Proteomics Computational Analyses Suggest that the Envelope Glycoproteins of Segmented Jingmen Flavi-Like Viruses Are Class II Viral Fusion Proteins (β-Penetrenes) with Mucin-Like Domains

Abstract

Jingmen viruses are newly described segmented flavi-like viruses that have a worldwide distribution in ticks and have been associated with febrile illnesses in humans. Computational analyses were used to predict that Jingmen flavi-like virus glycoproteins have structural features of class II viral fusion proteins, including an ectodomain consisting of beta-sheets and short alpha-helices, a fusion peptide with interfacial hydrophobicity and a three-domain architecture. Jingmen flavi-like virus glycoproteins have a sequence enriched in serine, threonine, and proline at the amino terminus, which is a feature of mucin-like domains. Several of the serines and threonines are predicted be modified by the addition of O-linked glycans. Some of the glycoproteins are predicted to have an additional mucin-like domain located prior to the transmembrane anchor, whereas others are predicted to have a stem consisting of two alpha-helices. The flavivirus envelope protein and Jingmen flavi-virus glycoproteins may have diverged from a common class II precursor glycoprotein with a mucin-like domain or domains acquired after divergence.

Geographical and Tick-Dependent Distribution of Flavi-Like Alongshan and Yanggou Tick Viruses in Russia

“…Segment 2 encodes VP1a, VP1b and the previously described nuORF [ 7 ] proteins. Since VP1a and VP1b are believed to be surface glycoproteins [ 5 , 6 ], we assumed that these proteins were responsible for the association with the vector species. For two strains, Miass502 and Miass506, high-throughput sequencing of the virus purified from the IRE/CTVM19 cell supernate was carried out in order to obtain full genomes, while for eight positive tick samples, partial sequences of segment 2 were obtained via Sanger sequencing using primers targeting segment 2 ( Table S3 ).…”

“…The representatives of the Jingmenvirus (JMV) group, such as the Jingmen tick virus (JMTV), Alongshan virus (ALSV), Yanggou tick virus (YGTV) and others, have segmented ssRNA(+) genomes, two segments of which have homology with the well-studied flavivirus RNA-dependent RNA polymerase NS5 (segment 1) and RNA helicase-protease NS3 (segment 3) [ 3 , 5 ]. The remaining two segments are specific only to JMVs and encode glycoproteins—a novel upstream open reading frame (nuORF), VP1a and VP1b proteins (segment 2) [ 5 , 6 , 7 ] and other virus proteins—VP2 and VP3 (segment 4) [ 2 , 3 , 5 ]. Excluding plant viruses, before the discovery of JMTVs [ 3 ], only representatives of the genus Omegatetravirus of the family Tetraviridae , which infect insects [ 8 ], and the genera Alphanodavirus and Betanodavirus of the family Nodaviridae , which infect insects and fish, respectively [ 9 ], were known to have a segmented ssRNA(+) genome.…”

Jingmen Tick Virus in Ticks from Kenya

“…The viruses of one group are transmitted by blood-feeding arthropods and are vertebrate pathogenic (arbo-jingmenviruses) such as JMTV, Mogiana tick virus (MGTV), and Yanggou tick virus (YGTV) [ 2 , 10 , 11 , 12 ]. The second group contains viruses that only infect arthropods (arthropod-specific jingmenviruses) exemplified by the Guaico Culex virus (GCXV), Wuhan aphid virus (WHAV), and Shuangao insect virus (SHIV) groups [ 8 , 10 , 12 ]. Jingmenviruses have a genome comprising four segments of positive-sense single-stranded RNA and are distantly related to flaviviruses [ 1 , 10 , 11 , 12 ].…”

“…The second group contains viruses that only infect arthropods (arthropod-specific jingmenviruses) exemplified by the Guaico Culex virus (GCXV), Wuhan aphid virus (WHAV), and Shuangao insect virus (SHIV) groups [ 8 , 10 , 12 ]. Jingmenviruses have a genome comprising four segments of positive-sense single-stranded RNA and are distantly related to flaviviruses [ 1 , 10 , 11 , 12 ]. JMTV has a multisegmented genome comprising three monocistronic segments (segments 1, 2, and 3) and two separate open reading frames (ORF) in one segment (segment 4) [ 1 , 10 , 12 ].…”

Sequence Relationships of RNA Helicases and Other Proteins Encoded by Blunervirus RNAs Highlight Recombinant Evolutionary Origin of Kitaviral Genomes

“…However, phylogenetic trees of "jivivirus" Met-HEL and RdRp domains revealed obvious similarity to virga-like viruses (Chiapello et al, 2020). Most strikingly, jivivirus RNA3 (around 2 Kb) encodes an SF2 RNA helicase with prominent sequence similarity to flavi-like insect jingmen viruses which contain the respective gene in RNA3 of a quadripartite genome (Chiapello et al, 2020;Garry and Garry, 2020) (Supplementary Figure 1 and Supplementary Table 1). Thus, the structure of "jivivirus" genomes formally corresponds to a reassortant between virga-like and flavi-like viruses and represents a second example among plant viruses when a single genome encodes both SF1 and SF2 RNA helicases.…”