Matthew Ballinger

Mississippi State University | MSU · Department of Biological Sciences

An understanding of the timescale of evolution is critical for comparative virology but remains elusive for many RNA viruses. Age estimates based on mutation rates can severely underestimate divergences for ancient viral genes that are evolving under strong purifying selection. Paleoviral dating, however, can provide minimum age estimates for ancie...

Unlabelled: Bunyaviridae is a large family of RNA viruses chiefly comprised of vertebrate and plant pathogens. We discovered novel bunyavirids that are approximately equally divergent from each of the five known genera. We characterized novel genome sequences for two bunyavirids, namely, Kigluaik phantom virus (KIGV), from tundra-native phantom mi...

Among eukaryotes with modified nuclear genetic codes, viruses are unknown. However, here we provide evidence of an RNA virus that infects a fungal host (Scheffersomyces segobiensis) with a derived nuclear genetic code where CUG codes for serine. The genomic architecture and phylogeny are consistent with infection by a double-stranded RNA virus of t...

The recent and surprising discovery of widespread NIRVs (non-retroviral integrated RNA viruses) has highlighted the importance of genomic interactions between non-retroviral RNA viruses and their eukaryotic hosts. Among the viruses with integrated representatives are the rhabdoviruses, a family of negative sense single-stranded RNA viruses. We iden...

Little is known of the biological significance and evolutionary maintenance of integrated non-retroviral RNA virus genes in eukaryotic host genomes. Here, we isolated novel filovirus-like genes from bat genomes and tested for evolutionary maintenance. We also estimated the age of filovirus VP35-like gene integrations and tested the phylogenetic hyp...

Parasitoid wasps are exceptionally diverse and use specialized adaptations capable of manipulating the physiology and behaviour of host organisms¹. In more than two centuries since the first records of Drosophila-parasitizing wasps, nearly 200 described and provisional parasitoid species of drosophilids have been identified². These include endopara...

In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished...

Vertically transmitted (VT) microbial symbionts play a vital role in the evolution of their insect hosts. A longstanding question in symbiont research is what genes help promote long-term stability of vertically transmitted lifestyles. Symbiont success in insect hosts is due in part to expression of beneficial or manipulative phenotypes that favor...

In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renam...

Cytoplasmic incompatibility (CI) is a form of reproductive manipulation caused by maternally inherited endosymbionts infecting arthropods, like Wolbachia, whereby matings between infected males and uninfected females produce few or no offspring. We report the discovery of a new CI symbiont, a strain of Spiroplasma causing CI in the parasitoid wasp...

Inherited mutualists, parasites, and commensals occupy one of the most intimate ecological niches available to invertebrate-associated microbes. How this transmission environment influences microbial evolution is increasingly understood for inherited bacterial symbionts, but in viruses, research on the prevalence of vertical transmission and its ef...

In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, a...

In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, a...

p>In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted...

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted,...

How insects combat RNA virus infection is a subject of intensive research owing to its importance in insect health, virus evolution, and disease transmission. In recent years, a pair of potentially linked phenomena have come to light as a result of this work-first, the pervasive production of viral DNA from exogenous nonretroviral RNA in infected i...

In February 2019, following the annual taxon ratification vote, the order Bunyavirales was amended by creation of two new families, four new subfamilies, 11 new genera and 77 new species, merging of two species, and deletion of one species. This article presents the updated taxonomy of the order Bunyavirales now accepted by the International Commit...

In October 2018, the order Bunyavirales was amended by inclusion of the family Arenaviridae, abolishment of three families, creation of three new families, 19 new genera, and 14 new species, and renaming of three genera and 22 species. This article presents the updated taxonomy of the order Bunyavirales as now accepted by the International Committe...

Defenses conferred by microbial symbionts play a vital role in the health and fitness of their animal hosts. An important outstanding question in the study of defensive symbiosis is what determines long term stability and effectiveness against diverse natural enemies. In this study, we combine genome and transcriptome sequencing, symbiont transfect...

DNA copies of many non-retroviral RNA virus genes or portions thereof (NIRVs) are present in the nuclear genomes of many eukaryotes. These have often been preserved for millions of years of evolution, suggesting that they play an important cellular function. One possible function is resistance to infection by related viruses. In some cases, this ap...

Middle panel of Fig. 1 raw data RTPCR with L1 RdRP primers of pYescp1, pYescp1 mutant, pG3cp1, pG3cp1mutant, and PC847 total RNAs

Raw data for uppermost panel of Fig. 1 Total RNA from pYescp1, pYescp1mutant, pG3cp1, pG3cp1mutant, PC847, and markers.

Bottom panel of Fig. 1 RTPCR with rps11b primers of pYescp1, pYescp1mutant, pG3cp1, pGccp1mutant, and PC847 total RNA.

Complete blot of Fig. 3 Figure 3 showing markers.

Tryptic peptides detected by GeLC-MS/MS in the experiment of Fig. 4 Tryptic peptides are highlighted in bold.

L1-LA but not La-LBC RNA is depleted from pG3cp1-treated S. cerevisiae Relative detection of La–LBC, L1–LA, and cp1 transcripts and genomic RNA by quantitative reverse transcription PCR. PC4391 cells were transformed with pG3cp1 encoding a wild type or a mutated cp1 gene. The pG3cp1 mutant sequence differs from the wild type optimized sequence by a...

Raw data of Supplemental File 1 Biorad data from which Supplemental File 1 was derived. Note that the data for M1 has been omitted from Fig. 1 and that “cp2” in the raw data is actually cp1 of File S1 and elsewhere in the article.

Microbial partners play important roles in the biology and ecology of animals. In insects, maternally transmitted symbionts are especially common and can have host effects ranging from reproductive manipulation to nutrient provisioning and defense against natural enemies. In this study, we report a genus-wide association of Myrmica ants with the in...

Hemipteran insects of the suborder Sternorrhyncha are plant-sap feeders, where each family is obligately associated with a specific bacterial endosymbiont that produces essential nutrients lacking in the sap. Coccidae (soft scale insects) is the only major sternorrhynchan family in which obligate symbiont(s) have not been identified. We studied the...

Little is known of the evolution of RNA viruses in aquatic systems. Here, we assess the genetic connectivity of two bunyaviruses (Kigluaik phantom orthophasmavirus or KIGV and Nome phantom orthophasmavirus or NOMV) with zooplanktonic hosts from subarctic ponds. We expected weak genetic structure among populations as the hosts (phantom midges) have...

While it has become increasingly clear that multicellular organisms often harbor microbial symbionts that protect their hosts against natural enemies, the mechanistic underpinnings underlying most defensive symbioses are largely unknown. Spiroplasma bacteria are widespread associates of terrestrial arthropods, and include strains that protect diver...

The planthopper Hyalesthes obsoletus (Hemiptera: Cixiidae) is the vector of yellows disease in grapevines, transmitting the phytopathogenic uncultivable bacterium Phytoplasma sp. (Mollicutes). In the current study, the bacterial community compositions of symbionts of this insect were examined. Two dominant bacterial genera were identified by mass s...

Most of the freshwater component of the Earth's surface is composed of shallow tundra ponds. These high latitude ecosystems have been exposed to a variety of abiotic disturbances associated with recent environmental change. However, the biological significance of these changes remains poorly understood. Here, we characterize the abiotic disturbance...

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The ecological model, Daphnia pulex (Cladocera: Daphniidae), is broadly distributed in Holarctic freshwater habitats and has been the subject of multidisciplinary study for over half a century, but never has a natural RNA virus infection been reported in daphnids. Here we report on a group of paleoviruses related to RNA dependent RNA polymerase in...

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