Andres Perez

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Jonathan Arzt

USDA Agricultural Research Service

Makerere University

University of Nairobi, Kenya

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Papers by Andres Perez

The role of African buffalo in the epidemiology of foot-and-mouth disease in sympatric cattle and buffalo populations in Kenya

Transmission of pathogens at wildlife-livestock interfaces poses a substantial challenge to the c... more Transmission of pathogens at wildlife-livestock interfaces poses a substantial challenge to the control of infectious diseases, including for foot-and-mouth disease virus (FMDV) in African buffalo and cattle. The extent to which buffalo play a role in the epidemiology of this virus in livestock populations remains unresolved in East Africa. Here, we show that FMDV occurs at high seroprevalence (~77%) in Kenyan buffalo. In addition, we recovered 80 FMDV VP1 sequences from buffalo, all of which were serotype SAT1 and SAT2, and seventeen FMDV VP1 sequences from cattle, which included serotypes A, O, SAT1 and SAT2. Notably, six individual buffalo were co-infected with both SAT1 and SAT2 serotypes. Our results suggest that transmission of FMDV between sympatric cattle and buffalo is rare. However, viruses from FMDV outbreaks in cattle elsewhere in Kenya were caused by viruses closely related to SAT1 and SAT2 viruses found in buffalo. We also show that the circulation of FMDV in buffalo i...

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Evaluation of the Performance of the IDvet IFN-Gamma Test for Diagnosis of Bovine Tuberculosis in Spain

Frontiers in veterinary science, 2018

In Spain, the national bovine tuberculosis (bTB) eradication program is based on yearly skin test... more In Spain, the national bovine tuberculosis (bTB) eradication program is based on yearly skin testing of every ≥6 weeks old animal using the single or comparative tuberculin test and parallel use of the interferon-gamma (IFN-γ) assay as an ancillary diagnostic test in infected herds. There are several versions of the latter. Recently, a new commercial IDvet IFN-γ assay has been authorized for use in the program, but there is limited scientific evidence about its performance in different epidemiological settings. Therefore, two studies to evaluate the performance of the IDvet assay were conducted. In study 1, a concordance analysis between the new IDvet and the Bovigam IFN-γ assay in use in Spain for over 10 years was conducted. In study 2, results from the IDvet assay when applied in tandem with a single intradermal tuberculin (SIT) test were used to evaluate the concordance between both tests and to estimate their sensitivity (Se) and specificity (Sp) using a Bayesian latent-class m...

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Bayesian estimation of ELISA and gamma interferon test accuracy for the detection of bovine tuberculosis in caudal fold test-negative dairy cattle in Kuwait

Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc, 2018

Bovine tuberculosis (TB) is endemic in Kuwait; cattle identified as TB-positive using the caudal ... more Bovine tuberculosis (TB) is endemic in Kuwait; cattle identified as TB-positive using the caudal fold test (CFT) are culled. We used a Bayesian approach to estimate the sensitivity (Se) and specificity (Sp) of the IFNγ assay and ELISA, which are not routinely used in Kuwait in CFT-negative dairy cattle. Blood samples from CFT-negative cattle ( n = 384) collected from 38 dairy farms were tested by IFNγ assay and ELISA. The Se and Sp (95% CI) of the IFNγ were 85.0% (67.6-95.3%) and 90.4% (86.7-95.3%), respectively, whereas estimates for the ELISA were 61.1% (33.1-84.6%) and 85.4% (81.7-88.8%). TB prevalence (95 CI%) in CFT-negative cattle was estimated as 2.6% (0.5-9.5%). The IFNγ assay may play a role as an ancillary test for the identification of Mycobacterium bovis-infected cattle that are undetected by CFT.

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Phylogeographic analysis of the 2000-2002 foot-and-mouth disease epidemic in Argentina

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, Jul 10, 2016

Foot-and-mouth disease (FMD) is a highly transmissible disease of hooved livestock. Although FMD ... more Foot-and-mouth disease (FMD) is a highly transmissible disease of hooved livestock. Although FMD has been eradicated from many countries, economic and social consequences of FMD reintroductions are devastating. After achieving disease eradication, Argentina was affected by a major epidemic in 2000-2002, and within few months, FMD virus spread throughout most of the country and affected >2500 herds. Available records and viral strains allowed us to assess the origins, spread and progression of this FMD epidemic, which remained uncertain. We used whole genome viral sequences and a continuous phylogeographic diffusion approach, which revealed that the viruses that caused the outbreaks spread fast in different directions from a central area in Argentina. The analysis also suggests that the virus that caused the outbreaks in the year 2000 was different from those found during the 2001 epidemic. To estimate if the approximate overall genetic diversity of the virus was related to diseas...

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Association of the presence of influenza A virus and porcine reproductive and respiratory syndrome virus in sow farms with post-weaning mortality

Preventive Veterinary Medicine, 2015

Influenza A virus (IAV) and porcine reproductive and respiratory syndrome virus (PRRSV) are among... more Influenza A virus (IAV) and porcine reproductive and respiratory syndrome virus (PRRSV) are among the most important pathogens affecting pigs worldwide. Their effect on post-weaning mortality can be substantial and may be potentiated by other concomitant factors. Here, the objective was to evaluate the association between IAV and PRRSV infection at weaning with post-weaning mortality observed in wean-to-finish farms in order to better quantify the full impact of their presence in breeding herds. IAV and PRRSV presence was assessed by real time reverse transcription (RRT)-PCR on oral fluid samples from suckling piglets in nine sow farms. Production data from 177 batches of growing pigs weaned one week before/after IAV and PRRSV testing were analyzed to measure the association between IAV and/or PRRSV test results and mortality recorded for a given batch through the use of Bayesian mixed effects negative binomial multivariable regression model. The model accounted for potential confounders such as flow, date at weaning, days on feed and batch size. A statistically important association between IAV (incidence ratio (IR)=1.18, 95% posterior probability interval 1.15-1.21) and PRRSV (IR=1.41, 95% PPI 1.30-1.52) with post-weaning mortality was detected, with season and number of days on feed also associated. Our results suggest that infection with IAV or PRRSV in the pre-weaning period is associated with an increase in post-weaning mortality. This association should be taken into consideration when measuring the impact of IAV and PRRSV in breeding herds.

Parameterization of the duration of infection stages of serotype O foot-and-mouth disease virus: an analytical review and meta-analysis with application to simulation models

Veterinary Research, 2010

Foot-and-mouth disease (FMD) is considered one of the most important infectious diseases of lives... more Foot-and-mouth disease (FMD) is considered one of the most important infectious diseases of livestock because of the devastating economic consequences that it inflicts in affected regions. The value of critical parameters, such as the duration of the latency or the duration of the infectious periods, which affect the transmission rate of the FMD virus (FMDV), are believed to be influenced by characteristics of the host and the virus. Disease control and surveillance strategies, as well as FMD simulation models, will benefit from improved parameter estimation. The objective of this study was to quantify the distributions of variables associated with the duration of the latency, subclinical, incubation, and infectiousness periods of FMDV transmission. A double independent, systematic review of 19 retrieved publications reporting results from experimental trials, using 295 animals in four reference laboratories, was performed to extract individual values related to FMDV transmission. Probability density functions were fitted to data and a set of regression models were used to identify factors associated with the assessed parameters. Latent, subclinical, incubation, and infectious periods ranged from 3.1 to 4.8, 2 to 2.3, 5.5 to 6.6, and 3.3 to 5.7 days, respectively. Durations were significantly (p < 0.05) associated independently with route of exposure, type of donor, animal species, strains, characteristics of sampling, and clinical signs. These results will contribute to the improvement of disease control and surveillance strategies and stochastic models used to simulate FMD spread and, ultimately, development of cost-effective plans to prevent and control the potential spread of the disease in FMD-free regions of the world.

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Modelling and Predicting Temporal Frequency of Foot-and-Mouth Disease Cases in Countries with Endemic Foot-and-Mouth Disease

Journal of the Royal Statistical Society Series A: Statistics in Society, 2011

Summary Foot-and-mouth disease (FMD) is a highly contagious viral disease that affects a variety ... more Summary Foot-and-mouth disease (FMD) is a highly contagious viral disease that affects a variety of cloven-hoofed animals. It spreads rapidly and results in considerable economic loss for agriculture in regions where the disease occurs. The main objective of this study is to develop statistical models that will reasonably predict temporal FMD case counts in endemic regions or countries, and which will also perform well under sporadic epidemic phases that increase FMD counts beyond background endemic circumstances. We used FMD data from Iran to develop correlated data models for predicting the number of FMD cases at future times and to assess the statistical importance of risk factors for increased frequency of FMD. Model selection and validation are accomplished by using the deviance information criterion and the mean absolute prediction error.

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