Fig. 1.
Geographical distribution of the commercial swine farms included in the study for detection of porcine parainfluenza virus 1, swine orthopneumovirus and swine influenza A virus. Farms are indicated by orange dots and capital letters (A–J)
Table 1.
Characteristics of the investigated farms and number of collected pig samples per farm. The presence of porcine parainfluenza virus 1, swine orthopneumovirus and swine influenza A virus was assessed
| Farm | Production type | Pig age group | OF | NS | OS |
|---|---|---|---|---|---|
| A* | multiplication farm | nursery | 0 | 27 | 0 |
| B | fattening farm | nursery | 1 | 0 | 1 |
| C | fattening farm | nursery | 0 | 0 | 1 |
| D | farrow-to-finish farm | nursery | 1 | 10 | 0 |
| E* | fattening farm | nursery | 7 | 35 | 0 |
| F | fattening farm | nursery | 1 | 0 | 0 |
| G* | farrow-to-finish farm | nursery | 5 | 0 | 0 |
| H | fattening farm | nursery | 0 | 15 | 0 |
| I* | farrow-to-finish farm | nursery | 11 | 12 | 2 |
| J | multiplication farm | nursery | 2 | 0 | 0 |
| Total sampled | 28 | 99 | 4 |
Table 2.
Porcine parainfluenza virus 1 F gene primer sequences
| Primer | Reference sequence nucleotides | Primer sequence |
|---|---|---|
| F-For1 | 4801–4826 | ACTTAGGTACAAGTTATCCAAAAA |
| F-For2 | 5537–5561 | GAGAGAAGCTTAACATTACAGGC |
| F-Rev1 | 5611–5636 | TCAATAATATCTGTATTCCCGATT |
| F-Rev2 | 6581–6603 | TCTGCCACCTAAGTTTTTCTTA |
Fig. 2.
Distribution of farms with overall results of detection of porcine parainfluenza virus 1, swine orthopneumovirus and swine influenza A virus represented by different colours: blue pin – farm with one detected virus (farm A); pink pins – farms with two viruses detected (farms D, E, G and J); yellow pin – farm with three viruses detected (farm I); orange pins – farms where none of the targeted viruses was present in the tested samples (B, C, F and H)
Table 3.
Results of real-time RT-PCR for detection of swine influenza A virus (SIV), porcine parainfluenza virus 1 (PPIV1) and swine orthopneumovirus (SOV) per farm
| Farm | SIV T | SIV OS+ | SIV OF+ | SIV NS+ | PPIV1 T | PPIV1 OS+ | PPIV1 OF+ | PPIV1 NS+ | SOV T | SOV OS+ | SOV OF+ | SOV NS+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A | 27 | 0 | 0 | 2 | 27 | 0 | 0 | 1 | 15 | 0 | 0 | 0 |
| B | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 0 |
| C | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| D | 11 | 0 | 1 | 0 | 11 | 0 | 0 | 0 | 11 | 0 | 0 | 0 |
| E | 42 | 0 | 2 | 7 | 42 | 0 | 3 | 5 | 12 | 0 | 0 | 0 |
| F | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| G | 5 | 0 | 3 | 0 | 5 | 0 | 3 | 4 | 5 | 0 | 0 | 0 |
| H | 15 | 0 | 0 | 0 | 15 | 0 | 0 | 0 | 10 | 0 | 0 | 0 |
| I | 25 | 0 | 8 | 3 | 25 | 0 | 4 | 1 | 18 | 0 | 0 | 0 |
| J | 2 | 0 | 1 | 0 | 2 | 0 | 1 | 0 | 2 | 0 | 0 | 0 |
| Total | 131 | 0 | 15 | 12 | 131 | 0 | 12 | 6 | 77 | 0 | 0 | 0 |
Table 4.
Results of gel-based RT-PCR for porcine parainfluenza virus 1 (PPIV1) and swine orthopneumovirus (SOV) per pig farm
| Farm | PPIV1 OF T | PPIV1 OF P | PPIV1 NS T | PPIV1 NS P | Accession No. | SOV NS T | SOV NS P | Accession No. |
|---|---|---|---|---|---|---|---|---|
| D | 1 | 0 | 0 | 0 | 0 | 0 | ||
| E | 3 | 0 | 5 | 2 | PX09864, PX098466 | 0 | 0 | |
| G | 4 | 0 | 0 | 0 | 0 | 0 | ||
| I | 4 | 0 | 1 | 1 | PX098465 | 2 | 2 | PX09833, PX09834 |
| J | 1 | 0 | 0 | 0 | 0 | 0 | ||
| Total | 12 | 0 | 6 | 3 | 2 | 2 |
Fig. 3.
Phylogenetic analysis of the partial F gene of 38 nucleotide sequences of porcine parainfluenza virus 1 (PPIV1). Only bootstrap values higher than 75 are shown, and these are at nodes. All positions containing gaps and missing data were eliminated. Red dot – sequence obtained in this research; two-letter, six-digit code – GenBank accession number; slash-separated fields – geographic origin/isolate identifier/year
Fig. 4.
Phylogenetic analysis of the partial G gene of swine orthopneumovirus (SOV). Only bootstrap values higher than 75 are shown, and these are at nodes. All positions containing gaps and missing data were eliminated. Red dot – sequence obtained in this research; two-letter, six-digit code – GenBank accession number; slash-separated fields – Orthopneumovirus species/geographic origin/isolate identifier/year