Sequencing protocol and bioinformatics pipeline for the avian influenza virus
Protokol za sekvenciranje i bioinformatičku analizu virusa avijarne influence
Authors
Gajdov, VladimirPetrović, Tamaš
Lazić, Gospava
Đurđević, Biljana
Pajić, Marko
Knežević, Slobodan
Nišavić, Jakov
Article (Published version)
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The avian influenza virus (AIV), traditionally confined to avian hosts, has recently been detected in various mammal species, raising significant concerns for both animal and public health, necessitating efficient and accurate methods for virus detection and characterization. This study presents a sequencing protocol combined with a comprehensive bioinformatics pipeline designed for the sequencing and analysis of AIV genomes. The presented streamlined approach encompasses whole genome PCR-amplification of the viral genome, enabling the genome characterization and detection of viral mutations with high precision. An amplicon-based MiniSeq sequencing workflow based on a set of PCR primers targeting all genome segments was developed. Three samples from H5 high pathogenic avian influenza (HPAI) outbreaks in Serbia were sequenced using the MiniSeq platform. The protocol involves optimized sample preparation, tailored specifically for AIV, library preparation and sequencing. This is compleme...nted by a robust bioinformatics pipeline that includes quality control, read mapping, consensus genome generation, subtyping and pathotyping, as well as statistical sequencing data. The pipeline efficiently processes raw sequencing data, ensuring high-quality genome assemblies and accurate identification of viral strains. The protocol was used on AIV samples from various avian species, demonstrating its applicability and reliability. The results highlight the protocol’s capability to generate comprehensive genomic data, which is crucial for monitoring viral evolution and informing public health interventions. The described integrated approach offers a powerful tool for AIV surveillance and research, facilitating timely and informed decision-making in response to avian influenza outbreaks. This protocol can be readily adapted for use in various laboratory settings, contributing to global efforts in combating avian influenza and enhancing our understanding of its genomic landscape.
Keywords:
avian influenza / high-throughput sequencing / bioinformatics / viral genomics / molecular characterizationSource:
Archives of Veterinary Medicine, 2024, 17, 1, 89-97Publisher:
- Novi Sad : Scientific Veterinary Institute "Novi Sad"
Funding / projects:
- Ministry of Science, Technological Development and Innovation of the Republic of Serbia, institutional funding - 200031 (Scientific Institute of Veterinary Medicine 'Novi Sad', Novi Sad) (RS-MESTD-inst-2020-200031)
- MetAvian - Exploring the Avian Microbial Frontier: MetagenomicSurveillance of Infectious Diseases and Antimicrobial Resistance in Wild Birds (RS-ScienceFundRS-Promis2023-10945)
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Fakultet veterinarske medicineTY - JOUR AU - Gajdov, Vladimir AU - Petrović, Tamaš AU - Lazić, Gospava AU - Đurđević, Biljana AU - Pajić, Marko AU - Knežević, Slobodan AU - Nišavić, Jakov PY - 2024 UR - https://vet-erinar.vet.bg.ac.rs/handle/123456789/4150 AB - The avian influenza virus (AIV), traditionally confined to avian hosts, has recently been detected in various mammal species, raising significant concerns for both animal and public health, necessitating efficient and accurate methods for virus detection and characterization. This study presents a sequencing protocol combined with a comprehensive bioinformatics pipeline designed for the sequencing and analysis of AIV genomes. The presented streamlined approach encompasses whole genome PCR-amplification of the viral genome, enabling the genome characterization and detection of viral mutations with high precision. An amplicon-based MiniSeq sequencing workflow based on a set of PCR primers targeting all genome segments was developed. Three samples from H5 high pathogenic avian influenza (HPAI) outbreaks in Serbia were sequenced using the MiniSeq platform. The protocol involves optimized sample preparation, tailored specifically for AIV, library preparation and sequencing. This is complemented by a robust bioinformatics pipeline that includes quality control, read mapping, consensus genome generation, subtyping and pathotyping, as well as statistical sequencing data. The pipeline efficiently processes raw sequencing data, ensuring high-quality genome assemblies and accurate identification of viral strains. The protocol was used on AIV samples from various avian species, demonstrating its applicability and reliability. The results highlight the protocol’s capability to generate comprehensive genomic data, which is crucial for monitoring viral evolution and informing public health interventions. The described integrated approach offers a powerful tool for AIV surveillance and research, facilitating timely and informed decision-making in response to avian influenza outbreaks. This protocol can be readily adapted for use in various laboratory settings, contributing to global efforts in combating avian influenza and enhancing our understanding of its genomic landscape. PB - Novi Sad : Scientific Veterinary Institute "Novi Sad" T2 - Archives of Veterinary Medicine T1 - Sequencing protocol and bioinformatics pipeline for the avian influenza virus T1 - Protokol za sekvenciranje i bioinformatičku analizu virusa avijarne influence VL - 17 IS - 1 SP - 89 EP - 97 DO - 10.46784/e-avm.v17i1.381 ER -
@article{ author = "Gajdov, Vladimir and Petrović, Tamaš and Lazić, Gospava and Đurđević, Biljana and Pajić, Marko and Knežević, Slobodan and Nišavić, Jakov", year = "2024", abstract = "The avian influenza virus (AIV), traditionally confined to avian hosts, has recently been detected in various mammal species, raising significant concerns for both animal and public health, necessitating efficient and accurate methods for virus detection and characterization. This study presents a sequencing protocol combined with a comprehensive bioinformatics pipeline designed for the sequencing and analysis of AIV genomes. The presented streamlined approach encompasses whole genome PCR-amplification of the viral genome, enabling the genome characterization and detection of viral mutations with high precision. An amplicon-based MiniSeq sequencing workflow based on a set of PCR primers targeting all genome segments was developed. Three samples from H5 high pathogenic avian influenza (HPAI) outbreaks in Serbia were sequenced using the MiniSeq platform. The protocol involves optimized sample preparation, tailored specifically for AIV, library preparation and sequencing. This is complemented by a robust bioinformatics pipeline that includes quality control, read mapping, consensus genome generation, subtyping and pathotyping, as well as statistical sequencing data. The pipeline efficiently processes raw sequencing data, ensuring high-quality genome assemblies and accurate identification of viral strains. The protocol was used on AIV samples from various avian species, demonstrating its applicability and reliability. The results highlight the protocol’s capability to generate comprehensive genomic data, which is crucial for monitoring viral evolution and informing public health interventions. The described integrated approach offers a powerful tool for AIV surveillance and research, facilitating timely and informed decision-making in response to avian influenza outbreaks. This protocol can be readily adapted for use in various laboratory settings, contributing to global efforts in combating avian influenza and enhancing our understanding of its genomic landscape.", publisher = "Novi Sad : Scientific Veterinary Institute "Novi Sad"", journal = "Archives of Veterinary Medicine", title = "Sequencing protocol and bioinformatics pipeline for the avian influenza virus, Protokol za sekvenciranje i bioinformatičku analizu virusa avijarne influence", volume = "17", number = "1", pages = "89-97", doi = "10.46784/e-avm.v17i1.381" }
Gajdov, V., Petrović, T., Lazić, G., Đurđević, B., Pajić, M., Knežević, S.,& Nišavić, J.. (2024). Sequencing protocol and bioinformatics pipeline for the avian influenza virus. in Archives of Veterinary Medicine Novi Sad : Scientific Veterinary Institute "Novi Sad"., 17(1), 89-97. https://doi.org/10.46784/e-avm.v17i1.381
Gajdov V, Petrović T, Lazić G, Đurđević B, Pajić M, Knežević S, Nišavić J. Sequencing protocol and bioinformatics pipeline for the avian influenza virus. in Archives of Veterinary Medicine. 2024;17(1):89-97. doi:10.46784/e-avm.v17i1.381 .
Gajdov, Vladimir, Petrović, Tamaš, Lazić, Gospava, Đurđević, Biljana, Pajić, Marko, Knežević, Slobodan, Nišavić, Jakov, "Sequencing protocol and bioinformatics pipeline for the avian influenza virus" in Archives of Veterinary Medicine, 17, no. 1 (2024):89-97, https://doi.org/10.46784/e-avm.v17i1.381 . .