Whole genome sequence phylogenetic analysis of four Mexican rabies viruses isolated from cattle

Spatial-temporal risk factors in the occurrence of rabies in Mexico

Rabies is a zoonotic disease that affects livestock worldwide. The distribution of rabies is highly correlated with the distribution of the vampire bat Desmodus rotundus, the main vector of the disease. In this study, climatic, topographic, livestock population, vampire distribution and urban and rural zones were used to estimate the risk for presentation of cases of rabies in Mexico by co- Kriging interpolation. The highest risk for the presentation of cases is in the endemic areas of the disease, i.e. the States of Yucatán, Chiapas, Campeche, Quintana Roo, Tabasco, Veracruz, San Luis Potosí, Nayarit and Baja California Sur. A transition zone for cases was identified across northern Mexico, involving the States of Sonora, Sinaloa, Chihuahua, and Durango. The variables topography, vampire distribution, bovine population and rural zones are the most important to explain the risk of cases in livestock. This study provides robust estimates of risk and spread of rabies based on geostatistical methods. The information presented should be useful for authorities responsible of public and animal health when they plan and establish strategies preventing the spread of rabies into rabies-free regions of México.

Descriptive and Time-Series Analysis of Rabies in Different Animal Species in Mexico

The spatio-temporal epidemiology of rabies has related the influence of environmental factors and anthropogenic changes on the movements of the hematophagous bat Desmodus rotundus. In Mexico, D. rotundus is the main transmitter of the rabies virus for different livestock species, modifying annually the fluctuation of the number of cases of rabies and its dissemination in subtropical areas and regions considered free of the disease. The purpose of this study was to perform a descriptive analysis of the distribution of cases of rabies in Mexico, and to perform a time-series analysis to evaluate stationarity and to predict the number of cases for the following year. A total of 3,469 cases were reported in the period of interest, of which the 89.1% occurred in cattle, 4.3% in horses, 1.5% in sheep, 0.6% in goats, 0.01% in pig, 3.1% in vampire bats, 0.3% in cervids, 0.2% in skunks, 0.1% in insectivorous bats, 0.1% in foxes, 0.1% in buffaloes, and 0.02% in coatis; 0.5% were not identified. The most frequent antigenic variants reported were AgV11, AgV5, and AgV3, associated with D. rotundus. The distribution of cases in bats correlates with the distribution of cases in domestic and wild animals; however, cases were observed in wild species in non-endemic areas of Mexico, like the State of Chihuahua. The additive model used in the time-series analysis showed a seasonal pattern with a peak of cases at the beginning of each year, from January to March. The model showed a good predicting value; the Pearson correlation coefficient R2 was 0.705. The highest probability for the occurrence of rabies cases in the different species estimated by Ordinary Kriging was in the coast of the Gulf of Mexico, involving the states of Tamaulipas, Veracruz, Tabasco, Chiapas, and Yucatan. This study confirms that rabies in domestic and wild species is endemic in tropical and subtropical areas—however, cases have been observed in new geographic areas—and provides useful information to support actions to stop the spread of the rabies virus or the reservoir, and for planning vaccination strategies considering time and place.

Development of a Dissemination Platform for Spatiotemporal and Phylogenetic Analysis of Avian Infectious Bronchitis Virus

Infecting large portions of the global poultry populations, the avian infectious bronchitis virus (IBV) remains a major economic burden in North America. With more than 30 serotypes globally distributed, Arkansas, Connecticut, Delaware, Georgia, and Massachusetts are among the most predominant serotypes in the United States. Even though vaccination is widely used, the high mutation rate exhibited by IBV is continuously triggering the emergence of new viral strains and hindering control and prevention measures. For that reason, targeted strategies based on constantly updated information on the IBV circulation are necessary. Here, we sampled IBV-infected farms from one US state and collected and analyzed 65 genetic sequences coming from three different lineages along with the immunization information of each sampled farm. Phylodynamic analyses showed that IBV dispersal velocity was 12.3 km/year. The majority of IBV infections appeared to have derived from the introduction of the Arkansas DPI serotype, and the Arkansas DPI and Georgia 13 were the predominant serotypes. When analyzed against IBV sequences collected across the United States and deposited in the GenBank database, the most likely viral origin of our sequences was from the states of Alabama, Georgia, and Delaware. Information about vaccination showed that the MILDVAC-MASS+ARK vaccine was applied on 26% of the farms. Using a publicly accessible open-source tool for real-time interactive tracking of pathogen spread and evolution, we analyzed the spatiotemporal spread of IBV and developed an online reporting dashboard. Overall, our work demonstrates how the combination of genetic and spatial information could be used to track the spread and evolution of poultry diseases, providing timely information to the industry. Our results could allow producers and veterinarians to monitor in near-real time the current IBV strain circulating, making it more informative, for example, in vaccination-related decisions.