Molecular epidemiology and evolution of type 2 porcine reproductive and respiratory syndrome virus in Ontario, Canada
Bibliographic record
Abstract
Recently, progress was made in collecting, classifying, and characterizing the genetic diversity of type 2 porcine reproductive and respiratory syndrome virus (PRRSV) using all known and publically available sequencing information. Despite this voluminous attempt, these analyses were largely na?ve of the Canadian contribution to circulating viruses. This represented a vital omission in the study of molecular epidemiology due to the fact that Canada had recorded the earliest evidence of the existence of type 2 PRRSV. To this end, the genetic diversity and evolutionary aspects of PRRSVs distributed in the Province of Ontario in Canada were characterized to abridge this existing knowledge gap on type 2 PRRSV. \n\n\n\nGenotyping of type 2 strains is primarily based on either a phylogenetic or restriction fragment length polymorphism (RFLP) approach. Classification of Ontario PRRSV field isolates (n = 505) from 1999 to 2010, based on a global type 2 PRRSV ORF5 phylogenetic framework, revealed genetic diversity comparable to PRRSV in the USA, with sequences assigned to five of nine lineages (1, 2, 5, 8 and 9). A majority (~85%) of these isolates were typed to the first two lineages (1 and 2). Despite a relatively smaller sample size to the USA, the topology of the phylogenetic tree indicated Canadian origins of these two lineages. Mapping RFLP patterns of Ontario isolates onto the phylogenetic tree revealed numerous examples of different patterns located within the same phylogenetic cluster. Examples of the non-specificity of RFLP patterns to any particular lineage or sub-lineage were abound. Statistical analysis showed occurrences where similar RFLP patterns masked diverse genetic distances and instances of close genetic proximity with divergent RFLP patterns. An examination of the most abundant 15 RFLP patterns revealed that the discrepancy between RFLP typing and genetic distances was not attributable to a single or few patterns but was rather a permeating feature.\n\n\n\nImportantly, the tree topology also indicated a Canadian ancestry for the highly virulent MN184-related strains that first emerged in 2001 in the USA. Selective pressure analyses highlighted a handful of positively selected sites most of which were located in the ORF5 ectodomains of outbreak strains, implicating the host immune system as the possible selective agent. This was in contrast to the closely-related Ontario strains which were subject to strong purifying selection. A broader survey of transmission dynamics in North America unveiled a higher virus flow from Canada to the USA with the primary targets being the Lake States and Corn Belt. In turn, these regions served to disseminate viruses to other swine production regions in the USA. Virus flow from the USA to Canada occurred on a much smaller scale.\n\n\n\nCollectively, extensive genetic diversity prevails in type 2 PRRSV in one region of the North American swine industry and it is not described adequately by RFLP typing which might have some value in differentiating strains at the local farm level, instead. For diagnostic and research purposes, phylogenetic typing should be the preferred method. Finally, stronger surveillance needs to be adopted to minimize cross-border virus transmission.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".