BIOLOGICAL FEATURES OF SARS-CoV-2 AND CURRENT APPROACHES TO ANTIVIRAL THERAPY AND VACCINATION: A REVIEW

Since the first description of patients with pneumonia of unknown origin in Wuhan in December 2019, unprecedented efforts of the international scientific community led to the identification and molecular characterization of its etiological agent, e.g. SARS-CoV-2. The global pandemic of COVID-19 represents an outstanding challenge for the scientists and medical professionals worldwide. In this review, we discuss the most important aspects of SARS-CoV-2 biology and virology including antiviral and immunomodulatory treatment strategies as well as vaccine development

A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies

Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.Peer reviewe

Molecular identification of a phytoplasma infecting grapevine in the Republic of Macedonia

Phytoplasmas from the ribosomal subgroup 16SrXII-A (stolbur) were identified by PCR and RFLP analyses of 16S rRNA gene and elongation factor-Tu phytoplasma gene (tuf) in symptomatic grapevines from the Veles and Skopje areas in Macedonia. Two methods were used for nucleic acid extraction. Amplification and RFLP results of 16S rDNA were not influenced by the method used, but RFLP patterns of tuf gene revealed additional bands if a less time consuming method was applied. The possible origin of these bands is discussed. This is the first report of the presence of the stolbur phytoplasma in cvs Chardonnay and Vranac in Macedonia

After the data deluge: biological characterization of the new variants and viral species identified by HTS

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Multilocus sequence analysis reveals the genetic diversity of European fruit tree phytoplasmas and supports the existence of inter-species recombination

The genetic diversity of three temperate fruit tree phytoplasmas ‘Candidatus Phytoplasma prunorum’, ‘Ca. P. mali’ and ‘Ca. P. pyri’ has been established by multilocus sequence analysis. Among the four genetic loci used, the genes imp and aceF distinguished 30 and 24 genotypes, respectively, and showed the highest variability. Percentage of substitution for imp ranged from 50 to 68% according to species. Percentage of substitution varied between 9 and 12% for aceF, whereas it was between 5 and 6% for pnp and secY. In the case of ‘Ca P. prunorum’ the three most prevalent aceF genotypes were detected in both plants and insect vectors, confirming that the prevalent isolates are propagated by insects. The four isolates known to be hypo-virulent had the same aceF sequence, indicating a possible monophyletic origin. Haplotype network reconstructed by eBURST revealed that among the 34 haplotypes of ‘Ca. P. prunorum’, the four hypo-virulent isolates also grouped together in the same clade. Genotyping of some Spanish and Azerbaijanese ‘Ca. P. pyri’ isolates showed that they shared some alleles with ‘Ca. P. prunorum’, supporting for the first time to our knowledge, the existence of inter-species recombination between these two species

East Adriatic: a reservoir region of severe Citrus tristeza virus strains

Citrus tristeza virus (CTV) represents one of the major threats to citrus production worldwide. In the East Adriatic region, CTV symptoms are mostly absent due to traditional citrus grafting on trifoliate orange (Poncirus trifoliata), a CTV-tolerant rootstock. Therefore, the virus has been continuously spreading by the propagation of infected material. The genetic variability of CTV was studied on nineteen citrus samples, collected from orchards in the coastal region of Croatia, Montenegro and Albania, that previously tested positive by ELISA and immunocapture RT-PCR. Single-strand conformation polymorphism of the amplified coat protein gene demonstrated the presence of different CTV variants in each amplicon, while sequence analysis of cloned CP gene variants confirmed their clustering into six out of the seven phylogenetic groups so far delineated. Four of these groups include sequences of severe quick decline, seedling yellows and stem-pitting (SP) isolates, thought to be found only rarely in the Mediterranean region. Regardless of the lack of symptoms in the field, CTV isolates from the East Adriatic displayed high genetic variability and pathogenic potential, additionally confirmed by biological characterisation. The high percentage of mixed infections suggest the potential for further diversification and a greater risk of severe variants spreading into new areas