DOI: 10.5061/dryad.3hd6sb6
title: Data from: Disentangling synergistic disease dynamics: Implications for the viral biocontrol of rabbits

description: European rabbits (Oryctolagus cuniculus) have been exposed to rabbit
 haemorrhagic disease virus (RHDV) and myxoma virus (MYXV) in their native
 and invasive ranges for decades. Yet, the long‐term effects of these
 viruses on rabbit population dynamics remain poorly understood. In this
 context, we analysed 17 years of detailed capture–mark–recapture data
 (2000–2016) from Turretfield, South Australia, using a probabilistic
 state‐space hierarchical modelling framework to estimate rabbit survival
 and epidemiological dynamics. While RHDV infection and disease‐induced
 death were most prominent during annual epidemics in winter and spring, we
 found evidence for continuous infection of susceptible individuals with
 RHDV throughout the year. RHDV‐susceptible rabbits had, on average, 25%
 lower monthly survival rates compared to immune individuals, while the
 average monthly force of infection in winter and spring was ~38%. These
 combined to result in an average infection‐induced mortality rate of 69%
 in winter and spring. Individuals susceptible to MYXV and immune to RHDV
 had similar survival probabilities to those having survived infections
 from both viruses, whereas individuals susceptible to both RHDV and MYXV
 had higher survival probabilities than those susceptible to RHDV and
 immune to MYXV. This suggests that MYXV may reduce the future survival
 rates of individuals that endure initial MYXV infection. There was no
 evidence for long‐term changes in disease‐induced mortality and infection
 rates for either RHDV or MYXV. We conclude that continuous, year‐round
 virus perpetuation (and perhaps heterogeneity in modes of transmission and
 infectious doses during and after epidemics) acts to reduce the efficiency
 of RHDV and MYXV as biocontrol agents of rabbits in their invasive range.
 However, if virulence can be maintained as relatively constant through
 time, RHDV and MYXV will likely continue realizing strong benefits as
 biocontrol agents.
description: Rabbit
 capture-mark-recapture and serology (disease) state dataRabbit
 capture-mark-recapture and serology (disease) state data of 2,200 selected
 rabbit individuals with unequivocal serology data for all capture events
 live-captured at Turretfield Agricultural Research Centre (34°33′S,
 138°50′E, South Australia) between January 2000 and August 2016 at 8-12
 week intervals. All live captures were uniquely marked with serially
 numbered ear tags, weighed to the nearest 10 g and sexed. Blood was
 collected from an ear vein for serological tests of rabbit haemorrhagic
 disease virus (RHDV) and myxoma virus (MYXV) antibodies. Additionally, the
 study area and warrens were regularly surveyed for dead rabbits at
 intervals ≤ four weeks, increasing to weekly searches during spring
 (Sept-Nov) when epizootics were most likely to occur, and at 1-7 day
 intervals following any evidence of disease-related mortality. Capture
 events are assigned to capture session (n = 83) The date of the capture
 session was calculated as the median date of all captures made during a
 capture session and given as the number of days elapsed after the first
 date of capture (i.e. 19/01/2000 corresponds to day count ‘1’). Capture
 sessions were also assigned to one of the following (southern hemispheric)
 seasons according to local climate: 1 = Autumn: Mar – May, 2 = Winter: Jun
 – Aug, 3 = Spring: Sept-Nov, 4 = Summer: Dec-Feb. The full data set with
 further details is hold by Biosecurity SA, Adelaide, Australia. Data are
 arranged in 7 spreadsheets with the content described below. 1) ‘y’ Table
 of capture events/ individual encounter histories y, denoting the capture
 of individuals in the different capture session as “1” if an individual
 has been captured and “0” otherwise. Individuals are identified in the
 column “indNo”, the columns entitled “trip_1” to “trip_83” refer to the
 different capture session. 2) ‘z’ Table of the (partially known) state
 variable z, denoting of whether an individual is known to be 1= alive, 0 =
 dea or NA = in an unknown state. Individuals are identified in the column
 “indNo”, the columns entitled “trip_1” to “trip_83” refer to the different
 capture session. 3) ‘d_RHDV' Table of RHDV disease state, classifying
 rabbits as 1 = seronegative (“susceptible”) 2 = seropositive kittens with
 maternal antibodies (“protected young”) and 3 = seropositive due to
 previous infection (“immune”). Individuals are identified in the column
 “indNo”, the columns entitled “trip_1” to “trip_83” refer to the different
 capture session. 4) ‘d_MYXV' Table of MYXV disease state, classifying
 rabbits as 1 = seronegative with no detectable antibodies and therefore
 susceptible to infection/disease (“susceptible”) or 2 = seropositive with
 antibodies against disease. Individuals are identified in the column
 “indNo”, the columns entitled “trip_1” to “trip_83” refer to the different
 capture session. 5) ‘individuals’ Table of individual attributes used in
 the capture-mark-recapture analysis, namely "sex": individual
 gender; "birthmin": minimum day count of possible birth date;
 "birthmax": maximum day count of possible birth date;
 "trip_LowerLimit": earliest capture session for which individual
 data are modelled according to unknown states variables z;
 "trip_UpperLimit": latest capture session for which individual
 data are modelled according to unknown state variables z. 6) ‘capture
 session’ Table of capture session classifications, with
 "trip_No": identification number of capture session “daycount”:
 day count of capture session; “season” season classification (see above);
 “year”: year of capture session (‘1’ corresponds to the year 2000);
 “deltaT”: scaling factor to account for unequal time intervals between
 capture sessions. 7) ‘individuals’ Table of body mass measures of rabbit
 individuals during various individual capture events with “indNo”:
 individual number; weight” body mass measure (in gram); “daycount”” day
 count of individual capture events.Data_Rabbit.Dz_CMR.analysis_Dryad.xlsx