method available for the differential diagnosis between classic and recombinant MYXV strains, also allowing the detection of co-infections. The system proves to be an essential and effective tool for monitoring the geographical spread of ha-MYXV in the hare and wild rabbit populations, supporting the management of both species in the field