Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships

Negative sense RNA viruses (NSV) include some of the most detrimental human pathogens, including the influenza, Ebola and measles viruses. NSV genomes consist of one or multiple single-stranded RNA molecules that are encapsidated into one or more ribonucleoprotein (RNP) complexes. Current evolutionary relationships within the NSV phylum are based on alignment of conserved RNA-dependent RNA polymerase (RdRp) domain amino acid sequences. However, the RdRp-based phylogeny does not address whether other core proteins in the NSV genome evolved along the same trajectory. Moreover, the current classification of NSVs does not consistently match the segmented and non-segmented nature of negative-sense virus genomes. Viruses belonging to e.g. the Serpentovirales have a segmented genome but are classified among the non-segmented negative-sense RNA viruses. We hypothesized that RNA genome segmentation is not coupled to the RdRp domain, but rather to the nucleocapsid protein (NP) that forms RNP complexes with the viral RNA. Because NP sequences are too short to infer robust phylogenetic relationships, we here used experimentally-obtained and AlphaFold 2.0-predicted NP structures to probe whether evolutionary relationships can be estimated using NSV NP sequences and potentially improve our understanding of the relationships between NSV subphyla and the NSV genome organization. Following flexible structure alignments of modeled structures, we find that the structural homology of the NSV NPs reveals phylogenetic clusters that are consistent with the currently accepted NSV taxonomy based on RdRp sequences with one key difference: the NPs of the segmented Serpentovirales cluster with the other segmented NSV. In addition, we were able to assign viruses for which RdRp sequences are currently missing to phylogenetic clusters. Overall, our results suggest that the NSV RdRp and NP genes largely evolved along similar trajectories, that NP-based clustering is better correlated with the NSV genome structure organization, and that even short pieces of genetic, protein-coding information can be used to infer evolutionary relationships, potentially making metagenomic analyses more valuable.

Vesicular Stomatitis Virus Elicits Early Transcriptome Response in Culicoides sonorensis Cells

Viruses that are transmitted by arthropods, or arboviruses, have evolved to successfully navigate both the invertebrate and vertebrate hosts, including their immune systems. Biting midges transmit several arboviruses including vesicular stomatitis virus (VSV). To study the interaction between VSV and midges, we characterized the transcriptomic responses of VSV-infected and mock-infected Culicoides sonorensis cells at 1, 8, 24, and 96 h post inoculation (HPI). The transcriptomic response of VSV-infected cells at 1 HPI was significant, but by 8 HPI there were no detectable differences between the transcriptome profiles of VSV-infected and mock-infected cells. Several genes involved in immunity were upregulated (ATG2B and TRAF4) or downregulated (SMAD6 and TOLL7) in VSV-treated cells at 1 HPI. These results indicate that VSV infection in midge cells produces an early immune response that quickly wanes, giving insight into in vivo C. sonorensis VSV tolerance that may underlie their permissiveness as vectors for this virus.

A Virus Is a Community: Diversity within Negative-Sense RNA Virus Populations

Negative-sense RNA virus populations are composed of diverse viral components that interact to form a community and shape the outcome of virus infections. At the genomic level, RNA virus populations consist not only of a homogeneous population of standard viral genomes but also of an extremely large number of genome variants, termed viral quasispecies, and nonstandard viral genomes, which include copy-back viral genomes, deletion viral genomes, mini viral RNAs, and hypermutated RNAs. At the particle level, RNA virus populations are composed of pleomorphic particles, particles missing or having additional genomes, and single particles or particle aggregates. As we continue discovering more about the components of negative-sense RNA virus populations and their crucial functions during virus infection, it will become more important to study RNA virus populations as a whole rather than their individual parts. In this review, we will discuss what is known about the components of negative-sense RNA virus communities, speculate how the components of the virus community interact, and summarize what vaccines and antiviral therapies are being currently developed to target or harness these components.

High Plains wheat mosaic virus: An enigmatic disease of wheat and corn causing the High Plains disease

BRIEF HISTORY

In 1993, severe mosaic and necrosis symptoms were observed on corn (maize) and wheat from several Great Plains states of the USA. Based on the geographical location of infections, the disease was named High Plains disease and the causal agent was tentatively named High Plains virus. Subsequently, researchers renamed this virus as maize red stripe virus and wheat mosaic virus to represent the host and symptom phenotype of the virus. After sequencing the genome of the pathogen, the causal agent of High Plains disease was officially named as High Plains wheat mosaic virus. Hence, High Plains virus, maize red stripe virus, wheat mosaic virus, and High Plains wheat mosaic virus (HPWMoV) are synonyms for the causal agent of High Plains disease.

TAXONOMY

High Plains wheat mosaic virus is one of the 21 definitive species in the genus Emaravirus in the family Fimoviridae.

VIRION

The genomic RNAs are encapsidated in thread-like nucleocapsids in double-membrane 80-200 nm spherical or ovoid virions.

GENOME CHARACTERIZATION

The HPWMoV genome consists of eight single-stranded negative-sense RNA segments encoding a single open reading frame (ORF) in each genomic RNA segment. RNA 1 is 6,981-nucleotide (nt) long, coding for a 2,272 amino acid protein of RNA-dependent RNA polymerase. RNA 2 is 2,211-nt long and codes for a 667 amino acid glycoprotein precursor. RNA 3 has two variants of 1,439- and 1,441-nt length that code for 286 and 289 amino acid nucleocapsid proteins, respectively. RNA 4 is 1,682-nt long, coding for a 364 amino acid protein. RNA 5 and RNA 6 are 1,715- and 1,752-nt long, respectively, and code for 478 and 492 amino acid proteins, respectively. RNA 7 and RNA 8 are 1,434- and 1,339-nt long, code for 305 and 176 amino acid proteins, respectively.

BIOLOGICAL PROPERTIES

HPWMoV can infect wheat, corn (maize), barley, rye brome, oat, rye, green foxtail, yellow foxtail, and foxtail barley. HPWMoV is transmitted by the wheat curl mite and through corn seed.

DISEASE MANAGEMENT

Genetic resistance against HPWMoV in wheat is not available, but most commercial corn hybrids are resistant while sweet corn varieties remain susceptible. Even though corn hybrids are resistant to virus, it still serves as a green bridge host that enables mites to carry the virus from corn to new crop wheat in the autumn. The main management strategy for High Plains disease in wheat relies on the management of green bridge hosts. Cultural practices such as avoiding early planting can be used to avoid mite buildup and virus infections.

Visualization of Double-Stranded RNA Colocalizing With Pattern Recognition Receptors in Arenavirus Infected Cells

An important step in the initiation of the innate immune response to virus infection is the recognition of non-self, viral RNA, including double-stranded RNA (dsRNA), by cytoplasmic pattern recognition receptors (PRRs). For many positive-sense RNA viruses and DNA viruses, the production of viral dsRNA, and the interaction of viral dsRNA and PRRs are well characterized. However, for negative-sense RNA viruses, viral dsRNA was thought to be produced at low to undetectable levels and PRR recognition of viral dsRNA is still largely unclear. In the case of arenaviruses, the nucleocaspid protein (NP) has been identified to contain an exoribonuclease activity that preferentially degrades dsRNA in biochemical studies. Nevertheless, pathogenic New World (NW) arenavirus infections readily induce an interferon (IFN) response in a RIG-I dependent manner, and also activate the dsRNA-dependent Protein Kinase R (PKR). To better understand the innate immune response to pathogenic arenavirus infection, we used a newly identified dsRNA-specific antibody that efficiently detects viral dsRNA in negative-sense RNA virus infected cells. dsRNA was detected in NW arenavirus infected cells colocalizing with virus NP in immunofluorescence assay. Importantly, the dsRNA signals also colocalized with cytoplasmic PRRs, namely, PKR, RIG-I and MDA-5, as well as with the phosphorylated, activated form of PKR in infected cells. Our data clearly demonstrate the PRR recognition of dsRNA and their activation in NW arenavirus infected cells. These findings provide new insights into the interaction between NW arenaviruses and the host innate immune response.