SARS-CoV-2 Mu variant in dogs visiting veterinary clinics during the third pandemic peak in Eastern Colombia.

The global presence of SARS-CoV-2 in household pets is acknowledged, yet documentation remains scarce, leaving many regions unexplored. Thus, our study sought to fill this gap by investigating SARS-CoV-2 presence in dogs visiting veterinary clinics during the third pandemic peak in eastern Colombia. We collected and analyzed 43 oropharyngeal and rectal swabs using real-time PCR assays targeting the Envelope Gene of SARS-CoV-2. Out of these, two dogs tested positive, indicating an infection rate of 4.7%. Further examination through complete sequencing and phylogenetic analysis revealed the lineage B.1.621 for the SARS-CoV-2 genome. Consequently, our study unveils the first documented cases of Canis lupus familiaris infected with the Mu variant of SARS-CoV-2, the variant with the most death burden during the whole pandemic in Colombia. Remarkably, these cases presented mild and reversible respiratory and gastrointestinal symptoms, or no clinical manifestations at all. This sheds light on the virus's interaction with our four-legged companions, offering valuable insights into its transmission dynamics and potential effects on animal health.

Seroprevalence and coprological prevalence of liver fluke Fasciola hepatica in cattle and sheep from Santander department, Colombia.

Fasciola hepatica is a parasite with a worldwide distribution that affects several mammals, including humans, and is considered a public health problem. Therefore, the aim of this study was to determine the prevalence of Fasciola hepatica in humans, cattle and sheep, as well as to evaluate factors associated with the prevalence. A total of 185 serum samples from sheep, 290 from cattle, and 114 from humans were collected and processed using an in-house developed ELISA to detect IgG antibodies against F. hepatica. Additionally, 185 stool samples from sheep and 290 from cattle were examined using a Dennis sedimentation technique. Risk factors were analyzed using epidemiological surveys. The overall seroprevalence was 46.5% (86/185) in sheep, 32.5% (94/289) in cattle, and no humans tested positive for the infection. The coprological prevalence was 47.7% (86/180) in sheep and 33.7% (98/290) in cattle. Female gender and cattle living with alternate grazing management showed 2.5 and 6.5 times higher probability of infection, respectively. Bovines coexisting with sheep exhibited a higher risk of infection (odds ratio [OR]=4.3) compared to those without sheep. We concluded that F. hepatica in cattle and sheep has an endemic behavior, and therefore represents a problem of public health for rural communities.

The first report of Dirofilaria repens infection in dogs from Colombia.

Dirofilariasis is a mosquito-borne disease caused by Dirofilaria parasites, affecting both wild and domestic animals, including humans considered as accidental hosts. Dirofilaria repens is the principal causative agent of dirofilariasis in the Old World, with increasing reports of the parasite in countries where it has not been previously identified, due to several factors such as the expansion of mosquito vectors' geographical distribution. By utilizing newly designed primers for molecular detection and confirming through next-generation sequencing, here, we report the first plausible cases of D. repens in dogs from Colombia. Our results support the classification of this species as an emergent pathogen in the Americas. Finally, we encourage an increase in diagnostic and surveillance efforts to prevent and control the current and future dirofilariasis cases in this region.

Sow mortality in a pig production system in the midwestern USA: Reasons for removal and factors associated with increased mortality.

BACKGROUND: Sow mortality has become a growing concern in the pig production industry over the past decade. Therefore, we aimed to describe sow mortality and associated factors in a production system in the midwestern USA. METHODS: Mortality records from 2009 to 2018 for four farrow-to-wean farms were described. Environmental, farm- and individual-level factors associated with weekly mortality and individual risk of dying throughout a sow's lifetime were assessed. RESULTS: Deaths occurred at a median of 116 days from last service, or 26 days postpartum. The median parity upon death was two. Overall, the main reasons for death were locomotion (27%) and reproduction (24%). A higher weekly number of deaths was associated with spring (incidence rate ratio [IRR] 1.27, compared to winter). Sows had a higher mortality when they were exposed to at least one porcine reproductive and respiratory syndrome (PRRS) outbreak during their lifetime (IRR 1.55) and when housed in groups (pens) during gestation (IRR 1.32). Conversely, they had  a lower mortality when housed in filtered farms (IRR 0.76), accounting for an interaction term between parity at removal and PRRS outbreak exposure. LIMITATIONS: Issues with data completion and information accuracy were present, and prospective data collection throughout sows' lifetimes is still needed. CONCLUSION: Efforts to reduce infectious diseases within the herd and manage environmental stressors should help reduce mortality.

Identification of Multiple Blastocystis Subtypes in Domestic Animals From Colombia Using Amplicon-Based Next Generation Sequencing.

Blastocystis is frequently reported in fecal samples from animals and humans worldwide, and a variety of subtypes (STs) have been observed in wild and domestic animals. In Colombia, few studies have focused on the transmission dynamics and epidemiological importance of Blastocystis in animals. In this study, we characterized the frequency and subtypes of Blastocystis in fecal samples of domestic animals including pigs, minipigs, cows, dogs, horses, goats, sheep, and llama from three departments of Colombia. Of the 118 fecal samples included in this study 81.4% (n = 96) were positive for Blastocystis using a PCR that amplifies a fragment of the small subunit ribosomal RNA (SSU rRNA) gene. PCR positive samples were sequenced by next generation amplicon sequencing (NGS) to determine subtypes. Eleven subtypes were detected, ten previously reported, ST5 (50.7%), ST10 (47.8%), ST25 (34.3%), ST26 (29.8%), ST21 (22.4%), ST23 (22.4%), ST1 (17.9%), ST14 (16.4%), ST24 (14.9%), ST3 (7.5%), and a novel subtype, named ST32 (3.0%). Mixed infection and/or intra -subtype variations were identified in most of the samples. Novel ST32 was observed in two samples from a goat and a cow. To support novel subtype designation, a MinION based sequencing strategy was used to generate the full-length of the SSU rRNA gene. Comparison of full-length nucleotide sequences with those from current valid subtypes supported the designation of ST32. This is the first study in Colombia using NGS to molecularly characterize subtypes of Blastocystis in farm animals. A great diversity of subtypes was observed in domestic animals including subtypes previously identified in humans. Additionally, subtype overlap between the different hosts examined in this study were observed. These findings highlight the presence of Blastocystis subtypes with zoonotic potential in farm animals indicating that farm animals could play a role in transmission to humans.

Comparison between five coprological methods for the diagnosis of Balantidium coli cysts in fecal samples from pigs.

BACKGROUND AND AIM: Balantidium coli is a protozoan that can infect humans and non-human primates, being the domestic pigs the animals most affected by this parasite. This study aimed to compare the performance of five coprological methods for diagnosis of Balantidium coli cysts in fecal samples from pigs. MATERIALS AND METHODS: From September to December 2019, 558 fecal samples were collected from the rectum of backyard pigs in the Bucaramanga metropolitan area, Colombia. The average age of the sampled animals was 3-4 months. Fecal samples collected were tested using the following coprological techniques: Direct examination with Lugol's iodine solution, buffered saline, centrifugation/flotation and McMaster techniques, and Ziehl-Neelsen method. RESULTS: The results indicate that B. coli cysts were diagnosed most frequently through direct examination with Lugol's iodine solution (52.7% of the samples) followed by direct examination with a buffered saline solution (37.6%). Moderate concordance (k=0.41; p<0.05) was determined between direct method with Lugol's iodine and buffered saline solution, McMaster and buffered saline (k=0.35; p<0.05), and centrifugation/flotation and buffered saline (k=0.28; p<0.05) showed a fair degree of concordance. The rest of the comparisons were classified as poor. The flotation techniques (centrifugation/flotation and McMaster) did not show good recovery of cysts. CONCLUSION: It is concluded that the most efficient method for diagnosing this parasitosis was to an association between direct examination with Lugol's iodine solution and buffered saline.

A survey for potentially zoonotic parasites in backyard pigs in the Bucaramanga metropolitan area, Northeast Colombia.

BACKGROUND AND AIM: Backyard pigs farming is a rearing system associated with poor hygienic and sanitary conditions of the pig, often causing public health and food safety problems. Therefore, this study was conducted to investigate the occurrence of potentially zoonotic parasites in population pig reared under backyard farming in the Bucaramanga metropolitan area, Northeast Colombia. MATERIALS AND METHODS: From September to December 2019, a total of 558 fecal samples from 64 backyard pig farms were examined for the presence of enteric protozoan infection. The coprological diagnosis was done by direct examination using Lugol's iodine solution, buffered saline solution, and Kinyoun technique. In addition, blood samples were collected from 200 pigs. Serum was collected and used for the detection of Trichinella spiralis and Taenia solium cysticercosis infections, using the enzyme-linked immunosorbent assay. RESULTS: The overall prevalence of zoonotic protozoa in the Bucaramanga metropolitan area was 65.2%, reporting 52.7% prevalence for Balantidium coli, 33.7% for Entamoeba coli, and 5.7% for Cryptosporidium spp. Regarding the prevalence by municipalities, there was no statistical association (p>0.05), indicating that the prevalence was similar in the region under study. Pigs >7 months of age showed to be a risk factor for B. coli infection, indicating that the prevalence increases with the age, while pigs raised at >1000 masl and access to latrines, increased infection risk for E. coli and Cryptosporidium spp. infections. In the present study, T. spiralis infection was not detected in the analyzed sera, while T. solium cysticercosis infection was found to be 40.5%. CONCLUSION: The high prevalence of protozoan infections and porcine cysticercosis reported in this study could be due to poor facilities, and lack of hygiene in the facilities, and suggests the possible transmission of these parasite populations between pigs and humans, thus increasing the transmission of parasites zoonotic potential. Therefore, appropriate sanitary management practices and deworming programs should be adopted to reduce the prevalence of these infectious agents.

Prevalence of Dirofilaria immitis in shelter dogs in Bucaramanga metropolitan area, Colombia.

The heartworm Dirofilaria immitis is the causative agent of cardiopulmonary dirofilariosis in dogs and cats and also infects humans. The current knowledge about this parasite in South America is scarce compared to North America and Europe. Nevertheless, this parasite has been reported in some regions of Colombia. The objective of this study was to determine the prevalence and risk factors associated with D. immitis infection in shelter dogs from Bucaramanga metropolitan area. We performed a cross-sectional study using blood samples from shelter dogs. Microfilariae testing of whole blood included a blood smear and modified Knott's test. Antigen testing of serum was performed using the Anigen Rapid HW Ag Test Kit 2.0 ®. A descriptive analysis and univariable logistic regression analysis were applied. A total of 207 whole blood samples, from 7 shelters dogs in the Bucaramanga metropolitan area, were utilized. The overall prevalence of D. immitis observed in shelter dogs in the Bucaramanga metropolitan area by blood smears and modified Knott's test was 6.3% (13/ 207) and 0.5% (1/207) by immunochromatography test kit. Regarding the prevalence by municipalities, there was a statistical association (P < .05), indicating that the prevalence was higher in dogs in Girón municipality. Likewise, there was a statistical association (P < .05) between the prevalence with respect to heartworm knowledge and mosquito control. For prevalence by gender, age group, dog breed, and hair length, there was no statistical association (P > .05). For Girón municipality there was a 7.1 times (OR = 7.1; CI95% 0.8-59.2; P < .05) increased infection risk. This study provides current data and the first known report of the prevalence of D. immitis microfilaremia and antigenemia in shelter dogs in the Bucaramanga metropolitan area, and these results could be useful for designing new control measures for this infection. We observed that the prevalence of both microfilaremia and antigenemia was significantly lower in these sampled dogs compared to previous reports.

Current status of prevalence and risk factors associated with liver fluke Fasciola hepatica in cattle raised in different altitudinal regions of Colombia.

Fasciola hepatica is a trematode parasite with a worldwide distribution that affects mammals, including humans, and is considered a major food safety and public health problem. A research was conducted in three hundred eighty-five livestock farms located in different altitudinal regions of Colombia between February 2017 and March 2018 with the aim to determine the coprological prevalence, seroprevalence (SP) and risk factors associated with liver fluke F. hepatica. A total of 5620 fecal sample were collected from cattle and processed using sedimentation technique. Additionally, 597 blood samples were collected and processed by an ELISA test. The coprological prevalence of F. hepatica in animals and herds was 6.4% and 38.4%, respectively. Regarding the prevalence by municipalities, there was statistical association (P < .05), indicating that the prevalence was higher in those municipalities above 2000 masl (meters above sea level). Regarding risk factors, cattle raised in municipalities at 2000 to 3000 masl showed about 4 (OR = 3.96 [CI95% 3.1-5]; P < .05) times higher probability for infection than those raised at lower altitude. Cattle from 2 to 3 year of age, showed almost 4 times (OR = 3.7[CI95% 2.5-5.4]; P < .05), increased infection risk. Females and dairy breeds showed almost 2 (OR = 1.9 [CI95% 1.3-2.6]; P < .05) and 10 times (OR = 10 [CI95% 7.8-12.8]; P < .05), respectively, increased infection risk. The presence of antibodies anti- F. hepatica (SP = 37.8%; [CI95% 35.8-39.7]; P < .05) in cattle of the region under study is confirmed, which suggests an endemic behavior of this parasitosis. The present study provides current information on the prevalence of F. hepatica in different altitudinal regions of Colombia, and these findings could be useful for designing new holistic control measures for the liver fluke F. hepatica infection.

Prevalence and risk factors of gastrointestinal parasites in backyard pigs reared in the Bucaramanga Metropolitan Area, Colombia.

Backyard pigs have been associated with poor sanitary conditions and the development of parasitic diseases, often causing public health and food safety problems. Therefore, the aim of this study was to determine the prevalence and risk factors for gastrointestinal parasites in backyard pigs. 279 animals were sampled from thirty-two backyard pig farms located in the Bucaramanga, Floridablanca, Giron and Piedecuesta municipalities, from Bucaramanga Metropolitan Area, Colombia. Fecal samples were taken directly from the rectum and processed by four coprological techniques. The overall prevalence of gastrointestinal parasites was 91%, being the highest values for Balantidium coli and Eimeria sp. Regarding the prevalence by municipalities, there was no statistical association (p ≥ 0.05) indicating that the prevalence was similar in the region under study. Floridablanca municipality, free-ranging pigs, access to latrines, and consumption of spring water showed to be a risk factor for nematodes, while Giron municipality, pigs > 7 months of age and access to latrines, increased infection risk for coccidian. We concluded that there is a high prevalence of gastrointestinal parasites in backyard pigs from the Bucaramanga Metropolitan Area, and that it could be controlled by improving management practices and farm facilities.

Prevalence and risk factors associated with liver fluke Fasciola hepatica in cattle and sheep in three municipalities in the Colombian Northeastern Mountains.

Fasciola hepatica is a parasitic trematode of worldwide distribution, which affects cattle and a large number of mammals, including man. An investigation was carried out to the Colombian Northeastern Mountain between October 2017 and February 2018 with the aim to determine the prevalence and risk factors associated with Fasciola hepatica. Thirty-four farms whose owners agreed to participate in the study were included. Overall, 103 bovines and 97 sheep were examined. A fecal and blood sample was collected from each animal, and all the samples were identified and stored in a refrigerated box to be transported to the Parasitology laboratory for analysis. Fecal samples were processed with a coprological technique, and blood by ELISA test. A written epidemiological survey was applied on all farms. The results indicate 20.5% of coprological prevalence and 41.5% of seroprevalence (SP). Evidence of the parasite was demonstrated in the three municipalities; however, statistical differences were found (P < .05), with higher seropositivity in Duitama municipality (SP = 83.3%). Regarding risk factor, pure breeds of cattle showed 2.5 (SP = 56.1, OR = 2.5) times higher of infection than crossed breed. Cattle and sheep from 12 to 24 months of age, showed 2.5 (SP = 66.7%, OR = 2.5) and 5.9 times (SP = 44.2%, OR = 5.9), respectively, increased infection risk. The presence of snails on the farms had higher odds for testing F. hepatica-positive, therefore, showed to be an important risk factor. The presence of antibodies against F. hepatica in cattle and sheep from the region under study suggests it is endemic and should be controlled by control and prevention programs in the farms.

Prevalence and risk factors of gastrointestinal parasites in backyard pigs reared in the Bucaramanga Metropolitan Area, Colombia / Prevalência e fatores de risco de parasitos gastrointestinais em suínos criados na Área Metropolitana de Bucaramanga, Colombia

Abstract Backyard pigs have been associated with poor sanitary conditions and the development of parasitic diseases, often causing public health and food safety problems. Therefore, the aim of this study was to determine the prevalence and risk factors for gastrointestinal parasites in backyard pigs. 279 animals were sampled from thirty-two backyard pig farms located in the Bucaramanga, Floridablanca, Giron and Piedecuesta municipalities, from Bucaramanga Metropolitan Area, Colombia. Fecal samples were taken directly from the rectum and processed by four coprological techniques. The overall prevalence of gastrointestinal parasites was 91%, being the highest values for Balantidium coli and Eimeria sp. Regarding the prevalence by municipalities, there was no statistical association (p ≥ 0.05) indicating that the prevalence was similar in the region under study. Floridablanca municipality, free-ranging pigs, access to latrines, and consumption of spring water showed to be a risk factor for nematodes, while Giron municipality, pigs > 7 months of age and access to latrines, increased infection risk for coccidian. We concluded that there is a high prevalence of gastrointestinal parasites in backyard pigs from the Bucaramanga Metropolitan Area, and that it could be controlled by improving management practices and farm facilities.

Resumo Suínos criados em fundo de quintal têm sido associados às más condições sanitárias e ao desenvolvimento de doenças parasitárias, frequentemente causando problemas de saúde pública e segurança alimentar. Assim, o objetivo deste estudo foi determinar a prevalência e os fatores de risco para parasitos gastrointestinais em suínos criados em fundo de quintal. Foram amostrados 279 animais de 32 fazendas de suínos localizadas nos municípios de Bucaramanga, Floridablanca, Giron e Piedecuesta, da Área Metropolitana de Bucaramanga, Colômbia. As amostras fecais foram coletadas diretamente do reto e processadas por quatro técnicas coprológicas. A prevalência geral de parasitos gastrintestinais foi de 91%, sendo os maiores valores para Balantidium coli e Eimeria sp. Em relação à prevalência por municípios, não houve associação estatística (p≥ 0,05), indicando que a prevalência foi semelhante na região estudada. O município de Floridablanca, porcos caipiras, acesso a latrinas e consumo de água da nascente mostraram ser um fator de risco para os nematoides enquanto no município de Giron, porcos com mais de 7 meses de idade e acesso a latrinas, aumentou o risco de infecção por coccídios. Concluiu-se que há uma alta prevalência de parasitos gastrointestinais em suínos criados em fundo de quintal da Área Metropolitana de Bucaramanga, e que isso poderia ser controlado melhorando as práticas de manejo e as instalações agrícolas.

An Altered Circadian Clock Coupled with a Higher Photosynthesis Efficiency Could Explain the Better Agronomic Performance of a New Coffee Clone When Compared with a Standard Variety.

In a context where climate change is threatening coffee productivity, the management of coffee leaf rust is a challenging issue. Major resistant genes, which have been used for many years, are systematically being overcome by pathogens. Developing healthy plants, able to defend themselves and be productive even when attacked by the pathogen, should be part of a more sustainable alternative approach. We compared one hybrid (GPFA124), selected for its good health in various environments including a reduced rust incidence, and the cv. 'Caturra', considered as a standard in terms of productivity and quality but highly susceptible to rust, for phenotypic variables and for the expression of genes involved in the circadian clock and in primary photosynthetic metabolism. The GPFA124 hybrid showed increased photosynthetic electron transport efficiency, better carbon partitioning, and higher chlorophyll content. A strong relationship exists between chlorophyll a fluorescence and the expression of genes related to the photosynthetic electron transport chain. We also showed an alteration of the amplitude of circadian clock genes in the clone. Our work also indicated that increased photosynthetic electron transport efficiency is related to the clone's better performance. Chlorophyll a fluorescence measurement is a good indicator of the coffee tree's physiological status for the breeder. We suggest a connection between the circadian clock and carbon metabolism in coffee tree.

Point prevalence of gastrointestinal parasites in double purpose cattle of Rio de Oro and Aguachica municipalities, Cesar state, Colombia.

Gastrointestinal parasites are one of the most important health problems in cattle worldwide, as they cause economic losses in the herds. Twenty - seven double purpose herds were visited to determine the prevalence of gastrointestinal parasites in cattle at the Rio de Oro and Aguachica municipalities. Overall, 862 fecal samples were collected in three age groups: <12months, 12-24months and >24months. Stool samples were taken directly from the rectum and refrigerated until processing. For parasite determination, fecal samples were processed using coprological techniques. The parasitic genera were identified by egg or infective larval morphology. The global prevalence of gastrointestinal parasites was 83.2%, being the highest values for Eimeria sp. (77.9%), Strongyloides sp. (10.8%) and Haemonchus sp. (8.5%). Regarding the prevalence by municipalities, there was no statistical association (P>0.05) indicating that the prevalence was similar in the two municipalities. Regarding the results for Eimeria sp., different degrees of positivity were observed, reflecting that there was statistical association (P<0.05) with respect to the age group, suggesting that adult animals may act as infection source for calves. Likewise, there was statistical association (P<0.05) between the prevalence for Strongyloides sp., Haemonchus sp. and Trichostrongylus sp. with respect to the age group. It is concluded that there is a high prevalence of gastrointestinal parasites in dual-purpose cattle in the municipalities under study, and that it could be controlled by improving the hygienic conditions of the herds, and informing the farmer about parasite control programs.

Influence of Environmental Conditions and Genetic Background of Arabica Coffee (C. arabica L) on Leaf Rust (Hemileia vastatrix) Pathogenesis.

Global warming is a major threat to agriculture worldwide. Between 2008 and 2013, some coffee producing countries in South and Central America suffered from severe epidemics of coffee leaf rust (CLR), resulting in high economic losses with social implications for coffee growers. The climatic events not only favored the development of the pathogen but also affected the physiological status of the coffee plant. The main objectives of the study were to evaluate how the physiological status of the coffee plant modified by different environmental conditions impact on the pathogenesis of CLR and to identify indicators of the physiological status able to predict rust incidence. Three rust susceptible genotypes (one inbred line and two hybrids) were grown in controlled conditions with a combination of thermal regime (TR), nitrogen and light intensity close to the field situation before being inoculated with the rust fungus Hemileia vastatrix. It has been demonstrated that a TR of 27-22°C resulted in 2000 times higher sporulation than with a TR of 23-18°C. It has been also shown that high light intensity combined with low nitrogen fertilization modified the CLR pathogenesis resulting in huge sporulation. CLR sporulation was significantly lower in the F1 hybrids than in the inbred line. The hybrid vigor may have reduced disease incidence. Among the many parameters studied, parameters related to photosystem II and photosynthetic electron transport chain components appeared as indicators of the physiological status of the coffee plant able to predict rust sporulation intensity. Taken together, these results show that CLR sporulation not only depends on the TR but also on the physiological status of the coffee plant, which itself depends on agronomic conditions. Our work suggests that vigorous varieties combined with a shaded system and appropriate nitrogen fertilization should be part of an agro-ecological approach to disease control.