scholarly journals Analysis of Coinfections with A/H1N1 Strain Variants among Pigs in Poland by Multitemperature Single-Strand Conformational Polymorphism

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Krzysztof Lepek ◽  
Beata Pajak ◽  
Lukasz Rabalski ◽  
Kinga Urbaniak ◽  
Krzysztof Kucharczyk ◽  
...  
Keyword(s):  
Influenza A ◽  
Cost Effective ◽  
Single Strand ◽  
Surveillance Systems ◽  
Monitoring And Control ◽  
Influenza A Viruses ◽  
Single Strand Conformational Polymorphism ◽  
Conformational Polymorphism ◽  
Wide Range ◽  
Different Strains

Monitoring and control of infections are key parts of surveillance systems and epidemiological risk prevention. In the case of influenza A viruses (IAVs), which show high variability, a wide range of hosts, and a potential of reassortment between different strains, it is essential to study not only people, but also animals living in the immediate surroundings. If understated, the animals might become a source of newly formed infectious strains with a pandemic potential. Special attention should be focused on pigs, because of the receptors specific for virus strains originating from different species, localized in their respiratory tract. Pigs are prone to mixed infections and may constitute a reservoir of potentially dangerous IAV strains resulting from genetic reassortment. It has been reported that a quadruple reassortant, A(H1N1)pdm09, can be easily transmitted from humans to pigs and serve as a donor of genetic segments for new strains capable of infecting humans. Therefore, it is highly desirable to develop a simple, cost-effective, and rapid method for evaluation of IAV genetic variability. We describe a method based on multitemperature single-strand conformational polymorphism (MSSCP), using a fragment of the hemagglutinin (HA) gene, for detection of coinfections and differentiation of genetic variants of the virus, difficult to identify by conventional diagnostic.

ViDiT–CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications

2018 ◽  
Vol 64 (10) ◽  
pp. 761-773 ◽  
Author(s):  
Joost T.P. Verhoeven ◽  
Marta Canuti ◽  
Hannah J. Munro ◽  
Suzanne C. Dufour ◽  
Andrew S. Lang
Keyword(s):  
Influenza A ◽  
High Throughput Sequencing ◽  
Low Cost ◽  
Quality Data ◽  
Library Preparation ◽  
Virus Discovery ◽  
Influenza A Viruses ◽  
Wide Range ◽  
Functional Profiling ◽  
Biology Laboratory

High-throughput sequencing (HTS) technologies are becoming increasingly important within microbiology research, but aspects of library preparation, such as high cost per sample or strict input requirements, make HTS difficult to implement in some niche applications and for research groups on a budget. To answer these necessities, we developed ViDiT, a customizable, PCR-based, extremely low-cost (less than US$5 per sample), and versatile library preparation method, and CACTUS, an analysis pipeline designed to rely on cloud computing power to generate high-quality data from ViDiT-based experiments without the need of expensive servers. We demonstrate here the versatility and utility of these methods within three fields of microbiology: virus discovery, amplicon-based viral genome sequencing, and microbiome profiling. ViDiT–CACTUS allowed the identification of viral fragments from 25 different viral families from 36 oropharyngeal–cloacal swabs collected from wild birds, the sequencing of three almost complete genomes of avian influenza A viruses (>90% coverage), and the characterization and functional profiling of the complete microbial diversity (bacteria, archaea, viruses) within a deep-sea carnivorous sponge. ViDiT–CACTUS demonstrated its validity in a wide range of microbiology applications, and its simplicity and modularity make it easily implementable in any molecular biology laboratory, towards various research goals.

scholarly journals Eco-Epidemiological Evidence of the Transmission of Avian and Human Influenza A Viruses in Wild Pigs in Campeche, Mexico

Viruses ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 528
Author(s):  
Brenda Aline Maya-Badillo ◽  
Rafael Ojeda-Flores ◽  
Andrea Chaves ◽  
Saul Reveles-Félix ◽  
Guillermo Orta-Pineda ◽  
...  
Keyword(s):  
Influenza A ◽  
Influenza Viruses ◽  
Influenza A Viruses ◽  
Serum Samples ◽  
Fragmented Habitats ◽  
Wild Pigs ◽  
Wide Range ◽  
Influenza Transmission ◽  
Human Viruses ◽  
Positive Results

Influenza, a zoonosis caused by various influenza A virus subtypes, affects a wide range of species, including humans. Pig cells express both sialyl-α-2,3-Gal and sialyl-α-2,6-Gal receptors, which make them susceptible to infection by avian and human viruses, respectively. To date, it is not known whether wild pigs in Mexico are affected by influenza virus subtypes, nor whether this would make them a potential risk of influenza transmission to humans. In this work, 61 hogs from two municipalities in Campeche, Mexico, were sampled. Hemagglutination inhibition assays were performed in 61 serum samples, and positive results were found for human H1N1 (11.47%), swine H1N1 (8.19%), and avian H5N2 (1.63%) virus variants. qRT-PCR assays were performed on the nasal swab, tracheal, and lung samples, and 19.67% of all hogs were positive to these assays. An avian H5N2 virus, first reported in 1994, was identified by sequencing. Our results demonstrate that wild pigs are participating in the exposure, transmission, maintenance, and possible diversification of influenza viruses in fragmented habitats, highlighting the synanthropic behavior of this species, which has been poorly studied in Mexico.

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