Use of oral fluids for efficient monitoring of influenza viruses in swine herds in Colombia

Čiuoderis, Karl; Perez, Laura Sofia Thomas; Cardona, Andrés; Hernández-Ortíz, Juan P.; Osorio, Jorge E.

doi:10.17533/udea.rccp.v35n3a02

Cited by 6 publications

(4 citation statements)

References 21 publications

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“…The phylogenetic analysis of the Colombian viruses confirmed what has been previously proposed about the genetic and antigenic dominance of the pandemic clade over classical FLUAV in the country since 2008 with no indication of the introduction of new H1 lineages or phylogenetic clades [26][27][28][29]. Nevertheless, the results presented here also provide evidence of the maintenance of the classical virus in Colombian pigs until 2021.…”

Section: Discussionsupporting

confidence: 87%

“…Epidemiological studies based on serology indicated that both H1N1 and H3N2 have been circulating among pig herds for at least 50 years [ 25 ]. More recently, research studies led to the isolation, sequencing, and partial genetic characterization of H1N1 strains in the country [ 26 , 27 , 28 , 29 ]. Regarding the H3N2 subtype, neither molecular evidence nor sequence data have yet been obtained.…”

Section: Introductionmentioning

confidence: 99%

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Sequence-Based Antigenic Analyses of H1 Swine Influenza A Viruses from Colombia (2008–2021) Reveals Temporal and Geographical Antigenic Variations

Ospina-Jimenez,

Gomez,

Rincon-Monroy

et al. 2023

Viruses

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Swine influenza is a respiratory disease that affects the pork industry and is a public health threat. It is caused by type A influenza virus (FLUAV), which continuously undergoes genetic and antigenic variations. A large amount of information regarding FLUAV in pigs is available worldwide, but it is limited in Latin America. The HA sequences of H1 subtype FLUAV-positive samples obtained from pigs in Colombia between 2008–2021 were analyzed using sequence-based antigenic cartography and N-Glycosylation analyses. Of the 12 predicted global antigenic groups, Colombia contained five: four corresponding to pandemic strains and one to the classical swine H1N1 clade. Circulation of these clusters was observed in some regions during specific years. Ca2 was the immunodominant epitope among Colombian viruses. The counts of N-Glycosylation motifs were associated with the antigenic cluster ranging from three to five. The results show for the first time the existence of antigenic diversity of FLUAV in Colombia and highlight the impact of spatial and temporal factors on this diversity. This study provides information about FLUAV variability in pigs under natural conditions in the absence of vaccination and emphasizes the need for surveillance of its phylogenetic and antigenic characteristics.

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Section: Discussionsupporting

confidence: 87%

Section: Introductionmentioning

confidence: 99%

Sequence-Based Antigenic Analyses of H1 Swine Influenza A Viruses from Colombia (2008–2021) Reveals Temporal and Geographical Antigenic Variations

Ospina-Jimenez,

Gomez,

Rincon-Monroy

et al. 2023

Viruses

View full text Add to dashboard Cite

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“…The analyses of the first viral isolates in the country confirmed the presence of classic H1N1 from clade 1A in Antioquia in 2008 (34), as well as the introduction and dissemination of H1N1pdm09 to other major pig-producing regions since 2009 (33,37). Subsequent investigations validate the constant circulation of IAV, specifically H1N1pdm09 in Antioquia, Cundinamarca, Valle del Cauca, Meta, and the "Coffee Region" (formed by Caldas, Huila, Quindío, and Risaralda regions) (32,38,39). However, the change in IAV viral dynamics in the Colombian swine population after the introduction of H1N1pdm09 remains unclear.…”

Section: Introductionmentioning

confidence: 72%

Zooming in on the molecular characteristics of swine influenza virus circulating in Colombia before and after the H1N1pdm09 virus

et al. 2022

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Influenza is one of the most critical viral agents involved in the respiratory disease complex affecting swine production systems worldwide. Despite the absence of vaccination against swine influenza virus in Colombia, the serologic reactivity to classic H1N1 and H3N2 subtypes reported since 1971 indicates the virus has been circulating in the country's swine population for several decades. However, successful isolation and sequencing of field virus from pigs was nonexistent until 2008, when H1N1 classical influenza virus was identified. One year later, due to the emergence of the influenza A (H1N1) pdm09 virus, responsible for the first global flu pandemic of the 21st century, it was introduced in the country. Therefore, to understand the impact of the introduction of the H1N1pdm09 virus in Colombia on the complexity and dynamics of influenza viruses previously present in the swine population, we carried out a study aiming to characterize circulating viruses genetically and establish possible reassortment events that might have happened between endemic influenza viruses before and after the introduction of the pandemic virus. A phylogenetic analysis of ten swine influenza virus isolates from porcine samples obtained between 2008 and 2015 was conducted. As a result, a displacement of the classical swine influenza virus with the pdmH1N1 virus in the swine population was confirmed. Once established, the pandemic subtype exhibited phylogenetic segregation based on a geographic pattern in all the evaluated segments. The evidence presents reassortment events with classic viruses in one of the first H1N1pdm09 isolates. Thus, this study demonstrates complex competition dynamics and variations in Colombian swine viruses through Drift and Shift.

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“…Thus, more cost-efficient and convenient sampling methods with comparable sensitivity have been sought during the last decade. The groupbased approach of oral fluid sampling has become very popular because it is less time-consuming and does not require restriction of individual pigs, hence, it is considered a cost-effective and animal friendly diagnostic tool for swIAV detection [34][35][36][37][38][39]. However, although the diagnostic sensitivity of oral fluids for qualitative swIAV detection was comparable and the duration of viral RNA shedding was longer in group-based oral fluids compared to individual nasal swabs, the difficulty to isolate swIAV from oral fluids displayed a major drawback for surveillance purposes related to strain characterization [34,37,[40][41][42].…”

Section: Discussionmentioning

confidence: 99%

Influenza surveillance in pigs: balancing act between broad diagnostic coverage and specific virus characterization

Stadler,

Zwickl,

Gumbert

et al. 2024

Porc Health Manag

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Background Monitoring of infectious diseases on swine farms requires a high diagnostic sensitivity and specificity of the test system. Moreover, particularly in cases of swine influenza A virus (swIAV) it is desirable to include characterization of the virus as precisely as possible. This is indispensable for strategies concerning prophylaxis of swIAV and furthermore, to meet the requirements of a purposeful monitoring of newly emerging swIAV strains in terms of vaccine design and public health. Within the present cross-sectional study, we compared the diagnostic value of group samples (wipes of surfaces with direct contact to mouth/nose, dust wipes, udder skin wipes, oral fluids) to individual samples (nasal swabs, tracheobronchial swabs) for both swIAV identification and characterization. Sampling included different stages of pig production on 25 sow farms with attached nursery considered as enzootically infected with swIAV. Firstly, samples were analyzed for IAV genome and subsequently samples with Ct-values < 32 were subtyped by multiplex RT-qPCR. Results Nasal swabs of suckling piglets and nursery pigs resulted in a higher odds to detect swIAV (p < 0.001) and to identify swIAV subtypes by RT-qPCR (p < 0.05) compared to nasal swabs of sows. In suckling piglets, significant higher rates of swIAV detection could be observed for nasal swabs (p = 0.007) and sow udder skin wipes (p = 0.036) compared to contact wipes. In the nursery, group sampling specimens were significantly more often swIAV positive compared to individual samples (p < 0.01), with exception of the comparison between contact wipes and nasal swabs (p = 0.181). However, in general nasal swabs were more likely to have Ct-value < 32 and thus, to be suitable for subtyping by RT-qPCR compared to dust wipes, contact wipes, udder skin wipes and tracheobronchial swabs (p < 0.05). Interestingly, different subtypes were found in different age groups as well as in different specimens in the same holding. Conclusion Although population-based specimens are highly effective for swIAV monitoring, nasal swabs are still the preferable sampling material for the surveillance of on-farm circulating strains due to significantly higher virus loads. Remarkably, sampling strategies should incorporate suckling piglets and different age groups within the nursery to cover as many as possible of the on-farm circulating strains.

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Use of oral fluids for efficient monitoring of influenza viruses in swine herds in Colombia

Cited by 6 publications

References 21 publications

Sequence-Based Antigenic Analyses of H1 Swine Influenza A Viruses from Colombia (2008–2021) Reveals Temporal and Geographical Antigenic Variations

Sequence-Based Antigenic Analyses of H1 Swine Influenza A Viruses from Colombia (2008–2021) Reveals Temporal and Geographical Antigenic Variations

Zooming in on the molecular characteristics of swine influenza virus circulating in Colombia before and after the H1N1pdm09 virus

Influenza surveillance in pigs: balancing act between broad diagnostic coverage and specific virus characterization

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