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Disease Epidemiology in Farm Animal Production
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Disease Epidemiology in Farm Animal Production

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Veterinary Clinical Studies".

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 11987

Special Issue Editors

Dr. Gianmarco Ferrara

E-Mail Website
Guest Editor
Department of Veterinary Medicine and Animal Productions, University of Naples, Via Delpino 1, 80137 Naples, Italy
Interests: epidemiology in livestock and wildlife; infectious diseases; veterinary virology
Dr. Serena Montagnaro

E-Mail Website
Guest Editor
Department of Veterinary Medicine and Animal Productions, University of Naples, Via Delpino 1, 80137 Naples, Italy
Interests: veterinary epidemiology; veterinary virology; infectious disease and public health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Infectious diseases are thought to be the major cause of economic losses in livestock worldwide, with the greatest impact on animal growth performance (such as intestinal and respiratory infections) or fertility (such as pathogens that can cause reproductive disorders). In addition, certain infections are potential sources of zoonotic diseases that threaten both human and animal health. Epidemiological research and ongoing surveillance are, therefore, needed to gain new insights into the characteristics of infectious diseases.

This Special Issue focuses on epidemiological studies in livestock (including, but not limited to, molecular epidemiology, serological epidemiology, diagnosis, etc.) and incorporates original research and review articles designed to provide an overview of advances in the prevention and control of infectious diseases in livestock such as cattle, small ruminants, swine, buffalo, and others. Epidemiological research on emerging and re-emerging pathogens is also encouraged. In addition, we welcome original research and reviews that reveal new insights into the economic impact of infections.

Dr. Gianmarco Ferrara
Dr. Serena Montagnaro
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • veterinary epidemiology
  • infectious disease surveillance
  • prevention and control of pathogens of veterinary interest
  • emerging infectious diseases in livestock
  • re-emerging infectious diseases in livestock

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Published Papers (11 papers)

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Research

11 pages, 1050 KiB  
Article
Positivity Status and Molecular Characterization of Porcine Parvoviruses 1 Through 8 (PPV1-PPV8) from Slaughtered Pigs in China
by Dashi Zhao, Hong Lin, Zitao Huang, Yajie Zhou, Wenhao Qi, Meng Cui, Ming Qiu, Jianzhong Zhu and Nanhua Chen
Animals 2024, 14(22), 3238; https://doi.org/10.3390/ani14223238 - 12 Nov 2024
Viewed by 380
Abstract
Porcine parvoviruses one through eight (PPV1-PPV8) are prevalent in Chinese swine herds. However, the infection status of all these PPVs in slaughtered pigs is still unclarified. In this study, we detected PPV1-PPV8 in 353 tissue samples collected from slaughtered pigs from six regions [...] Read more.
Porcine parvoviruses one through eight (PPV1-PPV8) are prevalent in Chinese swine herds. However, the infection status of all these PPVs in slaughtered pigs is still unclarified. In this study, we detected PPV1-PPV8 in 353 tissue samples collected from slaughtered pigs from six regions of China in 2023. At least one species of PPV was detected in 79.32% of the samples (280 out of 353). Six PPV species were detected, except for PPV4 and PPV8, in slaughtered pigs, within which PPV3 (49.86%), PPV2 (42.49%), and PPV7 (42.21%) were predominant, followed by PPV1 (13.31%), PPV6 (13.31%), and PPV5 (8.22%). Noticeably, co-infection was frequently detected, with 67.50% of PPV-positive samples (189 out of 280) co-infecting with two to six PPVs. In addition, one representative genome for each detected PPV was determined. Multiple sequence alignment determined a large number of substitutions in capsid proteins of PPVs. Genome-based phylogenetic analysis confirmed the PCR detection results. Recombination detection identified two potential recombinants (PPV2 GDCZ2023-2088 strain and PPV3 HLJSYS2023-1654 strain) in slaughtered pigs. Overall, this study provides new insights into the prevalence and evolution of PPVs, particularly in slaughtered pigs in China. Full article
(This article belongs to the Special Issue Disease Epidemiology in Farm Animal Production)
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10 pages, 1043 KiB  
Article
Serological and Molecular Investigation of Infectious Laryngotracheitis Virus in Chickens from Robe Town, Southeastern Ethiopia
by Samuel Abebe, Gianmarco Ferrara, Belayneh Getachew, Eyob Hirpa and Nebyou Moje
Animals 2024, 14(22), 3227; https://doi.org/10.3390/ani14223227 - 11 Nov 2024
Viewed by 438
Abstract
Infectious laryngotracheitis virus (ILTV) is responsible for avian infectious laryngotracheitis (ILT), a highly contagious acute respiratory disease affecting chickens. However, there is limited information on ILTV and its distribution in Ethiopia, particularly in the southeastern region. The aim of this study was to [...] Read more.
Infectious laryngotracheitis virus (ILTV) is responsible for avian infectious laryngotracheitis (ILT), a highly contagious acute respiratory disease affecting chickens. However, there is limited information on ILTV and its distribution in Ethiopia, particularly in the southeastern region. The aim of this study was to establish the serological prevalence and molecular evidence in commercial and backyard chickens from Robe town, Southeastern Ethiopia. A cross-sectional study was conducted between December 2021 and June 2022, collecting 240 serum samples from randomly selected chickens belonging to eight kebeles (farms) using systematic random sampling. ILTV-specific antibodies were detected using a commercial indirect enzyme-linked immunosorbent assay (ELISA). From 240 serum samples, 26.7% were positive for ILTV antibodies. Logistic regression analysis identified the type of poultry farm (backyard) and the introduction of chickens from other farms as potential risk factors associated with ILTV exposure. Tracheal tissue and oropharyngeal and tracheal swabs were collected from suspected chickens for isolation and molecular detection. A total of six samples were successfully isolated in embryonated eggs (40%), with four of them verified with a specific PCR. These findings documented the presence of ILTV in the study area, which needs further insight to fully understand the actual spread of ILTV and quantify the damage caused to the poultry sector. Full article
(This article belongs to the Special Issue Disease Epidemiology in Farm Animal Production)
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20 pages, 561 KiB  
Article
Herd-Level Risk Factors Associated with Mycoplasma bovis Serostatus in Youngstock on Irish Dairy Farms
by Marie-Claire McCarthy, Luke O’Grady, Conor G. McAloon and John F. Mee
Animals 2024, 14(21), 3057; https://doi.org/10.3390/ani14213057 - 23 Oct 2024
Viewed by 578
Abstract
Mycoplasma bovis is a globally significant pathogen of cattle associated with a wide range of clinical syndromes, including respiratory disease, mastitis, arthritis, otitis, and reproductive failure. Since its detection in Ireland in 1994, M. bovis has become a significant contributor to morbidity and mortality [...] Read more.
Mycoplasma bovis is a globally significant pathogen of cattle associated with a wide range of clinical syndromes, including respiratory disease, mastitis, arthritis, otitis, and reproductive failure. Since its detection in Ireland in 1994, M. bovis has become a significant contributor to morbidity and mortality in Irish cattle. This study aimed to investigate herd-level risk factors associated with M. bovis seropositivity in replacement dairy heifers, using data from 105 Irish dairy herds. Ten heifers per herd were sampled on three occasions: spring 2018, spring 2019, and autumn 2019. Seropositivity was evaluated using two thresholds: ≥1 positive heifer (Model ≥ 1POS) and ≥3 positive heifers (Model ≥ 3POS). M. bovis seropositivity varied over time, with at least one positive heifer in 50.4% (95% confidence interval (CI): 40.5–60.3) of herds in spring 2018, 35.2% (95% CI: 26.2–45.1) in spring 2019, and 45.7% (95% CI: 36.0–55.7) in autumn 2019. Herds with three or more positive heifers increased from 31.4% (95%CI: 22.7–41.2) in spring 2018 to 42.9% (95% CI: 33.2–52.9) by autumn 2019. Risk factors for M. bovis seropositivity included the purchase of cattle, which significantly raised the odds of seropositivity across multiple visit periods (Model ≥ 1POS: Odds ratio (OR) 3.84, p = 0.02; Model ≥ 3POS: OR 3.69, p = 0.02). Managing more than three land parcels, housing heifer calves separately from bull calves, and sharing airspace between calves and older animals also increased seropositivity risks. Conversely, more colostrum feeds reduced the risk of seropositivity (Model ≥ 1POS: OR 0.81, p = 0.05), while colostrum quality assessment and feeding waste milk showed a trend toward increased risk. These findings suggest the importance of robust biosecurity measures, including limiting cattle purchases, improving calf management, and enhancing colostrum feeding practices, to control the spread of M. bovis. This study provides valuable insights into the epidemiology of M. bovis in Irish dairy herds, emphasising the need for targeted biosecurity and surveillance to safeguard herd productivity. Full article
(This article belongs to the Special Issue Disease Epidemiology in Farm Animal Production)
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9 pages, 561 KiB  
Article
First Molecular Detection and Genetic Characterization of Tetratrichomonas buttreyi and Pentatrichomonas hominis in Donkeys in Shanxi Province, China
by Han-Dan Xiao, Shuo Zhang, Yi-Han Lv, Ze-Dong Zhang, Nan Su, Liang-Liang Li, Xing-Quan Zhu, Shi-Chen Xie and Wen-Wei Gao
Animals 2024, 14(18), 2651; https://doi.org/10.3390/ani14182651 - 12 Sep 2024
Viewed by 497
Abstract
Two species of trichomonads, Tetratrichomonas buttreyi and Pentatrichomonas hominis, are common intestinal parasites that can impact animal health and productivity. Severe infection by these parasites can lead to diarrhea and wasting in affected animals. Notably, P. hominis is known to cause diarrhea [...] Read more.
Two species of trichomonads, Tetratrichomonas buttreyi and Pentatrichomonas hominis, are common intestinal parasites that can impact animal health and productivity. Severe infection by these parasites can lead to diarrhea and wasting in affected animals. Notably, P. hominis is known to cause diarrhea and has the potential to be transmitted between animals and humans. Donkeys hold significant economic importance in China’s agricultural sector. However, whether donkeys are infected with T. buttreyi and P. hominis remains unknown globally. To address this gap in knowledge, 815 fecal samples were collected from donkeys in three representative regions in Shanxi Province, North China. Then, the presence and genetic characteristics of T. buttreyi and P. hominis were examined using species-specific PCR primers amplifying the small subunit ribosomal RNA genes. The overall prevalence was detected to be 25.4% (207/815) for T. buttreyi and 0.7% (6/815) for P. hominis in donkeys in Shanxi Province. All obtained P. hominis sequences were identified as genotype CC1. Genetic analysis revealed that all P. hominis isolates from donkeys were clustered into the same branch with isolates detected in humans, suggesting possible zoonotic transmission. This study is the first to report the occurrence and prevalence of T. buttreyi and P. hominis in donkeys globally. These findings expand the host range of trichomonads and improve our understanding of their genetic diversity and zoonotic potential, providing essential baseline data for the prevention and control of these parasites in donkeys in the region. Full article
(This article belongs to the Special Issue Disease Epidemiology in Farm Animal Production)
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9 pages, 604 KiB  
Communication
Bovine Parainfluenza Virus 3 and Bovine Respiratory Syncytial Virus: Dominant Viral Players in Bovine Respiratory Disease Complex among Serbian Cattle
by Vesna Milićević, Sofija Šolaja, Dimitrije Glišić, Milan Ninković, Bojan Milovanović, Milan Đorđević, Snežana Ristevski, Filip Spasojević and Miroljub Dačić
Animals 2024, 14(10), 1458; https://doi.org/10.3390/ani14101458 - 14 May 2024
Cited by 1 | Viewed by 1348
Abstract
Bovine respiratory disease complex, a complex respiratory ailment in cattle, results from a combination of viral and bacterial factors, compounded by environmental stressors such as overcrowding, transportation, and adverse weather conditions. Its impact extends beyond mere health concerns, posing significant economic threats to [...] Read more.
Bovine respiratory disease complex, a complex respiratory ailment in cattle, results from a combination of viral and bacterial factors, compounded by environmental stressors such as overcrowding, transportation, and adverse weather conditions. Its impact extends beyond mere health concerns, posing significant economic threats to the cattle industry. This study presents an extensive investigation into viral pathogens associated with BRDC in Serbian cattle, utilizing serum samples and nasal swabs. A cross-sectional study was conducted in 2024 across 65 randomly selected dairy farms in Serbia, excluding farms with vaccinated cattle. The farms were categorized by their livestock count: small (≤50 animals), medium (51–200 animals), and large (>200 animals). Serum samples from adult cattle older than 24 months were tested for antibodies against BVDV, BHV-1, BRSV, and BPIV3. Nasal swab samples from the animals with respiratory signs were tested using PCR for viral genome detection. The results showed seropositivity for all four viruses across all of the farms, with BPIV3 exhibiting universal seropositivity. Medium-sized and large farms demonstrated higher levels of seropositivity for BRSV and BHV-1 compared to small farms (p < 0.05). Our true seroprevalence estimates at the animal level were 84.29% for BRSV, 54.08% for BVDV, 90.61% for BHV-1, and 84.59% for BPIV3. A PCR analysis of the nasal swabs revealed positive detections for BRSV (20%), BHV-1 (1.7%), BVDV (8%), and BPIV3 (10.9%). Influenza D virus was not found in any of the samples. This study provides critical insights into the prevalence and circulation of viral pathogens associated with BRDC in Serbian cattle, emphasizing the importance of surveillance and control measures to mitigate the impact of respiratory diseases in cattle populations. Full article
(This article belongs to the Special Issue Disease Epidemiology in Farm Animal Production)
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12 pages, 954 KiB  
Article
Determining the Economically Optimum Metaphylactic Strategy for Cattle Cohorts of Varied Demographic Characteristics
by Dannell J. Kopp, Robert L. Larson, Phillip A. Lancaster, Bradley J. White, Kristen J. Smith and Dustin L. Pendell
Animals 2024, 14(10), 1423; https://doi.org/10.3390/ani14101423 - 10 May 2024
Viewed by 876
Abstract
Metaphylactic antibiotic use in feeder cattle is a common practice to control respiratory disease. Antimicrobial stewardship is important to ensure continued efficacy and to protect animal welfare. The objective of this study is to identify characteristics of cohorts of cattle that had not [...] Read more.
Metaphylactic antibiotic use in feeder cattle is a common practice to control respiratory disease. Antimicrobial stewardship is important to ensure continued efficacy and to protect animal welfare. The objective of this study is to identify characteristics of cohorts of cattle that had not received metaphylaxis that would have benefited economically from the use of metaphylaxis. Cohorts (n = 12,785; 2,206,338 head) from 13 feedlots that did not receive metaphylaxis were modeled using an economic model to estimate net returns for three metaphylactic options. Logistic regression models with covariates for entry weight, sex, average daily weight gain, number of animals per cohort, and days on feed, with feedlot as a random effect, were used to determine the model-adjusted probability of cohorts benefiting economically from metaphylaxis. Most (72%) cohorts in this data set that had not received metaphylaxis at arrival would not economically benefit from metaphylaxis. Sex, entry weight category, number of cattle in the cohort, and average daily weight gain were associated with the likelihood of benefitting economically from metaphylaxis. The results illustrated that cattle cohort demographics influenced the probability that cohorts would benefit economically from metaphylaxis and the type of metaphylaxis utilized, and integrating this information has the potential to influence the metaphylaxis decision. Full article
(This article belongs to the Special Issue Disease Epidemiology in Farm Animal Production)
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25 pages, 915 KiB  
Article
Application of Epidemiological Methods in a Large-Scale Cross-Sectional Study in 765 German Dairy Herds—Lessons Learned
by Roswitha Merle, Martina Hoedemaker, Gabriela Knubben-Schweizer, Moritz Metzner, Kerstin-Elisabeth Müller and Amely Campe
Animals 2024, 14(9), 1385; https://doi.org/10.3390/ani14091385 - 6 May 2024
Cited by 1 | Viewed by 1501
Abstract
From 2016 to 2020, the “PraeRi” study, conducted by three German veterinary universities, was aimed at enhancing animal health and welfare in dairy farms. With 765 dairy farms visited and 101,307 animals examined, this study provided a basis for improving animal health and [...] Read more.
From 2016 to 2020, the “PraeRi” study, conducted by three German veterinary universities, was aimed at enhancing animal health and welfare in dairy farms. With 765 dairy farms visited and 101,307 animals examined, this study provided a basis for improving animal health and welfare. The study population comprised three different regions representing a broad variety of characteristics. To ensure representative estimates, a sample size of 250 farms was determined for each region, employing a stratified sampling plan based on farm size. According to the information provided by the farmers, the most commonly occurring disease in their herds was mastitis without general disorder (14.2% to 16.3% of the herd—depending on the region). For most disorders, prevalence data were lowest for the region South compared with the two remaining regions. Multivariable regression analyses were performed to identify risk factors for various target variables, and the results were communicated through individual reports and benchmarking flyers to participating farmers. The authors encountered challenges in management and communication due to the project’s size in terms of personnel, data, and farms examined. Harmonizing data management and hypothesis testing across all involved parties added complexity. Full article
(This article belongs to the Special Issue Disease Epidemiology in Farm Animal Production)
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15 pages, 1531 KiB  
Article
Epidemiology Tools to Evaluate the Control of Proliferative Enteropathy in Commercial Pig Herds
by Alison Collins and Cherie Collins
Animals 2024, 14(9), 1357; https://doi.org/10.3390/ani14091357 - 30 Apr 2024
Cited by 1 | Viewed by 923
Abstract
Proliferative enteropathy (PE) is characterized by diarrhea and reduced weight gains in growing pigs and intestinal hemorrhage in finishers. Vaccination, antibiotic medication, and improved hygiene can control PE, but their efficacy depends upon the epidemiology of PE. This study monitored the timing and [...] Read more.
Proliferative enteropathy (PE) is characterized by diarrhea and reduced weight gains in growing pigs and intestinal hemorrhage in finishers. Vaccination, antibiotic medication, and improved hygiene can control PE, but their efficacy depends upon the epidemiology of PE. This study monitored the timing and severity of PE in 84 commercial pens across seven treatments, including disinfection, vaccination, no treatment, medication with olaquindox (50, 25 and 12.5 ppm), and combined disinfection and vaccination. Vaccination with or without lime disinfection suppressed clinical signs of PE and reduced the number of excreted L. intracellularis relative to untreated pigs housed in cleaned or cleaned and disinfected pens between 9 and 17 weeks of age. Continuous olaquindox mediation to 17 weeks of age prevented L. intracellularis infection, leaving finisher pigs naïve. These finisher pigs suffered an outbreak of hemorrhagic enteropathy with significant reductions in weight gain, feed intake, and mortalities of 4.6%. Over the 13 week grow/finish period, vaccinated pigs housed in disinfected pens showed significantly higher weight gain and feed intake relative to all other treatments, equating to a weight gain difference of between 3.6 and 3.9 kg per pig. Monitoring the immune response and fecal excretion of L. intracellularis in pens of pigs enabled effective PE control strategies to be evaluated on the farm. Full article
(This article belongs to the Special Issue Disease Epidemiology in Farm Animal Production)
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9 pages, 2644 KiB  
Article
Surveillance of Sarcoptic Mange in Iberian Ibexes (Capra pyrenaica) and Domestic Goats (Capra hircus) in Southern Spain
by Félix Gómez-Guillamón, Débora Jiménez-Martín, Debora Dellamaria, Antonio Arenas, Luca Rossi, Carlo V. Citterio, Leonor Camacho-Sillero, Barbara Moroni, David Cano-Terriza and Ignacio García-Bocanegra
Animals 2024, 14(8), 1194; https://doi.org/10.3390/ani14081194 - 16 Apr 2024
Viewed by 1403
Abstract
Sarcoptic mange is a highly contagious skin disease caused by Sarcoptes scabiei. Sera were collected from 411 Iberian ibexes, comprising 157 individuals with sarcoptic mange skin lesions and 254 clinically healthy animals, in 13 population nuclei across Andalusia (southern Spain) between 2015 [...] Read more.
Sarcoptic mange is a highly contagious skin disease caused by Sarcoptes scabiei. Sera were collected from 411 Iberian ibexes, comprising 157 individuals with sarcoptic mange skin lesions and 254 clinically healthy animals, in 13 population nuclei across Andalusia (southern Spain) between 2015 and 2021. Skin samples from 88 of the 157 animals with mange-compatible lesions were also obtained. Moreover, 392 serum samples from domestic goats (Capra hircus) were collected in the same region and study period. Antibodies against S. scabiei were tested using an in-house indirect ELISA, while the presence of mites of S. scabiei was evaluated in the skin samples by potassium hydroxide digestion. Seropositivity was found in eight (3.1%) of the clinically healthy ibexes and in 104 (66.2%) of the animals with mange-compatible lesions. The presence of S. scabiei was confirmed in 57 (64.8%) out of the 88 skin samples analysed and anti-S. scabiei antibodies were found in 49 (86.0%) of these 57 mite-positive individuals. Seropositive animals were detected in population nuclei with previous records of sarcoptic mange, where S. scabiei mites were detected by potassium hydroxide digestion in individuals with sarcoptic mange-compatible external lesions. However, seropositivity was not observed in population nuclei that were historically free of this disease. None of the 392 domestic goats had antibodies against S. scabiei, suggesting an independent epidemiological cycle of sarcoptic mange in Iberian ibex populations in the study area, and a limited or null role of domestic goats in the transmission of the parasite to this wild species. Overall, our findings underscore the importance of maintaining and/or implementing integrated surveillance programs and control strategies in wildlife and livestock, to limit the risk of S. scabiei circulation in Iberian ibex populations. Full article
(This article belongs to the Special Issue Disease Epidemiology in Farm Animal Production)
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14 pages, 2515 KiB  
Article
Transmission Dynamics of Imported Vaccine-Origin PRRSV-2 within and between Commercial Swine Integrations in Hungary
by Szilvia Jakab, Krisztián Bányai, Krisztina Bali, Imre Nemes, Ádám Bálint and István Szabó
Animals 2023, 13(19), 3080; https://doi.org/10.3390/ani13193080 - 2 Oct 2023
Viewed by 1242
Abstract
This study reports on the molecular epidemiology of Ingelvac-PRRS-MLV-associated cases in Hungary for the period 2020–2021. Field epidemiology investigations led the experts to conclude that imported pigs, which were shipped through transit stations in Denmark, introduced the vaccine virus. The movement of fatteners [...] Read more.
This study reports on the molecular epidemiology of Ingelvac-PRRS-MLV-associated cases in Hungary for the period 2020–2021. Field epidemiology investigations led the experts to conclude that imported pigs, which were shipped through transit stations in Denmark, introduced the vaccine virus. The movement of fatteners and the neglect of disease control measures contributed to the spread of the virus to PRRS-free pig holdings in the vicinity. Deep sequencing was performed to genetically characterize the genes coding for the virion antigens (i.e., ORF2 through ORF7). The study isolates exhibited a range of 0.1 to 1.8% nucleotide sequence divergence from the Ingelvac PRRS MLV and identified numerous polymorphic sites (up to 57 sites) along the amplified 3.2 kilo base pair genomic region. Our findings confirm that some PRRSV-2 vaccine strains can accumulate very high number of point mutations within a short period in immunologically naive pig herds. Full article
(This article belongs to the Special Issue Disease Epidemiology in Farm Animal Production)
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12 pages, 1414 KiB  
Article
Co-Circulation of Multiple Coronavirus Genera and Subgenera during an Epizootic of Lethal Respiratory Disease in Newborn Alpacas (Vicugna pacos) in Peru: First Report of Bat-like Coronaviruses in Alpacas
by Luis Llanco, Karubya Retamozo, Noriko Oviedo, Alberto Manchego, César Lázaro, Dennis A. Navarro-Mamani, Norma Santos and Miguel Rojas
Animals 2023, 13(18), 2983; https://doi.org/10.3390/ani13182983 - 21 Sep 2023
Viewed by 1634
Abstract
Coronaviruses (CoVs) infect a wide range of hosts, including humans, domestic animals, and wildlife, typically causing mild-to-severe respiratory or enteric disease. The main objective of this study was to identify CoV genera and subgenera detected in Peruvian alpacas. Lung lavage specimens were collected [...] Read more.
Coronaviruses (CoVs) infect a wide range of hosts, including humans, domestic animals, and wildlife, typically causing mild-to-severe respiratory or enteric disease. The main objective of this study was to identify CoV genera and subgenera detected in Peruvian alpacas. Lung lavage specimens were collected from 32 animals aged 1 to 6 weeks. CoVs were identified by using RT-PCR to amplify a pan-CoV conserved region of the RNA-dependent RNA polymerase-encoding gene. A nested PCR was performed to identify β-CoVs. Then, β-CoV-positive samples were subjected to RT-PCR using specific primers to identify the Embecovirus subgenus. Out of 32 analyzed samples, 30 (93.8%) tested positive for at least one CoV genus. β-, α-, or unclassified CoVs were identified in 24 (80%), 1 (3.3%), and 1 (3.3%) of the positive samples, respectively. A CoV genus could not be identified in two (6.7%) samples. A mixture of different CoV genera was detected in two (6.7%) samples: one was co-infected with β- and α-CoVs, and the other contained a β- and an unclassified CoV. A sequence analysis of the amplicons generated by the PCR identified 17 β-CoV strains belonging to the subgenus Embecovirus and two α-CoV strains belonging to Decacovirus. A phylogenetic analysis of two strains revealed a relationship with an unclassified Megaderma BatCoV strain. A subgenus could not be identified in nine β-CoV samples. Our data show a high prevalence and a high genetic diversity of CoV genera and subgenera that infect alpacas, in which the β-CoV subgenus Embecovirus predominated. Our data also suggest a new role for bats in the dissemination and transmission of uncommon CoVs to alpacas raised in rural Peru. Full article
(This article belongs to the Special Issue Disease Epidemiology in Farm Animal Production)
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