Genetic Characterization of Frijoles and Chilibre Species Complex Viruses (Genus Phlebovirus; Family Phenuiviridae) and Three Unclassified New World Phleboviruses

Abstract

The genus Phlebovirus is a diverse group of globally occurring viruses, including tick-, mosquito-, and sand fly-borne pathogens. Phleboviruses have historically been classified by serological methods. However, molecular methods alone have been used to identify emergent novel and related strains in recent years. This makes reconciling the classification of historically and newly characterized viruses challenging. To address this in part, we describe the characterization of the genomes of the Frijoles and Chilibre species complex phleboviruses, and three unclassified phleboviruses isolated in the Americas: Caimito, Itaporanga, and Rio Grande viruses that had previously only been described at the serological level. With the exception of Itaporanga virus, the phleboviruses sequenced in this study are phylogenetically related to the current species Frijoles phlebovirus, Bujaru phlebovirus, or the Chagres antigenic complex. Unexpectedly, molecular and phylogenetic analysis suggests Chilibre and Caimito viruses are taxonomically related to the family Peribunyaviridae. These viruses have a genomic architecture similar to peribunyaviruses and form monophyletic groups within the genus Pacuvirus. Our data highlight the importance of reconciling serological and molecular taxonomic classification. In addition, we suggest the taxonomy of Chilibre and Caimito viruses should be revised.

Family Level Phylogenies Reveal Relationships of Plant Viruses within the Order Bunyavirales

“…The preGP also shows a strong phylogenetic relationship with Pacuvirus and Orthobunyavirus in group VI. This ML analysis supports the suggestion that the taxonomic identity for CHIV should be moved from the Phlebovirus to the Pacuvirus genus within Peribunyaviridae [ 54 ]. Inter-lineage reassortment, although unlikely, may only be considered for the assignment of Chilibre virus because these viruses share common reservoirs [ 55 ].…”

“…Members of the genus Phlebovirus are viruses that are borne by ticks, mosquitoes, and sandflies. Prior molecular characterization suggested that CHIV may be more related to the genus Pacuvirus within Peribunyaviridae [ 54 ]. Our ML analysis using a much larger dataset indicates that CHIV RdRp and N proteins share a specific relationship with the Pacuvirus within the Group I Peribunyaviridae.…”

Clinically Important Phleboviruses and Their Detection in Human Samples

“…Following isolation, identification and characterization of newly derived isolates were formerly provided by predominantly antibody-based methods, including complement fixation (CF), hemagglutination inhibition (HI), immunofluorescence assays (IFAs), and plaque reduction neutralization tests (PRNTs) [ 7 , 17 ]. In recent years, isolates have become increasingly characterized by nucleic-acid-based methods [ 18 , 19 , 20 ], including whole-genome sequencing, rather than serology. This transition has facilitated the more rapid identification of reassortant viruses [ 4 , 21 ] and allows for taxonomic classification based upon nucleic-acid-based criteria for demarcation [ 1 ].…”

Further Characterization of Rio Grande Virus and Potential for Cross Reactivity with Rift Valley Fever Virus Assays

“…Viruses within the genus Phlebovirus, family Phenuiviridae, include mosquito-, sand fly-, and tick-borne pathogens, and these viruses have three negative sense RNA segments (4). The first phlebovirus identified in the United States, Rio Grande virus (RGV), was isolated from southern plains woodrats (Neotoma micropus) in Texas [1,2], and was shown to be transmitted by a sand fly, Lutzomyia anthophora, in the laboratory [3].…”

“…No antibodies were found in 278 human serum samples tested, and sera from native wild ruminants were not tested [ 1 ]. Rio Grande virus is phylogenetically related to Anhanga virus, and is also grouped with Tapara virus in analyses based on the nucleocapsid protein (NP) [ 4 ]. Neotoma micropus , thought to be the natural host, ranges across North America from southeastern Colorado, east to central Kansas, west to the Arizona border, and south to the eastern coast of Mexico in northern Veracruz [ 5 ].…”