Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle.

Cattle have a significant impact on human societies in terms of both economics and health. Viral infections pose a relevant problem as they directly or indirectly disrupt the balance within cattle populations. This has negative consequences at the economic level for producers and territories, and also jeopardizes human health through the transmission of zoonotic diseases that can escalate into outbreaks or pandemics. To establish prevention strategies and control measures at various levels (animal, farm, region, or global), it is crucial to identify the viral agents present in animals. Various techniques, including virus isolation, serological tests, and molecular techniques like PCR, are typically employed for this purpose. However, these techniques have two major drawbacks: they are ineffective for non-culturable viruses, and they only detect a small fraction of the viruses present. In contrast, metagenomics offers a promising approach by providing a comprehensive and unbiased analysis for detecting all viruses in a given sample. It has the potential to identify rare or novel infectious agents promptly and establish a baseline of healthy animals. Nevertheless, the routine application of viral metagenomics for epidemiological surveillance and diagnostics faces challenges related to socioeconomic variables, such as resource availability and space dedicated to metagenomics, as well as the lack of standardized protocols and resulting heterogeneity in presenting results. This review aims to provide an overview of the current knowledge and prospects for using viral metagenomics to detect and identify viruses in cattle raised for livestock, while discussing the epidemiological and clinical implications.

High prevalence of Enterovirus E, Bovine Kobuvirus, and Astrovirus revealed by viral metagenomics in fecal samples from cattle in Central Colombia.

Livestock plays a crucial role in ensuring food security and driving the global economy. However, viral infections can have far-reaching consequences beyond economic productivity, affecting the health of cattle, as well as posing risks to human health and other animals. Identifying viruses present in fecal samples, a primary route of pathogen transmission, is essential for developing effective prevention, control, and surveillance strategies. Viral metagenomic approaches offer a broader perspective and hold great potential for detecting previously unknown viruses or uncovering previously undescribed agents. Ubaté Province is Colombia's dairy capital and a key center for livestock production in the country. Therefore, the purpose of this study was to characterize viral communities in fecal samples from cattle in this region. A total of 42 samples were collected from three municipalities in Ubaté Province, located in central Colombia, using a convenient non-probabilistic sampling method. We utilized metagenomic sequencing with Oxford Nanopore Technologies (ONT), combined with diversity and phylogenetic analysis. The findings revealed a consistent and stable viral composition across the municipalities, primarily comprising members of the Picornaviridae family. At the species level, the most frequent viruses were Enterovirus E (EVE) and Bovine Astrovirus (BoAstV). Significantly, this study reported, for the first time in Colombia, the presence of viruses with veterinary importance occurring at notable frequencies: EVE (59%), Bovine Kobuvirus (BKV) (52%), and BoAstV (19%). Additionally, the study confirmed the existence of Circular replicase-encoding single-stranded (CRESS) Virus in animal feces. These sequences were phylogenetically grouped with samples obtained from Asia and Latin America, underscoring the importance of having adequate representation across the continent. The virome of bovine feces in Ubaté Province is characterized by the predominance of potentially pathogenic viruses such as BoAstV and EVE that have been reported with substantial frequency and quantities. Several of these viruses were identified in Colombia for the first time. This study showcases the utility of using metagenomic sequencing techniques in epidemiological surveillance. It also paves the way for further research on the influence of these agents on bovine health and their frecuency across the country.

Serodiagnosis and Risk Factors Associated with Infectious Agents of Reproductive Diseases in Bovines of Chiquinquirá, District of Boyacá (Colombia).

The productivity of cattle farms is affected by infectious and noninfectious factors that generate economic losses and cause reproductive failure represented by low conception rates, embryonic mortality, abortions, and fetal mummification. The infectious agents that most impact the reproductive health of the bovine species from conception to birth are bovine herpesvirus type 1 (BoHV-1) causing infectious bovine rhinotracheitis (IBR), bovine viral diarrhea virus (BVDV), bovine parainfluenza virus type 3 (PI3), Neospora caninum and Leptospira spp. The objective of this study was to diagnose the presence of BoHV-1, bovine viral diarrhea (BVD), PI3, Neospora caninum, and Leptospira spp. by serology and identify the risk factors associated with infectious agents of reproductive interest in bovines of Boyacá (Colombia). A descriptive cross-sectional study was developed, with simple random sampling, where a sample size of 601 female cattle of Holstein, Jersey, and Normande breeds of different age groups was determined. Blood samples were taken and processed using the indirect ELISA technique (SYNBIOTICS®, SERELISA® BVD p80 Ab Mono Blocking, Ingezim R.12.NC.K, PRIMACHECK VPI-3®) and the MAT test for the diagnosis of bovine leptospirosis. The data were processed with the statistical program Epi Info™. The highest apparent seroprevalence was established for infectious bovine rhinotracheitis (61.1%), followed by BVD (37.6%), PI3 (40.9%), neosporosis (51.1%), and leptospirosis (14.8%). Variables such as age >4 years and Holstein breed for IBR and >4 years for BVD were established risk factors. Considering our results, we suggest implementing prevention and control plans that include vaccination as a prophylactic measure and biosecurity tools that reduce the probability of contagion and transmission of pathogens.

Seropositivity and risk factors associated with the presentation of bovine leukosis virus in Sotaquirá, Colombia.

BACKGROUND AND AIM: Enzootic bovine leukosis is a disease economically important to the dairy farming industry worldwide. The virus is of the Deltaretrovirus genus and is primarily transmitted iatrogenically. Most bovines infected with the virus remain asymptomatic with only 5-10% of cattle having lymphomas. This study aimed to determine the seroprevalence of bovine leukosis virus (BLV) in Sotaquirá, Boyacá, Colombia. MATERIALS AND METHODS: We conducted a descriptive, observational epidemiological cross-sectional study using the simple random sampling method with a sample size of 1000. Blood samples from random bovine were processed using the SERELISA® BLV Ab Mono Blocking indirect enzyme-linked immunosorbent assay kit (Zoetis, USA). The assay had a sensitivity of 97% and a specificity of 98%. The collected data were processed using Epi Info® (Centers for Disease Control and Prevention; Atlanta, Georgia). From the study, we could determine a high seroprevalence of BLV in Sotaquirá. RESULTS: We established a high seroprevalence on BLV in the municipality, with 31.1% apparent seroprevalence and 30.6% real seroprevalence rate. We found that male cattle more than 4 years old (39.4%) and the Ayrshire breed (45.5%) had the highest prevalence rates of the virus. In this study, we could establish statistically significant associations according to breed, age, and gender of the cattle under study. Moreover, we identified the risk factors for BLV infection. We found that in cattle aged <1 year and those older than 4 years of age and those of the Holstein breed, the presentation of infectious bovine rhinotracheitis, mucosal secretions, mastitis, fetal death, the presence of a corral, and the implementation of artificial insemination practices were risk factors for BLV infection. CONCLUSION: Determining the prevalence of BLV within the herd and identifying the associated risk factors for the disease are fundamental in developing efficient programs for the control and eradication of BLV within herds.

Seroprevalence of bovine viral diarrhea virus (BVDV) in cattle from Sotaquirá, Colombia.

Worldwide distributed Bovine Viral Diarrhea Virus (BVDV) represents a high risk of infection in most bovine farms, in which it is associated with gastrointestinal, respiratory, and reproductive diseases. The purpose of this research was to establish the seroprevalence and the main risk factors associated with the presentation of BVDV in the municipality of Sotaquirá, Colombia. Samples were taken from 1000 cattle of Holstein, Ayrshire, Jersey, Normande Gyr and Holstein x Gyr. Epidemiological surveys were implemented, reproductive and management variables were taken into consideration. Indirect ELISA was performed to detect specific antibodies against BVDV using the commercial kit SERELISA® BVD p80 Ab Mono Blocking. The overall seroprevalence of antibodies against BVDV was 42.5% (425/1000), where the Gyr breed (59.1% apparent prevalence (AP); 60.3% real prevalence (PR)) and the age group > 4 years (53.0% PA; 54.4% PR) presented the highest seroprevalences. A significant statistical association was found for the breed, age, management practices evaluated and the presentation of PI3 (p ≤ 0.05). Age group > 4 years, Normande breed, presentation of PI3 and grazing lease were established as risk factors associated with BVDV in the herds. These infections are mainly associated with dairy cattle and herds with many animals, so it is important to consider vaccination plans as a preventive system and follow up on the most common diseases.

Resistencia in vitro de la garrapata Rhipicephalus microplus a organofosforados, piretroides y amitraz en el Departamento de Boyacá, Colombia / In vitro Resistance of Rhipicephalus microplus ticks to Organophosphates, Pyrethroids and Amitraz in Boyacá Department, Colombia

El presente estudio evaluó la resistencia in vitro de la garrapata Rhipicephalus microplus a organofosforados (OF), piretroides sintéticos (PS) y amitraz (AM). Las garrapatas adultas fueron recolectadas en Boyacá, Colombia y sometidas a la prueba de inmersión para evaluar la eficacia de los fármacos, el efecto sobre la ovoposición y el porcentaje de eclosión larvaria. Se utilizó un diseño experimental completamente al azar con cinco grupos y tres repeticiones por tratamiento, con 10 garrapatas por repetición. Los resultados demostraron tasas de mortalidad a las moléculas evaluadas, encontrando 43, 56, 60 y 96% de mortalidad para el grupo control, PS, AM y OF, respectivamente, al día 21 del experimento. La inhibición de la ovoposición fue de 13,4% para el grupo control, 44,6% para AM, 45,5% para PS y 96% para OF. El porcentaje de eclosión de huevos fue de 88% para el grupo control, 16% para AM, 14% para PS y 4% para OF. El presente estudio in vitro representa el primer diagnóstico en el departamento de Boyacá, Colombia.

The present investigation evaluated the in vitro resistance of the Rhipicephalus microplus tick, to organophosphates (OP), synthetic pyretroids (SP), and amitraz. Adult ticks were collected in the Department of Boyacá, Colombia, and subjected to the immersion test, to assess the efficacy of drugs, their effect on oviposition, and the percentage of larvae eclosion. A completely randomized experimental design was used, with 5 groups and 3 replicates per group, with 10 ticks per replicate. The results showed that the mortality rates in terms of percentage (%) of the assessed molecules were: 43 for the control group; 56 for SP; 60 for AM, and 96 for OP, respectively, at day 21 of the study. The inhibition of oviposition was: 13.4% for the control group; 44.6% for AM; 45.5% for SP; and 96% for OP. The present in vitro study represents the first diagnostic of resistance in the Department of Boyacá, Colombia.

Evaluación de la eficacia de la CEPA MAF1309® de Metarhizium anisopliae en el control biológico de garrapatas adultas de Rhipicephalus microplus en Tunja, Colombia / Evaluation of efficacy of MaF1309® strain of Metarhizium anisopliae in biological control of adult ticks Rhipicephalus microplus in Tunja, Colombia

La garrapata del ganado Rhipicephalus microplus constituye el ectoparásito de mayor importancia en las ganaderías de regiones tropicales y subtropicales, al producir pérdidas directas por reducción de la producción de carne, leche y deterioro de las pieles así como a la transmisión de agentes patógenos para el ganado bovino tales como Babesia bovis, Babesia bigemina y Anaplasma marginale. El tratamiento químico ha sido efectivo para el control de las garrapatas; sin embargo,  su uso excesivo ha propiciado la selección de individuos resistentes y por tal motivo, se hace necesario el desarrollo de nuevas alternativas de control, tales como el uso de hongos entomopatógenos. El objetivo del presente estudio fue evaluar la eficacia in vitro de M. anisopliae para el control de la fase adulta de R. microplus, en Tunja, Colombia. Se usó la prueba de inmersión de adultas para evaluar la eficacia de la cepa MaF1309® de M. anisopliae a las siguientes concentraciones: 1x10(4), 1x10(6) y 1x10(8) conidias/mL. Se observó que en las garrapatas tratadas a una concentración de 1x10(8) conidias/mL se alcanzó el 100% de mortalidad a los 14 d postratamiento (PT), mientras que las concentraciones 1x10(6) y 1x10(4) conidias/mL alcanzaron el 100% de mortalidad a los días 16 y 20 PT, respectivamente. La mortalidad fue directamente proporcional a la concentración empleada del hongo, siendo las garrapatas tratadas con concentraciones mayores aquellas que alcanzaron una mortalidad en menor tiempo. Estos resultados in vitro son considerados el inicio de información de tipo local proyectados al diseño de programas de control para el departamento de Boyacá.

The livestock tick Rhipicephalus microplus is a high importance ectoparasite in cattle raised at tropical and sub-tropical regions producing direct losses since reduce meat and milk production and cause leather injury besides transmission of pathogenic agents such as Babesia bovis, Babesia bigemina y Anaplasma marginale. The chemical treatment has been effective to control tick  however the excessive use has selected resistant individuals; for that reason is important to develop new alternatives such as entomopathogen fungi to keep controlled those individuals. The objective of this research was to evaluate in vitro efficacy of M. anisopliae to control adult stage of R. microplus in Tunja, Colombia. The immersion test was used to evaluate efficacy of MaF1309® strain of M. anisopliae at concentrations of 1x10(4), 1x10(6) y 1x10(8) conidia/mL. The group of ticks treated with 1x10(8) conidia had 100% of mortality 14 post-treatment days (PT), otherwise 1x10(6) y 1x10(4) conidia/mL concentrations have 100% of mortality at 16 and 20 PT days, respectively. Mortality was directly proportional to fungus concentration used, the ticks treated with high concentrations reach high mortality in less time. Those in vitro results start in local information projected to design control programs for the department of Boyacá.

Estimación de los Valores de Hematocrito y Hemoglobina en Presencia de Haemonchus sp. en Ovinos de Oicatá, Colombia / Estimation of Hematocrit Packed Cell Volume and Hemoglobin with the Presence of Haemonchus sp. in Sheep of Oicatá, Colombia

La hemoncosis causada por el nemátodo del abomaso de rumiantes, Haemonchus contortus, representa uno de los mayores problemas en los sistemas ovinos debido a su impacto sobre la producción y el costo de los tratamientos. El objetivo del presente estudio fue determinar la prevalencia de Haemonchus sp. y la estimación de los valores de hematocrito (Hto) y hemoglobina (Hb) en ovinos pertenecientes al municipio de Oicatá, Colombia. Se realizó un muestreo aleatorio de 201 animales criollos que pertenecían a explotaciones extensivas. Se tomaron muestras de materia fecal que fueron analizadas por medio del método de concentración formol-éter y posteriormente se realizó la identificación de Haemonchus sp. En los mismos individuos se obtuvo una muestra de sangre de la vena cefálica, se estimaron y se realizaron hemogramas completos. Se escogieron cuatro parámetros hematológicos: hemoglobina (Hb), hematocrito (Hto), recuento de glóbulos rojos (RBC) y volumen corpuscular medio (VCM). Se observó una prevalencia de Haemonchus sp. del 31,3%. Solo el 6% de los animales mostró Hto por debajo de los valores normales, mientras que el 6,5% tenía valores de Hb anormal en presencia del helminto. Los valores de RBC y VCM no demostraron alteraciones en presencia de la infección. No se observó ninguna relación entre los parámetros hemáticos y la presencia de huevos de Haemonchus sp. en las heces ovinas.

Haemonchosis caused by the abomasal nematode of ruminants, Haemonchus contortus, represents one of the biggest problems in sheep farming by its impact on production losses and cost of anthelmintic treatments. The aim of the present study was to determine the prevalence of Haemonchus sp. and the estimated values of the hematocrit (Hto) and hemoglobin (Hb) of sheep from the municipality of Oicatá, Colombia. A random sampling of 201 creole animals belonging to extensive farms was carried out. Individual fecal samples were analyzed by the method of concentration formol-ether and the Haemonchus sp. infection determined. Blood samples from the same animals were obtained from the cephalic vein in EDTA containing tubes. Four hematological parameters were estimated: haemoglobin (Hb), haematocrit (Hto), red blood cells count (RBC) and mean corpuscular volume (MCV). Results were analyzed with the statistical package SPSS18 with a level of statistical significance of p<0.05. A prevalence of 31.3% was found for Haemonchus sp. Only 6% of the animals showed Hto below normal values, while 6.5% had abnormal Hb values in the presence of the helminth. RBC presented normal values in the presence of the parasite. In this study no correlation was found between the presence of the parasite and the haematological parameters determined.