Evolution and diversity of bat and rodent Paramyxoviruses from North America

Abstract

Paramyxoviruses are a diverse group of negative-sense, single-stranded RNA viruses of which several species cause significant mortality and morbidity. In recent years the collection of paramyxoviruses sequences detected in wild mammals has substantially grown, however little is known about paramyxovirus diversity in North American mammals. To better understand natural paramyxovirus diversity, host range, and host specificity, we sought to comprehensively characterize paramyxoviruses across a range of diverse co-occurring wild small mammals in Southern Arizona. We used highly degenerate primers to screen fecal and urine samples and obtained a total of 55 paramyxovirus sequences from 12 rodent species and 6 bat species. We also performed illumina RNA-seq and de novo assembly on 14 of the positive samples to recover a total of 5 near full-length viral genomes. We show there are at least 2 well-supported clades of rodent-borne paramyxoviruses, while bat-associated paramyxoviruses formed a putative single well-supported clade. Using structural homology modeling of the viral attachment protein, we infer that three of the five novel viruses likely bind sialic acid in a manner similar to other Respiroviruses, while the other two viruses from Heteromyid rodents likely bind a novel host receptor. We find no evidence for cross-species transmission, even among closely related sympatric host species. Taken together, these data suggest paramyxoviruses are a common viral infection in some bat and rodent species present in North America, and illuminate the evolution of these viruses.

The characterization of multiple novel paramyxovirus species highlights the diverse nature of the subfamily Orthoparamyxovirinae

“…Using our new assay, we found >33% of the animals in this study to be positive for paramyxoviruses. Even though this study had a limited sample size and the possibility of false negatives due to insufficient viral load or a too divergent sequence cannot be excluded, this percentage seems to fall in line with what has previously been reported in paramyxovirus screening studies of small mammals [18,30,43]. However, few previous studies have reported a similarly broad diversity as observed here, which might be attributable to the newly designed primer sets used in this study, as most previous studies were performed using the seminested assays developed by Tong and colleagues.…”

“…In recent years, many new orthoparamyxoviruses have been discovered and several of them are assumed to be pathogenic for animals or even humans. Especially the genus Jeilongvirus has seen a rapid expansion, with new member species being discovered primarily in rodents and bats, but also in carnivores and Eulipotyphla [9][10][11][12][13][14][15][16][17][18]. Furthermore, PCR-based screening studies have shown that much of the orthoparamyxovirus diversity remains to be properly characterized [19][20][21][22][23][24][25][26][27][28][29][30][31].…”

Discovery of three cycloviruses in fecal samples from silver-haired bats (Lasionycteris noctivagans) in Arizona (USA)

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RNA viruses [4][5][6]. However, limited discovery work has been done on bat-associated viruses in Arizona [7][8][9], even through southern Arizona harbors the greatest diversity of bats of any comparably sized region in the United States of America [2].Our field research was conducted in Madrean evergreenwoodland on Cave Creek in the Chiricahua Mountains (Cochise County, Arizona). To capture bats, we deployed mist nets (2.6, 4, and 6 m; Avinet Inc., Portland, ME) across areas of calm water on sections of Cave Creek where the Bats (order Chiroptera) are one of the most abundant and diverse groups of mammals, with 1,448 extant species currently recognized [1,2].

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“…RNA viruses [4][5][6]. However, limited discovery work has been done on bat-associated viruses in Arizona [7][8][9], even through southern Arizona harbors the greatest diversity of bats of any comparably sized region in the United States of America [2].…”