Distribution and prevalence of Sin Nombre hantavirus in rodent species in eastern New Mexico.

Orthohantaviruses are diverse zoonotic RNA viruses. Small mammals, such as mice and rats are common chronic, asymptomatic hosts that transmit the virus through their feces and urine. In North America, hantavirus infection primarily causes hantavirus cardiopulmonary syndrome (HCPS), which has a mortality rate of nearly 36%. In the United States of America, New Mexico (NM) is leading the nation in the number of HCPS-reported cases (N = 129). However, no reported cases of HCPS have occurred within eastern NM. In this study, we assessed the prevalence of Sin Nombre virus (SNV) in rodent assemblages across eastern NM, using RT-qPCR. We screened for potential rodent hosts in the region, as well as identified areas that may pose significant infection risk to humans. We captured and collected blood and lung tissues from 738 rodents belonging to 23 species. 167 individuals from 16 different species were positive for SNV RNA by RT-qPCR, including 6 species unreported in the literature: Onychomys leucogaster (Northern grasshopper mouse), Dipodomys merriami (Merriam's kangaroo rat), Dipodomys ordii (Ord's kangaroo rat), Dipodomys spectabilis (Banner-tailed kangaroo rat), Perognathus flavus (Silky pocket mouse), and Chaetodipus hispidus (Hispid pocket mouse). The infection rates did not differ between sexes or rodent families (i.e., Cricetidae vs. Heteromyidae). Generalized linear model showed that disturbed habitat types positively influenced the prevalence of SNV at sites of survey. Overall, the results of this study indicate that many rodent species in east New Mexico have the potential to maintain SNV in the environment, but further research is needed to assess species specific infectivity mechanisms and potential risk to humans

A summary of RT-qPCR results tested for Sin Nombre Virus (SNV) across all rodents captured during 2020 and 2021 surveys in east New Mexico.

Each species is split according to the sex category. “+” represents the number of positive individuals within the category.</p

Fig 2 -

Map of the state of New Mexico (left) highlighting counties that have reported cases of hantavirus cardiopulmonary syndrome based on the New Mexico Department of Health data in relation to 20 sites surveyed for rodents across east New Mexico in 2020 and 2021. Map of east New Mexico (right) including the relative proportion of Cricetid and Heteromyid rodents captured across the 20 survey sites. Site numbers correspond to Table 1. Level II Ecoregion GIS data was sourced from the freely available United States Environmental Protection Agency—Ecoregion database (https://www.epa.gov/eco-research/ecoregions-north-america).</p

A summary of 20 sites surveyed for rodents from March 2020 to May 2021 across east New Mexico.

The sites were surveyed over three-consecutive nights, and the second date of survey is depicted in the table. Specific coordinates are not provided in the table due to landowner privacy. Habitat type was determined by combining the results of vegetation surveys and evaluating dominant vegetation types. Habitats that were used to grow crops, graze livestock or heavily altered by human activity in other ways were classified as disturbed.</p

A table containing the rodent capture data for 738 samples captured between 2020–2021 in eastern New Mexico, USA.

GPS coordinates were excluded from the table as some sites were on privately owned land. Results of ELISA testing are listed as "1" if the samples was seropositive for SNV and "0" if it was not. Similarly, results of qPCR are represented as "0" if SNV was not genetically detected through RT-qPCR, and "1" if it was. (XLSX)</p

Fig 3 -

Map of the state of New Mexico (left) highlighting counties that have reported cases of hantavirus cardiopulmonary syndrome based on the New Mexico Department of Health data in relation to 20 sites surveyed for rodents across east New Mexico in 2020 and 2021. Map of east New Mexico (right) displaying the SNV positivity rate of rodents captured at each survey site based on results from the RT-qPCR analyses using SNV specific primers. Site numbers correspond to Table 1. Level II Ecoregion GIS data was sourced from the freely available United States Environmental Protection Agency—Ecoregion database (https://www.epa.gov/eco-research/ecoregions-north-america).</p

A summary of the rodent species that tested positive for SNV specific antibodies through enzyme-linked immunosorbent assays (ELISAs) on the blood samples collected from the samples during this study, including the number of seropositive individuals (“+” sign) per sex as well as the overall prevalence.

Species that did not test seropositive were excluded from this table. Rodents were surveyed from March 2020 to May 2021 across 20 sites in east New Mexico.</p

A chi-square results comparing the differences in the number of SNV positive individuals based on qPCR among sex classes (i.e., male, female, and juvenile) for each site and for the overall captures between 2020–2021 in eastern New Mexico, USA.

A chi-square results comparing the differences in the number of SNV positive individuals based on qPCR among sex classes (i.e., male, female, and juvenile) for each site and for the overall captures between 2020–2021 in eastern New Mexico, USA.</p

The mean, standard deviation (SD), minimum, and maximum values of the continuous and frequency for categorical explanatory variables used in generalized linear models to estimate the prevalence of Sin Nombre Virus (SNV) in rodents of east New Mexico.

The mean, standard deviation (SD), minimum, and maximum values of the continuous and frequency for categorical explanatory variables used in generalized linear models to estimate the prevalence of Sin Nombre Virus (SNV) in rodents of east New Mexico.</p

Output of the top model that best explained the proportion of Sin Nombre Virus (SNV) positive rodents in east New Mexico based on results from the RT-qPCR analyses using SNV specific primers.

Parameter estimates and standard errors are reported on the logit scale. Disturbed land was the reference category for the habitat type.</p