Virology: a scientific discipline facing new challenges

Using AlphaFold Predictions in Viral Research

Elucidation of the tertiary structure of proteins is an important task for biological and medical studies. AlphaFold, a modern deep-learning algorithm, enables the prediction of protein structure to a high level of accuracy. It has been applied in numerous studies in various areas of biology and medicine. Viruses are biological entities infecting eukaryotic and procaryotic organisms. They can pose a danger for humans and economically significant animals and plants, but they can also be useful for biological control, suppressing populations of pests and pathogens. AlphaFold can be used for studies of molecular mechanisms of viral infection to facilitate several activities, including drug design. Computational prediction and analysis of the structure of bacteriophage receptor-binding proteins can contribute to more efficient phage therapy. In addition, AlphaFold predictions can be used for the discovery of enzymes of bacteriophage origin that are able to degrade the cell wall of bacterial pathogens. The use of AlphaFold can assist fundamental viral research, including evolutionary studies. The ongoing development and improvement of AlphaFold can ensure that its contribution to the study of viral proteins will be significant in the future.

Status of Novel Coronavirus Disease 2019 (COVID-19) and Animal Production

In December 2019, a severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that caused severe disease clusters was first reported in Wuhan, the capital of China's Hubei province. This viral disease, which is reported to originate from a seafood market where wild animals are illegally sold, has been transmitted among humans worldwide through close contact. Given the growing number of infected people worldwide and the disastrous consequences in all aspects of life, COVID-19 is a serious public health issue that requires special attention. In some countries, the epidemic curve of infection which was in the plateau phase or decreasing phase during the lockdown period increases day by day since the reopening, indicating the second phase of contamination. Therefore, the preventive measures recommended by the World Health Organization (WHO) must be respected to stop the spread of the disease. The international crisis due to the COVID-19 pandemic negatively affects many sectors, including animal production and its related industries. Indeed, with the cessation of imports and exports between countries, it is not possible to provide feeds that are considered as basic raw materials in livestock raising. This situation impairs animal movements, decreases production inputs availability, and negatively affects the economy. The sustainability of animal production is also affected by a shortage of workers due to the lockdown/curfew, the strong decrease in the purchasing power of the consumer, and the intensification of health care tasks. To prevent contamination of animal products and the spread of the disease with food, the U.S. Centers for Disease Control and Prevention (CDC) recommends frequent disinfection of food and human contact surfaces at production sites using an appropriate antiseptic. The purpose of this review article is to describe the current status of COVID-19 and investigate its effects on animal production. We propose potential approaches to keep animal products processing units and staff safe from SARS-CoV-2 infection and some strategies to improve animal production quantity and economy.

RNA interference identifies domesticated viral genes involved in assembly and trafficking of virus-derived particles in ichneumonid wasps

There are many documented examples of viral genes retained in the genomes of multicellular organisms that may in some cases bring new beneficial functions to the receivers. The ability of certain ichneumonid parasitic wasps to produce virus-derived particles, the so-called ichnoviruses (IVs), not only results from the capture and domestication of single viral genes but of almost entire ancestral virus genome(s). Indeed, following integration into wasp chromosomal DNA, the putative and still undetermined IV ancestor(s) evolved into encoding a ‘virulence gene delivery vehicle’ that is now required for successful infestation of wasp hosts. Several putative viral genes, which are clustered in distinct regions of wasp genomes referred to as IVSPERs (Ichnovirus Structural Protein Encoding Regions), have been assumed to be involved in virus-derived particles morphogenesis, but this question has not been previously functionally addressed. In the present study, we have successfully combined RNA interference and transmission electron microscopy to specifically identify IVSPER genes that are responsible for the morphogenesis and trafficking of the virus-derived particles in ovarian cells of the ichneumonid wasp Hyposoter didymator. We suggest that ancestral viral genes retained within the genomes of certain ichneumonid parasitoids possess conserved functions which were domesticated for the purpose of assembling viral vectors for the delivery of virulence genes to parasitized host animals.

Thousands of parasitic wasp from the ichneumonid family rely on virus-derived particles, named Ichnoviruses (Polydnavirus family), to ensure their successful development. The particles are produced in a specialized ovarian tissue of the female wasp named calyx. Virions are assembled in the calyx cell nuclei and stored in the oviduct before being transferred to the parasitoid host upon female wasp oviposition. Genes encoding proteins associated with the particles had been previously identified. These genes are localized in clusters of genes in the wasp genome (named IVSPER for “Ichnovirus structural proteins encoding regions”), they are specifically transcribed in the calyx but not encapsidated. IVSPER genes were thus hypothesized to derive from the integration of a virus, however still undetermined. Indeed, none of the identified genes had similarity to known sequence, making in addition unclear their function in particle production. In this work, we use the RNA interference technology to decipher the function of six IVSPER genes from the ichneumonid wasp Hyposoter didymator. Thanks to this approach, combined with transmission electron microscopy, we show that the studied IVSPER genes are required in different steps of particle morphogenesis and trafficking, and that their functions are those expected of a typical virus.