Abstract:

Marsh rice rats were captured and dissected in June 2013-2017 at four oiled, three unoiled, and three reference sites. Blood was collected from mark and release animals, and a subset of rice rats were dissected for tissue samples. Total RNA was isolated from lung and kidney tissues so that viral RNA (belonging to a hantavirus strain, called Bayou virus) might be detected by qRT-PCR. Whole blood or serum samples were screened by immunofluorescent assays to detect antibodies for hantaviruses. In addition to this data, sample collection information is also reported.

Suggested Citation:

Perez-Umphrey, A., Taylor, S.. 2020. Bayou virus screening data of marsh rice rats (Oryzomys palustris) trapped on oiled and unoiled plots in Plaquemines Parish, Louisiana, 2013-06-03 to 2017-07-02. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-383p-6k11

Purpose:

Marsh rice rats are the primary reservoir host for Bayou virus, a hantavirus which causes a fatal disease in humans. We screened for viral RNA and antibodies in marsh rice rats to determine which individuals were infected with the virus. These animals were collected from sites differentially affected by the 2010 Deepwater Horizon oil spill.

Data Parameters and Units:

Date collected: Date animal was dissected (DD-MM-YYYY); Ear Tag (L): Unique numeric identifier of tags placed on left ear (NA=no ear tag present); Ear Tag (R): Unique numeric identifier of tags placed on right ear (NA=no ear tag present); PIT Tag ID: Unique alphanumeric identifier of the tag placed subcutaneously between the shoulder blades (NA=no PIT tag present); Diss ID: Unique identifier given to an animal that died during handling but was a new capture (i.e. had no other ID). NA=not applicable; Site: User-defined site identifier; Latitude: Latitude of the center of the sampling plot in decimal degrees; Longitude: Longitude of the center of the sampling plot in decimal degrees; Sex: Animal sex identified in the field using secondary sexual characteristics (F=female, M=male); Age: Animal age identified by weight class (J=juveniles-animals less than 30g, SA=subadults-animals 30-44g, A=adults-animals over 45g); Tissue: Tissue type used in viral RNA screening by qRT-PCR (Lung, Kidney). NA=not applicable; Date RNA extraction: Date that total RNA was extracted from tissue (DD-MMM-YY). NA=not applicable; Date qRTPCR: Date that total RNA was screened for viral RNA by qRT-PCR (DD-MMM-YY). NA=not applicable; Mean Ct value (Sample): A value between 0-40 that indicates the mean qPCR cycle threshold for that sample (values over 40 could not be read by the machine and are designated as "UNDETERMINED"). NA=not applicable; Mean Ct (Standard 10^1): A value between 0-40 that indicates the mean qPCR cycle threshold for plasmid diluted to 10^1. (values over 40 could not be read by the machine and are designated as "UNDETERMINED"). NA=not applicable; Mean Ct (Standard 10^2): A value between 0-40 that indicates the mean qPCR cycle threshold for plasmid diluted to 10^2. (values over 40 could not be read by the machine and are designated as "UNDETERMINED"). NA=not applicable; Mean Ct (Standard 10^3): A value between 0-40 that indicates the mean qPCR cycle threshold for plasmid diluted to 10^3. (values over 40 could not be read by the machine and are designated as "UNDETERMINED"). NA=not applicable; Mean Ct (Standard 10^4): A value between 0-40 that indicates the mean qPCR cycle threshold for plasmid diluted to 10^4. (values over 40 could not be read by the machine and are designated as "UNDETERMINED"). NA=not applicable; Mean Ct (Standard 10^5): A value between 0-40 that indicates the mean qPCR cycle threshold for plasmid diluted to 10^5. (values over 40 could not be read by the machine and are designated as "UNDETERMINED"). NA=not applicable; Mean Ct (Standard 10^6): A value between 0-40 that indicates the mean qPCR cycle threshold for plasmid diluted to 10^6. (values over 40 could not be read by the machine and are designated as "UNDETERMINED"). NA=not applicable; Mean Ct (Standard 10^7): A value between 0-40 that indicates the mean qPCR cycle threshold for plasmid diluted to 10^7. (values over 40 could not be read by the machine and are designated as "UNDETERMINED"). NA=not applicable; Mean Ct (Standard 10^8): A value between 0-40 that indicates the mean qPCR cycle threshold for plasmid diluted to 10^8. (values over 40 could not be read by the machine and are designated as "UNDETERMINED"). NA=not applicable; Final Score (qRT-PCR): Infection status decided by the user according to the mean Ct value in the qRT-PCR run (NEG=negative/uninfected, POS=positive/ infected, UNKNOWN=test was inconclusive or failed). NA=not applicable; Blood Type: Type of blood sample used in immunofluorescent assays (Whole Blood, Serum, Clots). NA=not applicable; Date IFA: Date that a blood sample was screened for antibodies to hantavirus by immunofluorescent assay (DD-MMM-YY). NA=test not run for this sample; Final Score (IFA): Infection status decided by the user according to the presence of fluorescent antibodies in the immunofluorescent assay at a 1 to 10 dilution (NEG=negative/uninfected, POS=positive/infected). NA=not applicable; Titires: End-point antibody titres for ‘POS’ individuals. NA=not applicable. NYT=not yet tested.

Methods:

Marsh rice rats were trapped on oiled and unoiled sites in Barataria Bay from 2013 to 2017. They were trapped using Sherman live traps. If an individual was a recapture, that animal’s unique ear tag and/or PIT tag identification was recorded. If the individual was a new capture, it received either ear tags on one ear (the 2013 field season), both ears (2014-2016 field seasons), or if it was an adult over 30g, a PIT tag (the 2017 field season). PIT tags were implanted subcutaneously between the shoulder blades using a spring-loaded implanter and 12-gauge needles. All animals were scanned using a PIT tag reader to detect any implanted tags. Captured adults over 30g were bled via the retro-orbital venous complex. A subset of animals caught on the final day of trapping at each site was dissected for tissue and blood harvest. Animals were euthanized by asphyxiation with isoflurane followed by decapitation. Tissues were removed, placed in cryovials, and flash-frozen in liquid nitrogen then stored at -80C until processing. Blood was collected following decapitation with capillary tubes, then placed in cryovials, and flash-frozen in liquid nitrogen then stored at -80C until processing. Total RNA was extracted from tissue samples which were then screened by qRT-PCR (quantitative real-time polymerase chain reaction) for viral RNA using the QuantStudio 6 System. Blood samples were screened for hantavirus-specific antibodies by immunofluorescent assay, where, if antibodies were present, they would fluoresce under magnification with a fluorescent microscope.

Instruments:

Sherman live traps: Used to trap marsh rice rats; Ear tag applier: Used to tag marsh rice rat ears; 1cm ear tags: Metal tags used to identify individual marsh rice rats; PIT tag implanter: Spring-loaded implanter to implant PIT tags subcutaneously between the shoulder blades using disposable needles; 12.5mm PIT tags: Passive integrated transponder tags used to identify individual marsh rice rats; PIT tag reader: Handheld tag reader used to scan marsh rice rats for implanted PIT tags; Liquid nitrogen tank: Used to flash freeze collected blood and tissue samples; Cryovials: Tubes to store tissue and blood samples in liquid nitrogen; Dissection scissors: Laboratory scissors used to decapitate and remove tissues from the body cavity of marsh rice rats; Dissection tweezers: Laboratory tweezers used to remove tissues from the body cavity of marsh rice rats; puC57 plasmid: Diluted in 10-fold dilutions to generate a standard curve against which to measure qRT-PCR data against QuantStudio 6 Real-Time PCR System: Quantitative PCR machine to measure the quantity of viral RNA in marsh rice rat tissues; Leica DM6B Fluorescent Microscope: Microscope used to detect antibodies in the blood of infected marsh rice rats; Biological Safety Cabinet: A laboratory hood where potentially infected tissue and blood samples could be safely handled.

Individual Files: