Probability of detecting influenza A virus subtypes H1N1 and H3N2 in individual pig nasal swabs and pen-based oral fluid specimens over time

Influenza A virus (IAV) active surveillance in pigs prior to weaning is commonly conducted by collecting individual samples, mostly nasal swabs. Recently, the use of udder skin wipes collected from lactating sows was identified as an effective sampling method to indicate IAV status of suckling piglets prior to weaning. However, there is limited information on the effect of pooling multiple udder wipes on the ability to detect IAV. We evaluated the effect of pooling 3, 5, or 10 udder wipes on the sensitivity of detecting IAV and compared the results with testing the wipes individually. The likelihood of detecting positive udder wipes decreased with pooling when the initial positive cycle threshold value was ≥31.5; pooling of up to 3 samples could be performed without affecting sensitivity significantly. Our results support pooling of udder skin wipes to conduct surveillance of IAV in pigs prior to weaning.

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N-Linked Glycan Sites on the Influenza A Virus Neuraminidase Head Domain Are Required for Efficient Viral Incorporation and Replication

Journal of Virology ◽

10.1128/jvi.00874-20 ◽

2020 ◽

Vol 94 (19) ◽

Cited By ~ 1

Author(s):

Henrik Östbye ◽

Jin Gao ◽

Mira Rakic Martinez ◽

Hao Wang ◽

Jan-Willem de Gier ◽

...

Keyword(s):

Influenza A Virus ◽

Surface Antigen ◽

Influenza A ◽

Surface Antigens ◽

Secretory Protein ◽

Enveloped Viruses ◽

Virion Incorporation ◽

Head Domain ◽

Glycosylation Sites ◽

Over Time

ABSTRACT N-linked glycans commonly contribute to secretory protein folding, sorting, and signaling. For enveloped viruses, such as the influenza A virus (IAV), large N-linked glycans can also be added to prevent access to epitopes on the surface antigens hemagglutinin (HA or H) and neuraminidase (NA or N). Sequence analysis showed that in the NA head domain of H1N1 IAVs, three N-linked glycosylation sites are conserved and that a fourth site is conserved in H3N2 IAVs. Variable sites are almost exclusive to H1N1 IAVs of human origin, where the number of head glycosylation sites first increased over time and then decreased with and after the introduction of the 2009 pandemic H1N1 IAV of Eurasian swine origin. In contrast, variable sites exist in H3N2 IAVs of human and swine origin, where the number of head glycosylation sites has mainly increased over time. Analysis of IAVs carrying N1 and N2 mutants demonstrated that the N-linked glycosylation sites on the NA head domain are required for efficient virion incorporation and replication in cells and eggs. It also revealed that N1 stability is more affected by the head domain glycans, suggesting N2 is more amenable to glycan additions. Together, these results indicate that in addition to antigenicity, N-linked glycosylation sites can alter NA enzymatic stability and the NA amount in virions. IMPORTANCE N-linked glycans are transferred to secretory proteins upon entry into the endoplasmic reticulum lumen. In addition to promoting secretory protein maturation, enveloped viruses also utilize these large oligosaccharide structures to prevent access to surface antigen epitopes. Sequence analyses of the influenza A virus (IAV) surface antigen neuraminidase (NA or N) showed that the conservation of N-linked glycosylation sites on the NA enzymatic head domain differs by IAV subtype (H1N1 versus H3N2) and species of origin, with human-derived IAVs possessing the most variability. Experimental analyses verified that the N-linked glycosylation sites on the NA head domain contribute to virion incorporation and replication. It also revealed that the head domain glycans affect N1 stability more than N2, suggesting N2 is more accommodating to glycan additions. These results demonstrate that in addition to antigenicity, changes in N-linked glycosylation sites can alter other properties of viral surface antigens and virions.

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Detection of Influenza A Virus Nucleoprotein Antibodies in Oral Fluid Specimens From Pigs Infected Under Experimental Conditions Using a Blocking ELISA

Transboundary and Emerging Diseases ◽

10.1111/tbed.12019 ◽

2012 ◽

Vol 61 (2) ◽

pp. 177-184 ◽

Cited By ~ 14

Author(s):

Y. Panyasing ◽

C. K. Goodell ◽

C. Wang ◽

A. Kittawornrat ◽

J. R. Prickett ◽

...

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

Oral Fluid ◽

Experimental Conditions ◽

Blocking Elisa

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Influenza A Virus Surveillance Based on Pre-Weaning Piglet Oral Fluid Samples

Transboundary and Emerging Diseases ◽

10.1111/tbed.12307 ◽

2014 ◽

Vol 63 (5) ◽

pp. e328-e338 ◽

Cited By ~ 12

Author(s):

Y. Panyasing ◽

C. Goodell ◽

A. Kittawornrat ◽

C. Wang ◽

I. Levis ◽

...

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

Oral Fluid ◽

Virus Surveillance

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Shedding and transmission of a live attenuated influenza A virus vaccine in pre-weaned pigs under field conditions

PLoS ONE ◽

10.1371/journal.pone.0246690 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0246690

Author(s):

Gustavo Lopez Moreno ◽

Jayaveeramuthu Nirmala ◽

Christa Goodell ◽

Marie Culhane ◽

Montserrat Torremorell

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

Rt Pcr ◽

Pcr Assay ◽

Post Vaccination ◽

Nasal Swabs ◽

Common Strategy ◽

Low Levels ◽

Live Attenuated Influenza Virus ◽

Pig Health

Influenza A virus (IAV) is one of the most important respiratory viruses affecting pig health and vaccination is the most common strategy to control influenza infections. In this field study we assessed the onset and duration of shedding of a live attenuated influenza virus (LAIV) vaccine, its ability to transmit to non-vaccinated pigs and whether the LAIV could be aerosolized and detected in the environment. Thirty-three litters (n = 33) of a farm using the LAIV vaccine were selected for the study, a subset of them (n = 12) were left unvaccinated and a subset of piglets (n = 3) in vaccinated litters were also left unvaccinated to serve as sentinels. Selected piglets from the litters were sampled multiple days post vaccination (DPV) by collecting nasal swabs and blood, and were tested using a LAIV vaccine specific RT-PCR assay and hemagglutination inhibition assay against the LAIV strains respectively. Environmental specimens consisting of air and surface wipes were also collected. One hundred percent (21/21) of the vaccinated litters tested LAIV positive 1 DPV and until 6 DPV. In contrast, only five (5/33) of the thirty-three non-vaccinated pigs tested positive during the course of the study. Viable LAIV was confirmed in vaccinated pigs by cell culture and whole genome sequencing. In addition, low levels of LAIV RNA (RT-PCR Ct values ranging between 33 and 38) were detected in all air specimens collected on the day of vaccination and until 6 DPV (3/10). Pigs had maternally derived antibodies reactive against the LAIV strains which may have influenced the degree of shedding observed. Under the conditions of this study, shedding of the LAIV from vaccinated pigs was limited in time, resulted in minimal transmission to non-vaccinated pigs and was detected in low levels in aerosols collected in the vaccinated rooms likely influenced by the presence of maternally derived antibodies against the LAIV strains.

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Microbiome disturbance and resilience dynamics of the upper respiratory tract in response to influenza A virus infection in humans and ferrets

10.1101/325324 ◽

2018 ◽

Author(s):

Drishti Kaul ◽

Raveen Rathnasinghe ◽

Marcela Ferres ◽

Gene S. Tan ◽

Aldo Barrera ◽

...

Keyword(s):

Influenza Virus ◽

Virus Infection ◽

Respiratory Tract ◽

Influenza A Virus ◽

Influenza A ◽

Cellular Damage ◽

Upper Respiratory Tract ◽

Upper Respiratory ◽

Influenza A Virus Infection ◽

Over Time

AbstractInfection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation because of host responses and cellular damage. The native upper respiratory tract (URT) microbiome likely plays a role, yet the effects of influenza infection on the URT microbiome are largely unknown. We performed a longitudinal study to assess the temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes had stable “heathy ecostate” communities both within and between individuals. In contrast, infected patients and ferrets exhibited large changes in bacterial community composition over time and between individuals. The “unhealthy” ecostates of infected individuals progressed towards the “healthy ecostate” over time, coinciding with viral clearance and recovery. Blooms of Pseudomonas were a statistically associated constant in the disturbed microbiomes of infected individuals. The dynamic and resilient nature of the microbiome during influenza virus infection in multiple hosts provides a compelling rationale for the maintenance of the microbiome homeostasis as a potential therapeutic target to prevent IAV associated bacterial co-infections.One Sentence SummaryDynamics of the upper respiratory tract microbiome during influenza A virus infection

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1350. Therapeutic Effects of Baloxavir Marboxil against Influenza A Virus Infection in Ferrets

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy210.1181 ◽

2018 ◽

Vol 5 (suppl_1) ◽

pp. S413-S413

Author(s):

Mitsutaka Kitano ◽

Takanobu Matsuzaki ◽

Ryoko Oka ◽

Kaoru Baba ◽

Takahiro Noda ◽

...

Keyword(s):

Body Temperature ◽

Oral Administration ◽

Influenza A Virus ◽

Influenza A ◽

Virus Titer ◽

Therapeutic Effects ◽

Single Oral Administration ◽

Influenza A Virus Infection ◽

Oseltamivir Phosphate ◽

Over Time

Abstract Background Baloxavir marboxil (BXM) is a novel small molecule inhibitor of cap-dependent endonuclease that is essential for influenza virus transcription and replication. In this study, pharmacokinetic profiles of BXM and baloxavir acid (BXA), an active form of BXM, were first examined in ferrets, and then the therapeutic effects of BXM against influenza A virus infection were compared with that of oseltamivir phosphate in ferrets. Methods The plasma exposure of BXA and BXM was examined after a single oral administration of BXM at doses of 10 and 30 mg/kg. The concentrations in plasma were determined by liquid chromatography-tandem mass spectrometry(LC/MS/MS). For efficacy study, ferrets infected intranasally with A/Kadoma/2006 (H1N1) were administrated 10 or 30 mg/kg of BXM orally twice daily for 1 day, starting at 1 day post-infection (p.i.) or administrated 10 mg/kg of BXM orally twice daily for 1 day, starting at 2 days p.i.. Oseltamivir phosphate was administered at doses of 5 mg/kg orally twice daily for 2 days as a comparison. The virus titer in the nasal washes and body temperature change were monitored during infection. Results BXA was detected in ferret plasma after a single oral administration of BXM at 10 and 30 mg/kg, in more than a dose-proportional manner. When the treatment was initiated at 1 day p.i., BXM at 10 and 30 mg/kg showed reduction of virus titer to an undetectable level on day 2 p.i. and statistically significant reduction in virus titer over time from day 2 to 3 p.i. compared with vehicle and oseltamivir phosphate. Moreover, the change of body temperature over time from 8 hours after the first administration to 3 days p.i. was significantly lower in BXM at 10 and 30 mg/kg than vehicle and oseltamivir phosphate. These effects were also observed in ferrets treated with BXM at 10 mg/kg even when administered at 2 day p.i. where ferret exhibit fever that is more than 1 degree higher than on 1 day p.i.. Conclusion Single-day oral administration of BXM had beneficial effects on viral titer and symptoms in ferrets infected with influenza A virus, which were superior to those observed with oseltamivir phosphate and vehicle. Disclosures M. Kitano, Shionogi & Co., Ltd.: Employee, Salary. T. Matsuzaki, Shionogi & Co., Ltd.: Employee, Salary. R. Oka, Shionogi & Co., Ltd.: Employee, Salary. K. Baba, Shionogi TechnoAdvance Research & Co., Ltd.: Employee, Salary. T. Noda, Shionogi TechnoAdvance Research & Co., Ltd.: Employee, Salary. Y. Yoshida, Shionogi & Co., Ltd.: Employee, Salary. K. Sato, Shionogi & Co., Ltd.: Employee, Salary. R. Yoshida, Shionogi & Co., Ltd.: Employee, Salary. A. Sato, Shionogi & Co., Ltd.: Employee, Salary. H. Kamimori, Shionogi & Co., Ltd.: Employee, Salary. T. Shishido, Shionogi & Co., Ltd.: Employee, Salary. A. Naito, Shionogi & Co., Ltd.: Employee, Salary.

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Modeling gene sequences over time in 2009 H1N1 Influenza A Virus populations

Virology Journal ◽

10.1186/1743-422x-6-215 ◽

2009 ◽

Vol 6 (1) ◽

pp. 215 ◽

Cited By ~ 5

Author(s):

Natalia Goñi ◽

Alvaro Fajardo ◽

Gonzalo Moratorio ◽

Rodney Colina ◽

Juan Cristina

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

H1n1 Influenza ◽

Gene Sequences ◽

2009 H1n1 ◽

Over Time

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Comparative study of the hemagglutinin and neuraminidase genes of influenza A virus H3N2, H9N2, and H5N1 subtypes using bioinformatics techniques

Canadian Journal of Microbiology ◽

10.1139/w07-044 ◽

2007 ◽

Vol 53 (7) ◽

pp. 830-839 ◽

Cited By ~ 5

Author(s):

Insung Ahn ◽

Hyeon S. Son

Keyword(s):

Codon Usage ◽

Influenza A Virus ◽

Host Species ◽

Influenza A ◽

Synonymous Codon ◽

Gc Content ◽

Synonymous Codon Usage ◽

Codon Usage Pattern ◽

Evolutionary Patterns ◽

Over Time

To investigate the genomic patterns of influenza A virus subtypes, such as H3N2, H9N2, and H5N1, we collected 1842 sequences of the hemagglutinin and neuraminidase genes from the NCBI database and parsed them into 7 categories: accession number, host species, sampling year, country, subtype, gene name, and sequence. The sequences that were isolated from the human, avian, and swine populations were extracted and stored in a MySQL®database for intensive analysis. The GC content and relative synonymous codon usage (RSCU) values were calculated using JAVA codes. As a result, correspondence analysis of the RSCU values yielded the unique codon usage pattern (CUP) of each subtype and revealed no extreme differences among the human, avian, and swine isolates. H5N1 subtype viruses exhibited little variation in CUPs compared with other subtypes, suggesting that the H5N1 CUP has not yet undergone significant changes within each host species. Moreover, some observations may be relevant to CUP variation that has occurred over time among the H3N2 subtype viruses isolated from humans. All the sequences were divided into 3 groups over time, and each group seemed to have preferred synonymous codon patterns for each amino acid, especially for arginine, glycine, leucine, and valine. The bioinformatics technique we introduce in this study may be useful in predicting the evolutionary patterns of pandemic viruses.

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Detection of pandemic influenza A/H1N1/pdm09 virus among pigs but not in humans in slaughterhouses in Kenya, 2013–2014

BMC Research Notes ◽

10.1186/s13104-019-4667-4 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 3

Author(s):

Eric Mogaka Osoro ◽

Shirley Lidechi ◽

Jeremiah Nyaundi ◽

Doris Marwanga ◽

Athman Mwatondo ◽

...

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

Respiratory Illness ◽

Influenza A Viruses ◽

Serum Samples ◽

Cross Sectional ◽

Western Kenya ◽

Influenza A H1n1 ◽

Nasal Swabs ◽

Polymerase Chain

Abstract Objective We conducted four cross-sectional studies over 1 year among humans and pigs in three slaughterhouses in Central and Western Kenya (> 350 km apart) to determine infection and exposure to influenza A viruses. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from participants who reported acute respiratory illness (ARI) defined as fever, cough or running nose. Nasal swabs and blood samples were collected from pigs. Human NP/OP and pig nasal swabs were tested for influenza A virus by real-time reverse transcriptase polymerase chain reaction (PCR) and pig serum was tested for anti-influenza A antibodies by ELISA. Results A total of 288 participants were sampled, 91.3% of them being male. Fifteen (5.2%) participants had ARI but the nine swabs collected from them were negative for influenza A virus by PCR. Of the 1128 pigs sampled, five (0.4%) nasal swabs tested positive for influenza A/H1N1/pdm09 by PCR whereas 214 of 1082 (19.8%) serum samples tested for Influenza A virus antibodies. There was higher seroprevalence in colder months and among pigs reared as free-range. These findings indicate circulation of influenza A/H1N1/pdm09 among pigs perhaps associated with good adaptation of the virus to the pig population after initial transmission from humans to pigs.

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