Young Ki Choi

Prevalence of swine influenza virus subtypes on swine farms in the United States

Summary Serologic and virologic prevalence of infection with different swine influenza virus (SIV) subtypes was investigated using swine sera, nasal swabs and lung samples that had been submitted for a diagnosis to the Minnesota Veterinary Diagnostic Laboratory. A total of 111,418 pig sera were tested for SIV antibody between 1998 and 2000, and 25,348 sera (22.8%) were found to be positive by the hemagglutination inhibition (HI) test. Of the positive samples, 16,807 (66.7%) and 8,541 (33.7%) had antibody to H1 and H3 subtypes, respectively. Between January 1998 and May of 2001, a total of 3,561 nasal swabs or lung samples were examined for the presence of SIV, and SIV was isolated from 1,124 samples (31.7%). Of these isolates, 869 (77.3%) and 255 (22.7%) were subtyped as H1 and H3, respectively, by the HI method. For further characterization, 120 SIV isolates each from 1998 to 2001 were randomly selected from a culture collection and their hemagglutinin (HA) and neuraminidase genes examined by reverse transcription-PCR and sequencing. Of the 480 isolates, 322 (67.1%), 22 (4.6%) and 129 (26.9%) were subtyped as H1N1, H1N2 and H3N2, respectively. The remaining 7 samples (1.5%) were found to contain both H1N1 and H3N2 viruses. The SIV H1N2 subtype was isolated from 1, 8, and 13 samples in 1999, 2000, and 2001, respectively. The 22 H1N2 isolates originated from 9 different states of the United States. Genetic screening of the HA genes of 12 selected H1N2 isolates showed that 8 of them had a close phylogenetic relationship with the Indiana isolate of H1N2 (A/Swine/Indiana/9K035/99), while 4 isolates were closely related to classical SIV H1N1.

Detection and subtyping of swine influenza H1N1, H1N2 and H3N2 viruses in clinical samples using two multiplex RT-PCR assays

A total of 360 type A swine influenza virus-positive samples including cell culture isolates, nasal swabs or lung tissues along with 30 virus-negative samples were tested for the detection and subtyping of H1N1, H1N2 or H3N2 by two multiplex reverse transcription (RT)-PCR assays. The positive samples had been collected between 1999 and 2001 from pigs with respiratory diseases, and type A influenza virus was isolated and subtyped by hemagglutination inhibition (HI) test at the Minnesota Veterinary Diagnostic Laboratory (MVDL). Two multiplex RT-PCR assays specific for H1 and H3, and N1 and N2 were developed. RT-PCR products with unique sizes characteristic of each subtype of influenza A virus were sequenced, and the sequences were demonstrated to be specific for H1N1, H1N2 or H3N2. Genomic RNAs or DNAs from 12 common swine pathogens other than type A influenza viruses were not amplified when the PCR assays were performed with these primer sets. Positive amplification reaction could be visualized with RNA extracted from up to 10(-5) dilution of each reference virus with original infectivity titer of 10(5) TCID(50)/ml. Of the 360 samples tested, swine influenza virus H1N1, H1N2 and H3N2 were identified in 200, 13 and 139 samples, respectively. The remaining eight samples were positive for both H1N1 and H3N2 viruses. The results of multiplex RT-PCR were 100% in agreement with those of virus isolation. These results demonstrate the usefulness of multiplex RT-PCR for detection and identification of influenza A virus subtypes. The results also indicate an increased occurrence of H1N2 in US swine population.

Phylogenetic analysis of H1N2 isolates of influenza A virus from pigs in the United States

Twenty-four H1N2 influenza A viruses were newly isolated from pigs in the United States. These isolates originated from 19 farms in 9 different swine producing states between 1999 and 2001. All farms had clinical histories of respiratory problem and/or abortion. The viral isolates were characterized genetically to determine the origin of all eight gene segments. The results showed that all H1N2 isolates were reassortants of classical swine H1N1 and triple reassortant H3N2 viruses. The neuraminidase (NA) and PB1 genes of the H1N2 isolates were of human origin, while the hemagglutinin (HA), nucleoprotein (NP), matrix (M), non-structural (NS), PA and PB2 polymerase genes were of avian or swine origin. Fifteen of the 24 H1N2 isolates were shown to have a close phylogenic relationship and high amino acid homology with the first US isolate of H1N2 (A/SW/IN/9K035/99). The remaining nine isolates had a close phylogenic relationship with classical swine influenza H1N1 in the HA gene. All other genes including NA, M, NP, NS, PA, PB1 and PB2 showed a close phylogenic relationship with the H1N2 (A/SW/IN/9K035/99) strain and triple reassortant H3N2 viruses. However, PB1 genes of two isolates (A/SW/KS/13481-S/00, A/SW/KS/13481-T/00) were originated from avian influenza A virus lineage. These results suggest that although there are some variations in the HA genes, the H1N2 viruses prevalent in the US swine population are of a similar genetic lineage.

Experimental in Utero Inoculation of Late-Term Swine Fetuses with Porcine Circovirus Type 2

All 37 fetuses of 3 laparotomized pregnant sows at 86, 92, and 93 days of gestation were inoculated intramuscularly through the uterine wall with porcine circovirus type 2 (PCV-2). The sows were allowed to farrow, and blood and tissue samples were collected from their piglets before and after suckling colostrum. Thirteen fetuses from 2 sows at 90 and 103 days of gestation were used as controls. Of the 37 PCV-2 inoculated fetuses, 24 were grossly normal and 13 were mummified, stillborn, or weak-born at farrowing. Infection with PCV-2 was demonstrated in various tissues of grossly normal and abnormal fetuses by virus isolation, polymerase chain reaction, and immunohistochemical methods. Antibodies specific to PCV-2 were also detected from the sera or thoracic fluids of abnormal fetuses and unsuckled normal pigs. No evidence of PCV-2 infection was found in any control fetuses. The present results confirm previous findings that PCV-2 can infect late-term swine fetuses and may cause reproductive abnormalities.

Identification of Novel Helicobacter Species in Pig Stomachs by PCR and Partial Sequencing

ABSTRACT Evidence of infection with Helicobacter species in pig stomach was investigated by the use of a PCR withHelicobacter genus-specific primers. Forty pig stomachs, each of four different ulcer lesion grades, 0, 1, 2, and 3 in thepars esophagea area, were collected from a slaughterhouse in Minnesota. Of 160 stomach samples examined, 102 (63.8%) were positive by the PCR assay. The 40 samples each of lesion grades 0, 1, 2, and 3 showed 22.5, 52.5, 85.0, and 95.0% PCR-positive results, respectively. There was a significant trend (P ≤ 0.01) in the proportions of PCR-positive cases relative to severity of the lesion. About 80% of the 16S rRNA gene was amplified, and PCR-restriction fragment length polymorphism (RFLP) patterns were analyzed. Of 102 PCR-positive samples, the PCR-RFLP patterns resulted in four different types, 32 samples being classified into type MN 1, 16 samples into type MN 2, 43 samples into type MN 3, and 11 samples into type MN 4. When the sequences of each RFLP type were compared to those reported in databases by using BLAST software, types MN 1, MN 2, MN 3, and MN 4 showed homologies of 97.3, 95.4, 96.7, and 99.5% with the 16S ribosomal DNA of Helicobacter flexispira taxon 3,Helicobacter sp. strains MIT 94-022 and MZ 640285, andHelicobacter suis, respectively. None of the 102 samples positive for the Helicobacter genus were positive with a primer set specific for Helicobacter pylori. Attempts to culture the organisms from selected stomachs in vitro were unsuccessful.

Evaluation of a multiplex reverse transcription-polymerase chain reaction assay for subtyping hemagglutinin genes 1 and 3 of swine influenza type A virus in clinical samples.

A multiplex reverse transcription-polymerase chain reaction (RT-PCR) assay was developed to detect and identify subtypes of hemagglutinin (H) 1 and H3 swine influenza virus (SIV). Two oligonucleotide primer sets were prepared using published sequence data for H1N1 and H3N2. The PCR products with unique size characteristics of each subtype were sequenced, and the sequences were confirmed to be subtype specific for H gene 1 or 3. These primer sets did not amplify when RT-PCR assay was performed for genomic DNA or RNA from other common swine pathogens. The RT-PCR assay was able to detect viral RNA up to 1 tissue culture infective dose of reference SIV H1N1 or H3N2. The multiplex RT-PCR was applied to 30 SIV isolates subtyped by hemagglutination inhibition (HI) test. Forty-three positive and 20 negative swine field samples for SIV by virus isolation were also tested. Of these 73 SIV-positive samples tested, H1 and H3 were identified in 38 and 28 samples by the multiplex RT-PCR, respectively. The remaining 7 samples were positive for both H1 and H3 genes. No positive reaction was found for all 20 SIV-negative field samples. Subsequently, 235 random field samples from pigs with respiratory problems were tested by the multiplex RT-PCR, and 26 and 13 samples were found to be positive for H1 and H3, respectively. Results of these multiplex RT-PCR were comparable with those of the HI test. These results suggest that multiplex RT-PCR can be a useful test for detection and subtyping of SIV in clinical samples.