Getting a closer look at USDA swine influenza A ...

Getting a closer look at USDA swine influenza A surveillance: What can we learn from the genetic data that can help us on the f arm? Tavis K. Anderson; Pravina Kitikoon; Amy L. Vincent Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa such as timely vaccine and diagnostic updates, as well as providing insight into determinants of transmission that Among the influenza A viruses (IAV) circulating in the could be mitigated by changes in production practices or US swine population from 1930 to present are at least ten facility management. genetically and antigenically distinct hemagglutinin (HA) lineages: three classical swine lineages H1α, H1β, H1γ; two Methods lineages derived from human seasonal H1 viruses H1δ1, rom 2009-2013 samples were collected from swine across H1δ2; the H1pdm09; and H3 cluster I-IV viruses.1,2 The F primary implication of these antigenic differences is that the US and processed upon: a) observation of swine with controlling infection and transmission via vaccination may influenza-like illness (ILI); b) observation of swine epinot be optimal. Current swine IAV vaccines use multivalent demiologically linked to a human case of novel IAV; or formulations of field-sourced virus, each component repre- c) observation of swine with signs of ILI at “comingling senting one of the different lineages, but not all lineages are points.” Up to 10 samples per laboratory accession, either included.3 These vaccines elicit antibodies with a relatively from nasal swabs, lung tissues or oral fluids, were sent to narrow range of protection, and efficacy is equivocal for a participating NAHLN laboratory and screened with a matrix (M) gene PCR assay specific for IAV. For those drifted strains. submissions positive for IAV, up to 2 positive samples were Our best option in controlling disease is the development subjected to subtyping by PCR assays (H1 or H3, N1 or and appropriate application of effective vaccines. It is es- N2, and/or undetermined), and virus isolation. Successful sential that these vaccine strains match viruses circulating virus isolations were further characterized by sequencing in the swine population, and achieving this is predicated on of the HA, neuraminidase (NA), and M genes and subavailability of robust viral surveillance data. As a model, sequently deposited into the Influenza Virus Resource, the global surveillance program administered by the World National Center for Biotechnology Information’s online Health Organization for human influenza vaccine design sequence repository.7 conducts large-scale phylogenetic and antigenic analyses of thousands of HA1 sequences and hemagglutination Nucleotide sequences from 1210 HA segments, 1175 NA inhibition (HI) results collected from >100 countries segments, and 1197 M segments were analyzed from on a semi-annual basis to inform selection of strains for IAV from US swine during 2009-2013. Viruses were colmultivalent vaccine compositions.4 Although vaccine mis- lected from swine in 25 US states (Arkansas, Colorado, matches occasionally occur, a robust surveillance system Iowa, Illinois, Indiana, Kentucky, Michigan, Minnesota, has resulted in vaccines that tend to protect well against Missouri, Mississippi, Montana, North Carolina, North circulating viruses, reducing morbidity and mortality in Dakota, Nebraska, New York, Ohio, Oklahoma, Oregon, the human population.5 Prior to 2009 such an approach Pennsylvania, South Dakota, Tennessee, Texas, Virginia, would not have been feasible in the swine IAV system; Wisconsin, and Wyoming). however, capacity building efforts in North America, led From these data, five sequence alignments were constructby the United States Department of Agriculture (USDA) ed using MUSCLE v.3.8.31:8 an alignment of H3 and H1 and implemented through the voluntary National Animal HA sequences, an alignment of N1 and N2 neuraminidase Health Laboratory Network (NAHLN) has redressed sequences, and an alignment of the M sequences. Based concerns about the insufficient quantity of virological and upon the H1 phylogeny, H1N1 and H1N2 isolates were molecular surveillance of IAV in swine.6 Consequently, it assigned to one of six previously described H1 antigenic is now possible to provide insight into the patterns of swine lineages, H1α, H1β, H1γ, H1δ1, H1δ2, H1pdm09.9,10 H3N2 IAV spread, genetic diversity throughout the year, and isolates were assigned to one of four main clusters based the dynamics of IAV evolution in North America. These upon the H3 phylogeny,2 and H3 Cluster IV isolates to one data allow for the identification of intervention strategies of 6 recently designated “clades”.2 Within and between

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Introduction

Tavis K. Anderson; Pravina Kitikoon; Amy L. Vincent clade nucleotide distances were calculated using MEGA.11 To clarify the evolutionary history of the H3N2 viruses, sequences from randomly selected H3 Cluster I, II and III viruses in Genbank were included in addition to the USDA system H3N2 isolates. For each of the alignments a maximum likelihood tree was inferred using RAxML (v7.4.2;)12 employing a general time-reversible (GTR) model of nucleotide substitution with G-distributed rate variation among sites. The starting tree was generated under parsimony methods, with the best-scoring tree and statistical support values obtained with the rapid bootstrap algorithm (1,000 replications).

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We also detected a seasonal trend in clinical swine IAV within the US We observe a primary seasonal peak that starts in September and peaks during November, and a secondary peak that begins in February and peaks in March. These peaks are coincident with changes in farm management. In the fall of each year when temperatures drop and daylight hours decrease, farms move from open-ventilation to closed-ventilation systems, with a concomitant change in indoor environmental conditions (i.e., reduced air exchange, decreased relative humidity). It is likely these factors facilitate transmission by exposing pigs to different climatic, airflow, and/or behavioral stress conditions; and management and control of transmission To study the seasonal patterns of swine IAV in the US, should take this into consideration. we conducted statistical analyses using the number of influenza isolates aggregated by month from 2009 to 2013. Swine IAV is commonly identified in diagnostic inFrequencies of monthly isolates were analyzed through vestigations of respiratory disease; these outbreaks and decomposition of the time series into seasonal, trend and endemic infections likely cause significant economic irregular components using Loess.13 Swine population burden on producers given the loss in growth potential estimates were sourced from the Quarterly Hogs and Pigs following infection.15 Vaccines that do not sufficiently report produced by the National Agricultural Statistics cover or match the observed diversity of IAV in the swine Service (USDA: http://usda.mannlib.cornell.edu/). population and, in relation, poorly timed vaccine use (i.e., In addition, using a Lotka–Euler framework, we relate when pigs have circulating maternal antibodies16) likely observed growth rate in the number of swine IAV cases contributes to the difficulty in controlling IAV in swine. in the surveillance system to the reproductive number.14 Given that we document seven genetically and antigeniIn this way the reproductive number, which represents cally distinct hemagglutinin lineages (H1α, H1β, H1γ, generation intervals and seasonal epidemic growth, pro- H1δ1, H1δ2, H1pdm09 and H3 cluster IV) circulating, vides insight into the strategies and efforts required to it is essential that we reconsider our approach to vaccine control swine IAV. updates and/or technology. Surveillance of IAV in US swine has progressed substantially since 2009, providing timely insight into co-circulating viral diversity. These Results and d iscussion data should be used to inform intervention strategies of The three IAV subtypes (H1N1, H1N2, and H3N2) envaccine and diagnostic updates and potential changes demic in the US swine population were detected every year swine health management. during our study period. The H1N1 and H1N2 subtypes were detected at similar frequencies across the 4 years, References representing 37.4% and 36.8% of all isolates respectively. Although the H3N2 represented less than 25% of the 1.Lorusso A, Vincent AL, Gramer MR, Lager KM, Ciacciidentified viruses during the total time period, this sub- Zanella JR. Contemporary Epidemiology of North American type represented an increasing proportion of sequenced Lineage Triple Reassortant Influenza A Viruses in Pigs. Curr Top Microbiol Immunol 2013; 370:113-32. isolates, from 25% in 2010 to 33% in 2012. Among the 2.Kitikoon P, Nelson MI, Killian ML, et al. Genotype patterns H1N1 and H1N2 subtype viruses in our study, 1.1% were of contemporary reassorted H3N2 virus in U.S. swine. J Gen H1α, 3.4% were H1β, 32.8% were H1γ, 43.3% were H1δ1, Virol 2013; 94: 1 236-1241. 3.9% were H1δ2, and 13.9% were H1pdm09. Of note, is 3.Van Reeth K, Ma W. Swine Influenza Virus Vaccines: To the rapid increase in the occurrence of H1δ1 in samples Change or Not to Change-That’s the Question. Curr Top Microsubmitted, with a concurrent decrease in H1pdm09 since biol Immunol 2013; 370:173-200. 2009. These data reveal year round circulation with a 4.Russell CA, Jones TC, Barr IG, et al. Influenza vaccine strain primary peak of sequenced isolates in October-November; selection and recent studies on the global migration of seasonal and in H1N1 and H1N2, a secondary peak in March. We influenza viruses. Vaccine 2008; 26 Suppl 4:D31-34. find that the reproductive number of H1N1, H1N2 and 5.Karlsson Hedestam GB, Fouchier RA, Phogat S, et al. The H3N2 across each year is larger than R = 1: in 2010 H1N1 = challenges of eliciting neutralizing antibodies to HIV-1 and to 2.31 (1.7-2.9); H1N2 = 3.14 (1.3-5.7); H3N2 = 3.55 (1.6-6.8) influenza virus. Nat Rev Microbiol 2008; 6:143-155. and in 2012 H1N1 = 2.75 (2.6-2.9); H1N2 = 2.67 (2.5-2.8); 6.Korslund JA, Pyburn DG, Swenson SL, et al. (2013) Summary of results: USDA surveillance for influenza A virus in swine. H3N2 = 6.05 (1.1-14.8). American Association of Swine Veterinarians, pp 507-512.

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