Modelling the time-dependent transmission rate for porcine circovirus type 2 (PCV2) in pigs using data from serial transmission experiments

Assessment of sow herd frequency of PCV-2 using placental umbilical cord serum and serology in 18 breeding farms in Brazil

Porcine circovirus type 2 (PCV-2) is the agent of one of the most important diseases in the swine industry. Although it has been controlled through vaccination, viremic piglets at birth may represent a risk by reducing vaccination efficacy. Since there are few reports on the viremic status of pre-suckling piglets regarding PCV-2 infection, we assessed the PCV-2 frequency in sows housed in 18 breeding farms with no history of clinical PCVAD in Brazil, using placental umbilical cord serum (PUCS). The selection criteria were: breeding farms with more than 1,000 sows; sows not vaccinated for PCV-2 at least for 2 years prior to the study; farms with no history of PCV-2 clinical disease in the last 12 months; and production systems with a maximum of two sites. Blood from the umbilical cords in sow placenta or directly from piglet's immediately after birth was collected from 30 litters on each farm for PCR. In addition, blood from 538 sows was collected for PCV-2 antibody detection. A total of 17.29% of the PUCS tested positive. The PCV-2 DNA was detected in PUCS from 94.4% of all farms. A total of 94.8% of the sows was positive for PCV-2 antibodies. However, seronegative sows were detected in 44.4% of farms. All 18 farms had at least 46.9% seropositive dams. A higher percentage of seronegative sows was observed for farms with more than 10% of PCV-2-positive litters compared to those with ≤10% of PCV-2 positive litters (8.9 +/-1.7% vs. 1.5 +/- 0.7%, p < 0.01, respectively).

Modelling infectious viral diseases in swine populations: a state of the art

Mathematical modelling is nowadays a pivotal tool for infectious diseases studies, completing regular biological investigations. The rapid growth of computer technology allowed for development of computational tools to address biological issues that could not be unravelled in the past. The global understanding of viral disease dynamics requires to account for all interactions at all levels, from within-host to between-herd, to have all the keys for development of control measures. A literature review was performed to disentangle modelling frameworks according to their major objectives and methodologies. One hundred and seventeen articles published between 1994 and 2020 were found to meet our inclusion criteria, which were defined to target papers representative of studies dealing with models of viral infection dynamics in pigs. A first descriptive analysis, using bibliometric indexes, permitted to identify keywords strongly related to the study scopes. Modelling studies were focused on particular infectious agents, with a shared objective: to better understand the viral dynamics for appropriate control measure adaptation. In a second step, selected papers were analysed to disentangle the modelling structures according to the objectives of the studies. The system representation was highly dependent on the nature of the pathogens. Enzootic viruses, such as swine influenza or porcine reproductive and respiratory syndrome, were generally investigated at the herd scale to analyse the impact of husbandry practices and prophylactic measures on infection dynamics. Epizootic agents (classical swine fever, foot-and-mouth disease or African swine fever viruses) were mostly studied using spatio-temporal simulation tools, to investigate the efficiency of surveillance and control protocols, which are predetermined for regulated diseases. A huge effort was made on model parameterization through the development of specific studies and methodologies insuring the robustness of parameter values to feed simulation tools. Integrative modelling frameworks, from within-host to spatio-temporal models, is clearly on the way. This would allow to capture the complexity of individual biological variabilities and to assess their consequences on the whole system at the population level. This would offer the opportunity to test and evaluate in silico the efficiency of possible control measures targeting specific epidemiological units, from hosts to herds, either individually or through their contact networks. Such decision support tools represent a strength for stakeholders to help mitigating infectious diseases dynamics and limiting economic consequences.

How mechanistic modelling supports decision making for the control of enzootic infectious diseases

Controlling enzootic diseases, which generate a large cumulative burden and are often unregulated, is needed for sustainable farming, competitive agri-food chains, and veterinary public health. We discuss the benefits and challenges of mechanistic epidemiological modelling for livestock enzootics, with particular emphasis on the need for interdisciplinary approaches. We focus on issues arising when modelling pathogen spread at various scales (from farm to the region) to better assess disease control and propose targeted options. We discuss in particular the inclusion of farmers' strategic decision-making, the integration of within-host scale to refine intervention targeting, and the need to ground models on data.

Tackling hepatitis E virus spread and persistence on farrow-to-finish pig farms: Insights from a stochastic individual-based multi-pathogen model

Hepatitis E virus (HEV) is a zoonotic agent of which domestic pigs have been recognised as the main reservoir in industrialised countries. The great variability in HEV infection dynamics described on different pig farms may be related to the influence of other pathogens, and in particular viruses affecting pigs' immune response. The objective of this study was to develop a multi-pathogen modelling approach to understand the conditions under which HEV spreads and persists on a farrow-to-finish pig farm taking into account the fact that pigs may be co-infected with an intercurrent pathogen. A stochastic individual-based model was therefore designed that combines a population dynamics model, which enables us to take different batch rearing systems into account, with a multi-pathogen model representing at the same time the dynamics of both HEV and the intercurrent pathogen. Based on experimental and field data, the epidemiological parameters of the HEV model varied according to the pig's immunomodulating virus status. HEV spread and persistence was found to be very difficult to control on a farm with a 20-batch rearing system. Housing sows in smaller groups and eradicating immunomodulating pathogens would dramatically reduce the prevalence of HEV-positive livers at slaughter, which would drop from 3.3% to 1% and 0.2% respectively (p-value < 0.01). It would also decrease the probability of HEV on-farm persistence from 0.6 to 0 and 0.34 respectively (p-value < 0.01) on farms with a 7 batch rearing system. A number of farming practices, such as limiting cross-fostering, reducing the size of weaning pens and vaccinating pigs against immunomodulating viruses, were also shown to be pivotal factors for decreasing HEV spread and persistence.

Natural viral co-infections in pig herds affect hepatitis E virus (HEV) infection dynamics and increase the risk of contaminated livers at slaughter

Hepatitis E virus (HEV) is a zoonotic pathogen, in particular genotype 3 HEV is mainly transmitted to humans through the consumption of contaminated pork products. This study aimed at describing HEV infection patterns in pig farms and at assessing the impact of immunomodulating co-infections namely Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Porcine Circovirus Type 2 (PCV2), as well as other individual factors such as piglets' immunity and litters' characteristics on HEV dynamics. A longitudinal follow-up was conducted in three farrow-to-finish farms known to be HEV infected. Overall, 360 piglets were individually monitored from birth to slaughter with regular blood and faecal sampling as well as blood and liver samples collected at slaughterhouse. Virological and serological analyses were performed to detect HEV, PCV2 and PRRSV genome and antibodies. The links between 12 explanatory variables and four outcomes describing HEV dynamics were assessed using cox-proportional hazard models and logistic regression. HEV infection dynamics was found highly variable between farms and in a lower magnitude between batches. HEV positive livers were more likely related to short time-intervals between HEV infection and slaughter time (<40 days, OR = 4.1 [3.7-4.5]). In addition to an influence of piglets' sex and sows' parity, the sequence of co-infections was strongly associated with different HEV dynamics: a PRRSV or PCV2/PRRSV pre- or co-infection was associated with a higher age at HEV shedding (Hazard Ratio = 0.3 [0.2-0.5]), as well as a higher age at HEV seroconversion (HR = 0.5 [0.3-0.9] and HR = 0.4 [0.2-0.7] respectively). A PCV2/PRRSV pre- or co-infection was associated with a longer duration of shedding (HR = 0.5 [0.3-0.8]). Consequently, a PRRSV or PCV2/PRRSV pre- or co-infection was strongly associated with a higher risk of having positive livers at slaughter (OR = 4.1 [1.9-8.9] and OR = 6.5 [3.2-13.2] respectively). In conclusion, co-infections with immunomodulating viruses were found to affect HEV dynamics in the farrow-to-finish pig farms that were followed in this study.

A commercial PCV2a-based vaccine significantly reduces PCV2b transmission in experimental conditions

Transmission characteristics of PCV2 have been compared between vaccinated and non-vaccinated pigs in experimental conditions. Twenty-four Specific Pathogen Free (SPF) piglets, vaccinated against PCV2 at 3weeks of age (PCV2a recombinant CAP protein-based vaccine), were inoculated at 15days post-vaccination with a PCV2b inoculum (6⋅10(5) TCID50), and put in contact with 24 vaccinated SPF piglets during 42days post-inoculation. Those piglets were shared in six replicates of a contact trial involving 4 inoculated piglets mingled with 4 susceptible SPF piglets. Two replicates of a similar contact trial were made with non-vaccinated pigs. Non vaccinated animals received a placebo at vaccination time and were inoculated the same way and at the same time as the vaccinated group. All the animals were monitored twice weekly using quantitative real-time PCR and ELISA for serology until 42days post-inoculation. The frequency of infection and the PCV2 genome load in sera of the vaccinated pigs were significantly reduced compared to the non-vaccinated animals. The duration of infectiousness was significantly different between vaccinated and non-vaccinated groups (16.6days [14.7;18.4] and 26.6days [22.9;30.4] respectively). The transmission rate was also considerably decreased in vaccinated pigs (β=0.09 [0.05-0.14] compared to β=0.19 [0.11-0.32] in non-vaccinated pigs). This led to an estimated reproduction ratio of 1.5 [95% CI 0.8 - 2.2] in vaccinated animals versus 5.1 [95% CI 2.5 - 8.2] in non-vaccinated pigs when merging data of this experiment with previous trials carried out in same conditions.

Modelling the within-herd transmission of Mycoplasma hyopneumoniae in closed pig herds

Background

A discrete time, stochastic, compartmental model simulating the spread of Mycoplasma hyopneumoniae within a batch of industrially raised pigs was developed to understand infection dynamics and to assess the impact of a range of husbandry practices. A ‘disease severity’ index was calculated based on the ratio between the cumulative numbers of acutely and chronically diseased and infectious pigs per day in each age category, divided by the length of time that pigs spent in this age category. This is equal to the number of pigs per day, either acutely or chronically infectious and diseased, divided by the number of all pigs per all days in the model. The impact of risk and protective factors at batch level was examined by adjusting ‘acclimatisation of gilts’, ‘length of suckling period’, ‘vaccination of suckling pigs against M. hyopneumoniae’, ‘contact between fattening pigs of different age during restocking of compartments’ and ‘co-infections in fattening pigs’.

Results

The highest ‘disease severity’ was predicted, when gilts do not have contact with live animals during their acclimatisation, suckling period is 28 days, no vaccine is applied, fatteners have contact with pigs of other ages and are suffering from co-infections. Pigs in this scenario become diseased/infectious for 26.1 % of their lifetime. Logistic regression showed that vaccination of suckling pigs was influential for ‘disease severity’ in growers and finishers, but not in suckling and nursery pigs. Lack of contact between gilts and other live pigs during the acclimatisation significantly influenced the ‘disease severity’ in suckling pigs but had less impact in growing and finishing pigs. The length of the suckling period equally affected the severity of the disease in all age groups with the strongest association in nursery pigs. The contact between fatteners of different groups influenced the course of infection among finishers, but not among other pigs. Finally, presence of co-infections was relevant in growers and finishers, but not in younger pigs.

Conclusion

The developed model allows comparison of different prevention programmes and strategies for controlling transmission of M. hyopneumoniae.

Electronic supplementary material

The online version of this article (doi:10.1186/s40813-016-0026-1) contains supplementary material, which is available to authorized users.

A novel epidemiological model to better understand and predict the observed seasonal spread of Pestivirus in Pyrenean chamois populations

Seasonal variations in individual contacts give rise to a complex interplay between host demography and pathogen transmission. This is particularly true for wild populations, which highly depend on their natural habitat. These seasonal cycles induce variations in pathogen transmission. The seasonality of these biological processes should therefore be considered to better represent and predict pathogen spread. In this study, we sought to better understand how the seasonality of both the demography and social contacts of a mountain ungulate population impacts the spread of a pestivirus within, and the dynamics of, this population. We propose a mathematical model to represent this complex biological system. The pestivirus can be transmitted both horizontally through direct contact and vertically in utero. Vertical transmission leads to abortion or to the birth of persistently infected animals with a short life expectancy. Horizontal transmission involves a complex dynamics because of seasonal variations in contact among sexes and age classes. We performed a sensitivity analysis that identified transmission rates and disease-related mortality as key parameters. We then used data from a long-term demographic and epidemiological survey of the studied population to estimate these mostly unknown epidemiological parameters. Our model adequately represents the system dynamics, observations and model predictions showing similar seasonal patterns. We show that the virus has a significant impact on population dynamics, and that persistently infected animals play a major role in the epidemic dynamics. Modeling the seasonal dynamics allowed us to obtain realistic prediction and to identify key parameters of transmission.

Transmission characteristics and optimal diagnostic samples to detect an FMDV infection in vaccinated and non-vaccinated sheep

We wanted to quantify transmission of FMDV Asia-1 in sheep and to evaluate which samples would be optimal for detection of an FMDV infection in sheep. For this, we used 6 groups of 4 non-vaccinated and 6 groups of 4 vaccinated sheep. In each group 2 sheep were inoculated and contact exposed to 2 pen-mates. Viral excretion was detected for a long period (>21 days post-inoculation, dpi). Transmission of FMDV occurred in the non-vaccinated groups (R0=1.14) but only in the first week after infection, when virus shedding was highest. In the vaccinated groups no transmission occurred (Rv<1, p=0.013). The viral excretion of the vaccinated sheep and the viral load in their pens was significantly lower than that of the non-vaccinated sheep. FMDV could be detected in plasma samples from 12 of 17 infected non-vaccinated sheep, for an average of 2.1 days, but in none of the 10 infected vaccinated sheep. In contrast, FMDV could readily be isolated from mouth swab samples from both non-vaccinated and vaccinated infected sheep starting at 1-3 dpi and in 16 of 27 infected sheep up till 21 dpi. Serologically, after 3-4 weeks, all but one of the infected sheep were detected using the NS-ELISA. We conclude that vaccination of a sheep population would likely stop an epidemic of FMDV and that the use of mouth swab samples would be a good alternative (instead of using vesicular lesions or blood samples) to detect an FMD infection in a sheep population both early and prolonged after infection.

Transmission of porcine circovirus type 2b (PCV2b) in Kunming mice

To investigate porcine circovirus type 2b (PCV2b) transmission by contact and vertical infection in Kunming mice (an outbred mouse stock deriving from Swiss albino mice with a high ratio of gene heterozygosis), four mice in cage 6 were inoculated with PCV2b and 25 mice without any treatment were placed into cages 1 to 5 (five mice in each cage). Seven days after being infected, the PCV2-binoculated mice were co-mingled with non-inoculated mice from cages 1 to 5 successively at 7, 14, 21, 28 and 35 days post infection (dpi), respectively, for 3 days. In addition, eleven pregnant mice were injected with PCV2b. Samples were collected from non-inoculated mice and three newborn mice from each litter for PCV2b detection by polymerase chain reaction (PCR) and immunohistochemistry (IHC). The PCR results showed that PCV2b transmission rate among mice in cages 1, 2, 3, 4 and 5 was 0/5, 2/5, 5/5, 5/5 and 1/5, respectively. PCV2b antigen signals generally appeared in most organs of the non-inoculated mice in which viruses were detected by PCR. PCV2b DNA was also detected in newborn mice of PCV2b-infected litters, and viral antigen signals were observed in their organs as well. PCV2b was transmitted in Kunming mice by contact, and it also caused vertical infection through the placenta.

Experimental airborne transmission of porcine postweaning multisystemic wasting syndrome

The objective of these studies was to investigate if porcine postweaning multisystemic wasting syndrome (PMWS) could be induced in healthy pigs following contact with air from pigs with clinical signs of PMWS. The pigs were housed in different units. Either 31 (study I) or 25 (study II) pigs with clinical symptoms of PMWS from a PMWS-affected herd and 25 healthy pigs from a PMWS-free, but PCV2-positive, herd were housed in unit A. Fifty pigs from a PMWS-free herd were housed in unit B, which were connected by pipes to unit A. In unit C, 30 pigs from a PMWS-free herd were housed as controls. In study II, the pigs in units A and B from the PMWS-free herd developed clinical signs of PMWS 2-3 weeks after arrival. PMWS was confirmed at necropsy and the diseased pigs had increased PCV2 load and increased antibody titers against PCV2 in serum that coincided with the development of clinical signs typical of PMWS. Sequence analysis revealed that the PCV2 isolate belonged to genotype 2b. In conclusion, the present study showed that PMWS can be induced in pigs from a PMWS-free herd by airborne contact with pigs from a PMWS-affected herd.

Infectiousness of pigs infected by the Porcine Reproductive and Respiratory Syndrome virus (PRRSV) is time-dependent

The time-dependent transmission rate of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and the correlation between infectiousness, virological parameters and antibody responses of the infected pigs were studied in experimental conditions. Seven successive transmission trials involving a total of 77 specific pathogen-free piglets were carried out from 7 to 63 days post-inoculation (dpi). A semi-quantitative real time RT-PCR was developed to assess the evolution of the viral genome load in blood and nasal swabs from inoculated and contact pigs, with time. Virus genome in blood was detectable in inoculated pigs from 7 to 77 dpi, whereas viral genome shedding was detectable from nasal swabs from 2 to 48 dpi. The infectiousness of inoculated pigs, assessed from the frequency of occurrence of infected pigs in susceptible groups in each contact trial, increased from 7 to 14 dpi and then decreased slowly until 42 dpi (3, 7, 2, 1 and 0 pigs infected at 7, 14, 21, 28 and 42 dpi, respectively). These data were used to model the time-dependent infectiousness by a lognormal-like function with a latency period of 1 day and led to an estimated basic reproduction ratio, R₀ of 2.6 [1.8, 3.3]. The evolution of infectiousness was mainly correlated with the time-course of viral genome load in the blood whereas the decrease of infectiousness was strongly related to the increase in total antibodies.

Naked PCV-2 cloned genomic DNA is infectious by mucosal (intratracheal or oro-nasal) inoculation

Porcine circovirus type 2 (PCV-2) is involved in several diseases named porcine circovirus-associated diseases and is transmitted by oro-faecal route. In this study we inoculated porcine-circovirus free piglets by mucosal routes (intratracheal or oro-nasal routes) with a plasmid carrying two copies of PCV-2 genomic DNA and compared the results to the intramuscular route. We observed that this PCV-2 naked DNA serves as template for viral replication and infectious PCV-2 particles are detected in the whole body after parenteral (intramuscular) or mucosal (intratracheal or oro-nasal) delivery. These results suggest that PCV-2 genome could play a role in in vivo transmission.

Estimation of transmission parameters of a fluoroquinolone-resistant Escherichia coli strain between pigs in experimental conditions

Antimicrobial resistance is of primary importance regarding public and animal health issues. Persistence and spread of resistant strains within a population contribute to the maintenance of a reservoir and lead to treatment failure. An experimental trial was carried out to study the horizontal transmission of a fluoroquinolone-resistant Escherichia coli strain from inoculated to naïve pigs. All naïve contact pigs had positive counts of fluoroquinolone-resistant E. coli after only two days of contact. Moreover, re-infections of inoculated pigs caused by newly contaminated animals were suspected. A maximum likelihood method, based on a susceptible-infectious-susceptible (SIS) model, was used to determine the transmission parameters. Two transmission levels were identified depending on the quantity of bacteria shed by infected individuals: (i) low-shedders with bacterial counts of resistant E. coli in the faeces between 5*10³ and 10⁶ CFU/g (β_L = 0.41 [0.27; 0.62]), (ii) high shedders with bacterial counts above 10⁶ CFU/g (β_H = 0.98 [0.59; 1.62]). Hence, transmission between animals could be pivotal in explaining the persistence of resistant bacteria within pig herds.

Epidemiology and horizontal transmission of porcine circovirus type 2 (PCV2)

Porcine circovirus type 2 (PCV2) is a small, non-enveloped, circular, single-stranded DNA virus of economic importance in the swine industry worldwide. Based on the sequence analyses of PCV2 strains, isolates can be divided into five subtypes (PCV2a–e). PCV2 is an ubiquitous virus based on serological and viremia data from countries worldwide. In addition, PCV2 DNA was discovered in archived samples prior to the first recognition of clinical disease. Recently, a worldwide shift in PCV2 subtype from PCV2a to PCV2b occurred. PCV2 DNA can be detected in fecal, nasal, oral and tonsillar swabs as well as in urine and feces from both naturally and experimentally infected pigs. PCV2 DNA can be detected early in the infectious process and persists for extended periods of time. The effectiveness of disinfectants for reducing PCV2in vitrois variable and PCV2 is very stable in the pig environment. Limited data exist on the horizontal transmission of PCV2. Direct transmission of PCV2 between experimentally or naturally infected animals and naïve animals has been documented and the incorporation of clinical or subclinically infected animals into a population represents a risk to the herd. Indirect transmission through the oral, aerosol or vaccine routes is likely a lesser risk for the transmission of PCV2 in most swine populations but may be worth evaluating in high heath herds. The objective of this review was to discuss data on the epidemiology and horizontal transmission of PCV2.

Model or meal? Farm animal populations as models for infectious diseases of humans

In recent decades, theory addressing the processes that underlie the dynamics of infectious diseases has progressed considerably. Unfortunately, the availability of empirical data to evaluate these theories has not grown at the same pace. Although laboratory animals have been widely used as models at the organism level, they have been less appropriate for addressing issues at the population level. However, farm animal populations can provide empirical models to study infectious diseases at the population level.

Influence of husbandry and control measures on porcine circovirus type 2 (PCV-2) dynamics within a farrow-to-finish pig farm: a modelling approach

We assessed, using a modelling approach, the influence of several management practices within a farrow-to-finish farm on the age of PCV-2 infection. The impact of PCV-2 vaccination with different vaccination schemes on infection dynamics, was also tested. A stochastic individual-based model describing the population dynamics in a typical French farrow-to-finish pig farm was built and coupled with an epidemiological model of PCV-2 infection. The parameters of the infectious model were mainly obtained from previous transmission experiments. Results were subjected to a survival analysis of time-to-infection. For each comparison, the reference situation was no vaccination followed by random mixing of piglets after birth and after weaning. The risk of early infection was significantly reduced when mixing of piglets was reduced at different stages (avoiding cross-fostering and grouping piglets by litters in small pens after weaning, hazard ratio (HR)=0.52 [0.46; 0.59]). Sow-targeted vaccination delayed the infectious process until the waning of passive immunity and piglet-targeted vaccination considerably decreased the force of infection leading to a dramatic decrease of the total number of infections (HR=0.44 [0.37; 0.54]). The effect was even more pronounced when strict management measures were applied (HR=0.24 [0.19; 0.31]). Changing from a low (3%) prevalence of PCV-2-infected semen to a higher one (18%) significantly increased the risk of early infections (HR=1.36 [1.2; 1.53]), whereas reducing replacement rate or changing sow housing from individual crates to group housing had a limited impact on PCV-2 dynamics.