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Meng W, Chen Z, Jiang Q, Chen J, Guo X, Ma Z, Jia K, Li S. A multiplex real-time fluorescence-based quantitative PCR assay for calf diarrhea viruses. Front Microbiol 2024; 14:1327291. [PMID: 38249490 PMCID: PMC10796610 DOI: 10.3389/fmicb.2023.1327291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Calf diarrhea is a significant condition that has a strong effect on the cattle industry, resulting in huge economic losses annually. Bovine torovirus (BToV), bovine enterovirus (BEV), bovine norovirus (BNoV), bovine coronavirus (BCoV), bovine rotavirus (BRV), and bovine viral diarrhea virus (BVDV) are key pathogens that have been implicated in calf diarrhea. Among these viruses, there remains limited research on BToV, BEV, and BNoV, with no available vaccines or drugs for their prevention and control. Although commercial vaccines exist for BCoV, BRV, and BVDV, the prevalence of these diseases remains high. Methods To address this issue, we developed a multiplex real-time fluorescence quantitative PCR method for detecting BToV, BEV, BNoV, BCoV, BRV, and BVDV. This method can be used to effectively monitor the prevalence of these six viruses and serve as a reference for future prevention and control strategies. In this study, we specifically designed primers and probes for the BNoV Rdrp, BEV 5'UTR, BToV M, BCoV N, BRV NSP5, and BVDV 5'UTR genes. Results This method was determined to be efficient, stable, and sensitive. The lowest detectable levels of plasmids for BNoV, BEV, BToV, BRV, BCoV, and BVDV were 1.91 copies/μL, 96.0 copies/μL, 12.8 copies/μL, 16.4 copies/μL, 18.2 copies/μL, and 65.3 copies/μL, respectively. Moreover, the coefficients of variation for all six detection methods were < 3%; they also exhibited a strong linear relationship (R2 ≥ 0.98), and an amplification efficiency of 90%-110%. A total of 295 fecal and anal swabs were collected from calves with diarrhea in Guangdong, China. The positive rates for BToV, BEV, BNoV, BCoV, BR, and BVDV were determined to be 0.34% (1/295), 6.10% (18/295), 0.68% (2/295), 1.36% (4/295), 10.85% (32/295), and 2.03% (6/295), respectively. Notably, BEV and BRV exhibited the highest prevalence. Discussion Additionally, this study identified the occurrence of BToV and BNoV in Guangdong for the first time. In summary, this study successfully established an effective method for detecting several important bovine viruses; ultimately, this holds strong implications for the future development of the cattle industry.
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Affiliation(s)
- Wenxin Meng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
| | - Zihan Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
| | - Qifeng Jiang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
| | - Jinping Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
| | - Xiaoying Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
| | - Zihang Ma
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
| | - Kun Jia
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
| | - Shoujun Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Technological Engineering Research Center for Pet, Guangzhou, China
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Silva CJD, Lima KPB, Monteiro JFDCLS, Silva AKSFD, Silva FJD, Pereira AMDS, Hernandes VP, Silva EDD, Silva CSDAGE, Brandão Filho SP, Brito MEFD. Leishmania V. braziliensis infection in asymptomatic domestic animals within an endemic region in the Northeast of Brazil. Rev Soc Bras Med Trop 2022; 55:e0600. [PMID: 35976338 PMCID: PMC9405948 DOI: 10.1590/0037-8682-0600-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/12/2022] [Indexed: 11/26/2022] Open
Abstract
Background: American cutaneous leishmaniasis is a commonly neglected, vector-borne tropical parasitic disease that is a major public health concern in Brazil. Leishmania (Viannia) braziliensis is the main species associated with the disease. Accurate diagnosis is based on epidemiological surveillance, clinical assessment, and laboratory testing. Leishmania (V.) braziliensis has been detected in several wild and synanthropic mammals. Their epidemiological role has not been entirely elucidated. This study aimed to assess potential L. braziliensis infections in asymptomatic domestic animals, by molecular and serological testing in endemic areas, in the metropolitan region of Recife. Methods: Blood samples and conjunctival fluids were collected from 232 animals (canids, felids, equines, and caprines) for the detection of L. braziliensis using molecular tests (conventional and real-time polymerase chain reaction [PCR and qPCR]). For immunological detection, blood samples from 115 dogs were assessed using enzyme-linked immunosorbent assay. Results: Real-time quantitative PCR showed positive results for blood and conjunctival samples in all investigated species. The results of the blood and conjunctival samples were 68.2% and 26.9% in Canis familiaris, 100% and 41.7% in Felis catus, 77.3% and 30.8% in Equus caballus/Equus asinus, and 50% and 33.3% in Capra hircus samples, respectively. Conclusions: Results from this study adds valuable information to our understanding of the role of asymptomatic domestic animals, L. braziliensis life cycle, and American cutaneous leishmaniasis in Northeast Brazil.
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Affiliation(s)
- Claudio Júlio da Silva
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Laboratório de Imunoparasitologia, Recife, PE, Brasil.,Núcleo de Vigilância em Saúde de Moreno, Moreno, PE, Brasil.,Universidade Fernando Pessoa, Faculdade de Ciência e Tecnologia, Porto, Portugal
| | - Karina Patricia Baracho Lima
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Laboratório de Imunoparasitologia, Recife, PE, Brasil
| | | | | | - Fernando José da Silva
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Laboratório de Imunoparasitologia, Recife, PE, Brasil
| | - Allana Maria de Souza Pereira
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Laboratório de Imunoparasitologia, Recife, PE, Brasil
| | - Valéria Pereira Hernandes
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Laboratório de Imunoparasitologia, Recife, PE, Brasil
| | - Elis Dionísio da Silva
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Laboratório de Imunoparasitologia, Recife, PE, Brasil
| | - Cláudia Sofia de Assunção Gonçalves E Silva
- Universidade Fernando Pessoa, Faculdade de Ciência e Tecnologia, Porto, Portugal.,Universidade Fernando Pessoa, Centro de Investigação em Biomedicina, Unidade de Investigação em Energia, Ambiente e Saúde, Porto, Portugal
| | - Sinval Pinto Brandão Filho
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Laboratório de Imunoparasitologia, Recife, PE, Brasil
| | - Maria Edileuza Felinto de Brito
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Laboratório de Imunoparasitologia, Recife, PE, Brasil
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Yang T, Song X, Zhong Y, Wang B, Zhou C. Field investigation‐ and dietary metabarcoding‐based screening of arthropods that prey on primary tea pests. Ecol Evol 2022; 12:e9060. [PMID: 35813924 PMCID: PMC9251880 DOI: 10.1002/ece3.9060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/30/2022] [Accepted: 06/10/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Tingbang Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Institute of Ecology China West Normal University Nanchong China
| | - Xuhao Song
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Institute of Ecology China West Normal University Nanchong China
| | - Yang Zhong
- School of Nuclear Technology and Chemistry & Biology Hubei University of Science and Technology Xianning China
- Hubei Engineering Research Center for Fragrant Plants Hubei University of Science and Technology Xianning China
| | - Bin Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Institute of Ecology China West Normal University Nanchong China
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Institute of Ecology China West Normal University Nanchong China
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Baroja U, Garin I, Vallejo N, Caro A, Ibáñez C, Basso A, Goiti U. Molecular assays to reliably detect and quantify predation on a forest pest in bats faeces. Sci Rep 2022; 12:2243. [PMID: 35145165 PMCID: PMC8831491 DOI: 10.1038/s41598-022-06195-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
Targeted molecular methods such as conventional PCR (cPCR) and quantitative PCR (qPCR), combined with species-specific primers and probes, are widely applied for pest species detection. Besides, the potential of qPCR to quantify DNA in samples makes it an invaluable molecular tool to infer the predation levels on specific prey by analysing predators’ stools. Nevertheless, studies on the diet of bats failed to find any empirical relationship, and it remains to be evaluated. Thus, we developed and evaluated two species-specific PCR assays to detect and quantify DNA of a major forest pest, the pine processionary, Thaumetopoea pityocampa, in bats’ faeces. Further, we empirically compared a range of different known DNA concentrations (input) of the target species mixed with mocks and bat faecal samples against DNA abundances yielded by qPCR (output) for a quantitative assessment. Overall, cPCR showed a lower detection rate than qPCR, but augmenting the replicate effort from one to three replicates led to a greater increase in the detection rate of the cPCR (from 57 to 80%) than the qPCR (from 90 to 99%). The quantitative experiment results showed a highly significant correlation between the input and output DNA concentrations (t = 10.84, p < 0.001) with a mean slope value of 1.05, indicating the accuracy of our qPCR assay to estimate DNA abundance of T. pityocampa in bat faeces. The framework of this study can be taken as a model to design similar assays applicable to other species of interest, such as agricultural pests or insects of public health concern.
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Affiliation(s)
- Unai Baroja
- Department of Zoology and Animal Cell Biology, Faculty of Science, University of the Basque Country, UPV/EHU, Leioa, Basque Country, Spain.
| | - Inazio Garin
- Department of Zoology and Animal Cell Biology, Faculty of Science, University of the Basque Country, UPV/EHU, Leioa, Basque Country, Spain
| | - Nerea Vallejo
- Department of Zoology and Animal Cell Biology, Faculty of Science, University of the Basque Country, UPV/EHU, Leioa, Basque Country, Spain
| | - Amaia Caro
- Department of Zoology and Animal Cell Biology, Faculty of Pharmacy, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Basque Country, Spain
| | - Carlos Ibáñez
- Department of Evolutionary Ecology, Estación Biológica de Doñana (CSIC), Avenida Américo Vespucio 26, 41092, Seville, Spain
| | - Andrea Basso
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università, 10, 35020, Legnaro, Padova, Italy
| | - Urtzi Goiti
- Department of Zoology and Animal Cell Biology, Faculty of Science, University of the Basque Country, UPV/EHU, Leioa, Basque Country, Spain
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Senevirathna JDM, Yonezawa R, Saka T, Igarashi Y, Funasaka N, Yoshitake K, Kinoshita S, Asakawa S. Selection of a reference gene for studies on lipid-related aquatic adaptations of toothed whales ( Grampus griseus). Ecol Evol 2021; 11:17142-17159. [PMID: 34938499 PMCID: PMC8668803 DOI: 10.1002/ece3.8354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 10/24/2021] [Accepted: 10/29/2021] [Indexed: 11/06/2022] Open
Abstract
Toothed whales are one group of marine mammals that has developed special adaptations, such as echolocation for predation, to successfully live in a dynamic aquatic environment. Their fat metabolism may differ from that of other mammals because toothed whales have acoustic fats. Gene expression in the metabolic pathways of animals can change with respect to their evolution and environment. A real-time quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for studying the relative expressions of genes. However, since the accuracy of RT-qPCR data is totally dependent on the reference gene, the selection of the reference gene is an essential step. In this study, 10 candidate reference genes (ZC3H10, FTL, LGALS1, RPL27, GAPDH, FTH1, DCN, TCTP, NDUS5, and UBIM) were initially tested for amplification efficiency using RT-qPCR. After excluding DCN, the remaining nine genes, which are nearly 100% efficient, were selected for the gene stability analysis. Stable reference genes across eight different fat tissue, liver, and muscle samples from Grampus griseus were identified by four algorithms, which were provided in Genorm, NormFinder, BestKeeper, and Delta CT. Finally, a RefFinder comprehensive ranking was performed based on the stability values, and the nine genes were ranked as follows: LGALS1 > FTL > GAPDH > ZC3H10 > FTH1 > NDUS5 > TCTP > RPL27 > UBIM. The LGALS1 and FTL genes were identified as the most stable novel reference genes. The third-ranked gene, GAPDH, is a well-known housekeeping gene for mammals. Ultimately, we suggest the use of LGALS1 as a reliable novel reference gene for genomics studies on the lipid-related aquatic adaptations of toothed whales.
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Affiliation(s)
- Jayan D. M. Senevirathna
- Laboratory of Aquatic Molecular Biology and BiotechnologyDepartment of Aquatic BioscienceGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
- Department of Animal ScienceFaculty of Animal Science and Export AgricultureUva Wellassa UniversityBadullaSri Lanka
| | - Ryo Yonezawa
- Laboratory of Aquatic Molecular Biology and BiotechnologyDepartment of Aquatic BioscienceGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Taiki Saka
- Laboratory of Aquatic Molecular Biology and BiotechnologyDepartment of Aquatic BioscienceGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Yoji Igarashi
- Department of Life Sciences and ChemistryGraduate School of BioresourcesMie UniversityMieJapan
| | - Noriko Funasaka
- Department of Life SciencesGraduate School of BioresourcesMie UniversityMieJapan
| | - Kazutoshi Yoshitake
- Laboratory of Aquatic Molecular Biology and BiotechnologyDepartment of Aquatic BioscienceGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Shigeharu Kinoshita
- Laboratory of Aquatic Molecular Biology and BiotechnologyDepartment of Aquatic BioscienceGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Shuichi Asakawa
- Laboratory of Aquatic Molecular Biology and BiotechnologyDepartment of Aquatic BioscienceGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
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Yang T, Song X, Xu X, Zhou C, Shi A. A comparative analysis of spider prey spectra analyzed through the next-generation sequencing of individual and mixed DNA samples. Ecol Evol 2021; 11:15444-15454. [PMID: 34765189 PMCID: PMC8571630 DOI: 10.1002/ece3.8252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 11/09/2022] Open
Abstract
As one of the most abundant predators of insects in terrestrial ecosystems, spiders have long received much attention from agricultural scientists and ecologists. Do spiders have a certain controlling effect on the main insect pests of concern in farmland ecosystems? Answering this question requires us to fully understand the prey spectrum of spiders. Next-generation sequencing (NGS) has been successfully employed to analyze spider prey spectra. However, the high sequencing costs make it difficult to analyze the prey spectrum of various spider species with large samples in a given farmland ecosystem. We performed a comparative analysis of the prey spectra of Ovia alboannulata (Araneae, Lycosidae) using NGS with individual and mixed DNA samples to demonstrate which treatment was better for determining the spider prey spectra in the field. We collected spider individuals from tea plantations, and two treatments were then carried out: (1) The DNA was extracted from the spiders individually and then sequenced separately (DESISS) and (2) the DNA was extracted from the spiders individually and then mixed and sequenced (DESIMS). The results showed that the number of prey families obtained by the DESISS treatment was approximately twice that obtained by the DESIMS treatment. Therefore, the DESIMS treatment greatly underestimated the prey composition of the spiders, although its sequencing costs were obviously lower. However, the relative abundance of prey sequences detected in the two treatments was slightly different only at the family level. Therefore, we concluded that if our purpose were to obtain the most accurate prey spectrum of the spiders, the DESISS treatment would be the best choice. However, if our purpose were to obtain only the relative abundance of prey sequences of the spiders, the DESIMS treatment would also be an option. The present study provides an important reference for choosing applicable methods to analyze the prey spectra and food web compositions of animal in ecosystems.
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Affiliation(s)
- Tingbang Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Institute of EcologyChina West Normal UniversityNanchongChina
| | - Xuhao Song
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Institute of EcologyChina West Normal UniversityNanchongChina
| | - Xiaoqin Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Institute of EcologyChina West Normal UniversityNanchongChina
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Institute of EcologyChina West Normal UniversityNanchongChina
| | - Aimin Shi
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
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