Reevaluation of the phylogenetic relationships among Neotomini rodents (Hodomys, Neotoma, and Xenomys) and comments on the woodrat classification.

The woodrats or packrats of the genus Neotoma have been the subject of a wide array of research including paleoecology, physiology, morphological evolution, systematics, speciation, and hybridization. In recent years, much work has been done to elucidate evolutionary relationships within and between closely related species of the genus; in particular the addition of newly collected specimens from critical geographic regions has provided new opportunities for taxonomic assessment. Given these new data and their potential, parsimony (PARS), maximum likelihood (ML), and Bayesian inference (BI) analyses were conducted on DNA sequences obtained from nine individual genes (four mitochondrial loci: 12S, 16S, CoII, and Cytb; five nuclear loci: AdhI2, BfibI7, En2, Mlr, and Myh6) to estimate the phylogenetic relationships among 23 species of Neotoma. Results of these analyses depicted a wide array of phylogenetic relationships among taxa; with substantial nodal support recovered in both the ML and PARS analyses at some mid-level and terminal positions. Several individual genes, particularly 12S, AdhI2, BfibI7, CoII, and Cytb, provided support at several basal positions; however, phylogenetic resolution was limited in the other genes. A final BI analysis where the nine genes were concatenated into a single data set produced several supported clades that corresponded to previously recognized species groups (floridana, micropus, mexicana, and lepida) and the subgenus Homodontomys. Levels of genetic divergence for within-species comparisons (estimated from the Cytb data set) ranged from 0.88% (N. magister) to 6.82% (N. fuscipes); for between sister species comparisons ranged from 4.68% (N. devia and N. lepida) to 12.70% (N. angustapalata and N. nelsoni); and for members within closely related clades ranged from 8.70% (N. bryanti and N. lepida) to 12.57% (N. goldmani and N. magister). Evaluations of generic, subgeneric, and species group boundaries were explored using phylogenetic principles on the DNA sequence data presented herein, as well as morphological findings from previous studies. Results obtained suggest that the most conservative taxonomic interpretation involves the abandonment of subgeneric delineations and relies on the recognition of eight species groups (cinerea, floridana, fuscipes, lepida, mexicana, micropus, phenax, and stephensi) as the backbone of the woodrat classification.

Las ratas cambalacheras del género Neotoma han sido estudiadas en varios tipos de investigaciones incluyendo paleoecología, fisiología, evolución morfológica, sistemática, especiación e hibridación. Recientemente, se han realizado numerosos estudios para elucidar las relaciones evolutivas dentro del género y entre especies cercanamente relacionadas al mismo; en particular la inclusión de nuevos especímenes provenientes de regiones geográficas críticas han brindado nuevas oportunidades para evaluaciones taxonómicas. A partir de estos nuevos datos se realizaron análisis de parsimonia (PARS), Máxima Verosimilitud (MV), e Inferencia Bayesiana (IB) en secuencias de ADN provenientes de nueve genes individuales (cuatro loci mitocondriales: 12S, 16S, CoII, y Cytb; cinco loci nucleares: Adh-I2, Bfib-I7, En2, Mlr, and Myh6) para determinar la relación filogenética de 23 especies de Neotoma. Los resultados de estos análisis presentan una amplia gama de relaciones filogenéticas entre taxa con un soporte nodal importante en los análisis de MV y PARS en algunas posiciones terminales de nivel medio. Varios genes individuales, en particular 12S, Adh-I2, Bfib-I7, CoII, and Cytb, ofrecieron soporte en varias posiciones basales; sin embargo, la resolución filogenética fue reducida en los demás genes. El último análisis de IB, en donde nueve genes se concatenaron en un solo conjunto de datos, produjo soporte en varios clados que correspondieron a especies de grupos previamente reconocidos (floridana, micropus, mexicana, y lepida) y el sub-género Homodontomys. Los niveles de divergencia genética para comparaciones intraespecíficas fluctuaron entre 0.88% (N. magister) y 6.82% (N. fuscipes); para especies hermanas (4.68%­N. devia y N. lepida hasta 12.70%­N. angustapalata y N. nelsoni); y para los miembros de clados cercanos (8.70%­N. bryanti y N. lepida hasta 12.57%­N. goldmani y N. magister). Las evaluaciones de los limites genéricos, subgenéricos y de grupos de especies fueron explorados usando principios filogenéticos en las secuencias de ADN de este trabajo, y también se basaron en las conclusiones morfológicas de estudios previos. Los resultados obtenidos sugieren que la interpretación taxonómica más conservadora incluye el abandono de las delineaciones subgenéricas y se depende en el reconocimiento de ocho grupos de especies (cinerea, floridana, fuscipes, lepida, mexicana, micropus, phenax, y stephensi) como el pilar central de la clasificación de las ratas cambalacheras.

Taxonomy of the order Bunyavirales: update 2019.

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 Committee on Taxonomy of Viruses (ICTV).

Taxonomy of the order Bunyavirales: second update 2018.

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 Committee on Taxonomy of Viruses (ICTV).

Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species.

The International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (phyla to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV's official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world, and therefore, have limited use for ICTV-devised taxa. Instead, these professionals look to the ICTV as an expert point source that provides the most current taxonomic affiliations of viruses of interests to facilitate document writing. These needs are currently unmet as an ICTV-supported, easily searchable database that includes all published virus names and abbreviations linked to their taxa is not available. In addition, in stark contrast to other biological taxonomic frameworks, virus taxonomy currently permits individual species to have several members. Consequently, confusion emerges among those who are not aware of the difference between taxa and viruses, and because certain well-known viruses cannot be located in ICTV publications or be linked to their species. In addition, the number of duplicate names and abbreviations has increased dramatically in the literature. To solve this conundrum, the ICTV could mandate listing all viruses of established species and all reported unclassified viruses in forthcoming online ICTV Reports and create a searchable webpage using this information. The International Union of Microbiology Societies could also consider changing the mandate of the ICTV to include the nomenclature of all viruses in addition to taxon considerations. With such a mandate expansion, official virus names and virus name abbreviations could be catalogued and virus nomenclature could be standardized. As a result, the ICTV would become an even more useful resource for all stakeholders in virology.

Muleshoe Virus and Other Hantaviruses Associated with Neotomine or Sigmodontine Rodents in Texas.

The broad objective of this study was to increase our knowledge of Muleshoe virus and other hantaviruses associated with cricetid rodents in Texas. Anti-hantavirus antibody was found in 38 (3.2%) of 1171 neotomine rodents and 6 (1.8%) of 332 sigmodontine rodents from 10 Texas counties; hantaviral RNA was detected in 23 (71.9%) of 32 antibody-positive rodents. Analyses of nucleocapsid protein gene sequences indicated Muleshoe virus infection in four hispid cotton rats (Sigmodon hispidus) from northern Texas; Bayou virus, three Texas marsh oryzomys (Oryzomys texensis) from the Gulf Coast; Limestone Canyon virus, five brush mice (Peromyscus boylii) from western Texas; and Sin Nombre virus-five Texas mice (P. attwateri), one Lacey's white-ankled deer mouse (P. laceianus), four white-footed mice (P. leucopus), and one fulvous harvest mouse (Reithrodontomys fulvescens) from northern, central, or southern Texas. The results of this study together with the results of a previous study revealed that Muleshoe virus, perhaps in association with S. hispidus, is distributed across northern Texas. Finally, the results of Bayesian analyses of glycoprotein precursor (GPC) gene sequences and pairwise comparisons of complete GPC (amino acid) sequences strengthened support for the notion that Muleshoe virus is distinct from Black Creek Canal virus, Bayou virus, and all other species included in the Bunyaviridae, genus Hantavirus.

Phylogenetic Relationship of Necoclí Virus to Other South American Hantaviruses (Bunyaviridae: Hantavirus).

The results of a previous study suggested that Cherrie's cane rat (Zygodontomys cherriei) is the principal host of Necoclí virus (family Bunyaviridae, genus Hantavirus) in Colombia. Bayesian analyses of complete nucleocapsid protein gene sequences and complete glycoprotein precursor gene sequences in this study confirmed that Necoclí virus is phylogenetically closely related to Maporal virus, which is principally associated with the delicate pygmy rice rat (Oligoryzomys delicatus) in western Venezuela. In pairwise comparisons, nonidentities between the complete amino acid sequence of the nucleocapsid protein of Necoclí virus and the complete amino acid sequences of the nucleocapsid proteins of other hantaviruses were ≥8.7%. Likewise, nonidentities between the complete amino acid sequence of the glycoprotein precursor of Necoclí virus and the complete amino acid sequences of the glycoprotein precursors of other hantaviruses were ≥11.7%. Collectively, the unique association of Necoclí virus with Z. cherriei in Colombia, results of the Bayesian analyses of complete nucleocapsid protein gene sequences and complete glycoprotein precursor gene sequences, and results of the pairwise comparisons of amino acid sequences strongly support the notion that Necoclí virus represents a novel species in the genus Hantavirus. Further work is needed to determine whether Calabazo virus (a hantavirus associated with Z. brevicauda cherriei in Panama) and Necoclí virus are conspecific.

Epizootiology of Tacaribe serocomplex viruses (Arenaviridae) associated with neotomine rodents (Cricetidae, Neotominae) in southern California.

The objective of this study was to advance our knowledge of the epizootiology of Bear Canyon virus and other Tacaribe serocomplex viruses (Arenaviridae) associated with wild rodents in California. Antibody (immunoglobulin G [IgG]) to a Tacaribe serocomplex virus was found in 145 (3.6%) of 3977 neotomine rodents (Cricetidae: Neotominae) captured in six counties in southern California. The majority (122 or 84.1%) of the 145 antibody-positive rodents were big-eared woodrats (Neotoma macrotis) or California mice (Peromyscus californicus). The 23 other antibody-positive rodents included a white-throated woodrat (N. albigula), desert woodrat (N. lepida), Bryant's woodrats (N. bryanti), brush mice (P. boylii), cactus mice (P. eremicus), and deer mice (P. maniculatus). Analyses of viral nucleocapsid protein gene sequence data indicated that Bear Canyon virus is associated with N. macrotis and/or P. californicus in Santa Barbara County, Los Angeles County, Orange County, and western Riverside County. Together, analyses of field data and antibody prevalence data indicated that N. macrotis is the principal host of Bear Canyon virus. Last, the analyses of viral nucleocapsid protein gene sequence data suggested that the Tacaribe serocomplex virus associated with N. albigula and N. lepida in eastern Riverside County represents a novel species (tentatively named "Palo Verde virus") in the genus Arenavirus.

Pneumonitis in Syrian golden hamsters (Mesocricetus auratus) infected with Rio Mamoré virus (family Bunyaviridae, genus Hantavirus).

Rio Mamoré virus is an etiological agent of hantavirus pulmonary syndrome in South America. The purpose of this study was to determine whether Rio Mamoré virus strain HTN-007 in Syrian golden hamsters is pathogenic. None of 37 adult hamsters infected by intramuscular injection of HTN-007, including 10 animals killed on Day 42 or 43 post-inoculation, exhibited any symptom of disease. Histological abnormalities included severe or moderately severe pneumonitis in 6 (46.2%) of the 13 animals killed on Day 7 or 10 post-inoculation. The primary target of infection in lung was the endothelium of the microvasculature. Collectively, these results indicate that Rio Mamoré virus strain HTN-007 in adult Syrian golden hamsters can cause a nonlethal disease that is pathologically similar to hantavirus pulmonary syndrome.

Diversity among Tacaribe serocomplex viruses (Family Arenaviridae) associated with the southern plains woodrat (Neotoma micropus).

The southern plains woodrat (Neotoma micropus) is the principal host of Catarina virus in southern Texas and a natural host of other North American Tacaribe serocomplex viruses. The objectives of this study were to increase our knowledge of the genetic diversity among Tacaribe serocomplex viruses associated with N. micropus and to define better the natural host relationships of these viruses. Pairwise comparisons of complete glycoprotein precursor gene sequences and complete nucleocapsid protein gene sequences revealed a high level of genetic diversity among Tacaribe serocomplex viruses associated with N. micropus in western Oklahoma, southern New Mexico, and northern and southern Texas. Collectively, the results of Bayesian analyses of nucleotide sequences and pairwise comparisons of amino acid sequences confirmed that the arenaviruses associated with N. micropus in Oklahoma and New Mexico should be included in the Whitewater Arroyo species complex, and indicated that that the arenaviruses associated with N. micropus in northern Texas are strains of a novel arenaviral species--tentatively named "Middle Pease River virus". Together, the results of assays for arenavirus and assays for anti-arenavirus antibody in 54 southern plains woodrats and 325 other rodents captured at 2 localities suggested that the southern plains woodrat is the principal host of Middle Pease River virus in northern Texas.

Ecology of Catarina virus (family Arenaviridae) in southern Texas, 2001-2004.

A total of 3941 rodents were captured during a 46-month prospective (mark-recapture) study on the ecology of Catarina virus in southern Texas. Antibody reactive against Catarina virus was found in 73 (11.9%) of 611 southern plains woodrats (Neotoma micropus) and none of 3330 other rodents; strains of Catarina virus were isolated from 6 antibody-negative and 9 antibody-positive southern plains woodrats; and the infections in at least 3 southern plains woodrats were chronic. These results affirm the notion that the southern plains woodrat is the principal host of Catarina virus and suggest that Catarina virus infection is highly specific to N. micropus.

Geographic distribution of hantaviruses associated with neotomine and sigmodontine rodents, Mexico.

To increase our knowledge of the geographic distribution of hantaviruses associated with neotomine or sigmodontine rodents in Mexico, we tested 876 cricetid rodents captured in 18 Mexican states (representing at least 44 species in the subfamily Neotominae and 10 species in the subfamily Sigmodontinae) for anti-hantavirus IgG. We found antibodies against hantavirus in 35 (4.0%) rodents. Nucleotide sequence data from 5 antibody-positive rodents indicated that Sin Nombre virus (the major cause of hantavirus pulmonary syndrome [HPS] in the United States) is enzootic in the Mexican states of Nuevo León, San Luis Potosí, Tamaulipas, and Veracruz. However, HPS has not been reported from these states, which suggests that in northeastern Mexico, HPS has been confused with other rapidly progressive, life-threatening respiratory diseases. Analyses of nucleotide sequence data from 19 other antibody-positive rodents indicated that El Moro Canyon virus and Limestone Canyon virus are geographically widely distributed in Mexico.

Ocozocoautla de espinosa virus and hemorrhagic fever, Mexico.

Arenavirus RNA was isolated from Mexican deer mice (Peromyscus mexicanus) captured near the site of a 1967 epidemic of hemorrhagic fever in southern Mexico. Analyses of nucleotide and amino acid sequence data indicated that the deer mice were infected with a novel Tacaribe serocomplex virus (proposed name Ocozocoautla de Espinosa virus), which is phylogenetically closely related to Tacaribe serocomplex viruses that cause hemorrhagic fever in humans in South America.

Duration of Catarina virus infection in the southern plains woodrat (Neotoma micropus).

Four adult male, 6 sub-adult, and 7 newborn southern plains woodrats (Neotoma micropus) each were inoculated subcutaneously with 3.1 log(10) median cell culture infectious doses (CCID(50)) of Catarina virus strain AV A0400135 (virus family Arenaviridae). The inoculated animals and the mothers of the newborn animals all became infected and remained asymptomatic. The infections in the adult male woodrats and in the mother woodrats were transient, the infections in 2 (33.3%) of the sub-adult woodrats persisted through month 4 post-inoculation, and 6 (85.7%) of the newborn woodrats were viruric through month 5 post-inoculation. Collectively these findings indicate that the duration of infection in the southern plains woodrat is dependent upon age at exposure to Catarina virus. The results of this study also indicate that chronically infected woodrats persistently shed Catarina virus into the environment.

Transmission of Guanarito and Pirital viruses among wild rodents, Venezuela.

Samples from rodents captured on a farm in Venezuela in February 1997 were tested for arenavirus, antibody against Guanarito virus (GTOV), and antibody against Pirital virus (PIRV). Thirty-one (48.4%) of 64 short-tailed cane mice (Zygodontomys brevicauda) were infected with GTOV, 1 Alston's cotton rat (Sigmodon alstoni) was infected with GTOV, and 36 (64.3%) of 56 other Alston's cotton rats were infected with PIRV. The results of analyses of field and laboratory data suggested that horizontal transmission is the dominant mode of GTOV transmission in Z. brevicauda mice and that vertical transmission is an important mode of PIRV transmission in S. alstoni rats. The results also suggested that bodily secretions and excretions from most GTOV-infected short-tailed cane mice and most PIRV-infected Alston's cotton rats may transmit the viruses to humans.

Diversity and phylogenetic relationships among the North American Tacaribe serocomplex viruses (family Arenaviridae).

The purpose of this study was to extend our knowledge of the genetic diversity and phylogenetic relationships among the North American Tacaribe serocomplex viruses. Analyses of glycoprotein precursor gene sequence data separated the North American arenaviruses into 7 major phylogenetic groups. The results of analyses of Z gene and nucleocapsid protein gene sequence data were not remarkably different from the glycoprotein precursor gene tree. In contrast, the tree generated from RNA-dependent RNA polymerase gene sequences differed from the glycoprotein precursor gene tree with regard to phylogenetic relationships among the viruses associated with woodrats captured in the western United States, Texas, or northern Mexico. Further analyses of the polymerase gene sequence data set suggested that the difference in topology was a consequence of incongruence among the gene tree data sets or chance rather than genetic reassortment or recombination between arenaviruses.

Novel arenavirus infection in humans, United States.

Immunoglobulin G against Whitewater Arroyo virus or lymphocytic choriomeningitis virus was found in 41 (3.5%) of 1,185 persons in the United States who had acute central nervous system disease or undifferentiated febrile illnesses. The results of analyses of antibody titers in paired serum samples suggest that a North American Tacaribe serocomplex virus was the causative agent of the illnesses in 2 persons and that lymphocytic choriomeningitis virus was the causative agent of the illnesses in 3 other antibody-positive persons in this study. The results of this study suggest that Tacaribe serocomplex viruses native to North America, as well as lymphocytic choriomeningitis virus, are causative agents of human disease in the United States.

The delicate pygmy rice rat (Oligoryzomys delicatus) is the principal host of Maporal virus (family Bunyaviridae, genus Hantavirus).

Choclo virus (CHOV) and Maporal virus (MAPV) are enzootic in Panama and western Venezuela, respectively. The results of previous studies suggested that the fulvous pygmy rice rat (Oligoryzomys fulvescens) is the principal host of both viruses. The results of an analysis of nucleotide sequence data in this study indicated that the rodent associated with CHOV is the Costa Rican pygmy rice rat (Oligoryzomys costaricensis) and that the rodent associated with MAPV is the delicate pygmy rice rat (Oligoryzomys delicatus). As such, MAPV is ecologically distinct from CHOV and should be considered a species separate from CHOV.

Geographical range of Rio Mamoré virus (family Bunyaviridae, genus Hantavirus) in association with the small-eared pygmy rice rat (Oligoryzomys microtis).

Hantavirus HTN.007 was originally isolated from a small-eared pygmy rice rat (Oligoryzomys microtis) captured in northeastern Peru. The results of analyses of nucleotide and amino acid sequence data in this study indicated that HTN.007 is a strain of Rio Mamoré virus (RIOMV) which is enzootic in small-eared pygmy rice rat populations in Bolivia. As such, the results of this study extend our knowledge of the geographical range of RIOMV and support the notion that the small-eared pygmy rice rat is the principal host of RIOMV.