Tiled PCR amplification-based Whole Genome Sequencing and Phylogenetic Classification Accelerate the Implementation of Respiratory Syncytial Virus Genomic surveillance in Canada as a Pilot Study
Bibliographic record
Abstract
ABSTRACT Whole genome sequencing (WGS) has emerged as a powerful tool to facilitate the study of existing and emerging infectious diseases. WGS-based genomic surveillance provides information on the genetic diversity and tracks the evolution of important viral pathogens including Respiratory Syncytial Virus (RSV). Development and implementation of robust tiled multiplex PCR amplification-based WGS assays will facilitate high-throughput RSV surveillance initiatives. In this study, we developed multiplex PCR assays for targeted enrichment of viral genomes using PrimalScheme ( http://primal.zibraproject.org ) to amplify over 97% of the genome in the majority of contemporaneous specimens tested. A pilot dataset comprising 52 RSVA and 37 RSVB genomes derived from Canadian clinical specimens during the 2022-2023 respiratory virus season were used to perform phylogenetic analyses using both near complete genome and Glycoprotein (G) sequences. Overall, the RSV phylogenetic tree built with whole genomes showed identical lineage clusters as that compared to the G gene, but showed more confidence and discriminatory features within individual lineage. Moreover, availability of whole genomes enabled the identification of a broader range of mutations, for instance the identified S377N, K272M, S276N, S211N, S206I and S209Q in Canadian fusion proteins that could be potentially associated with effectiveness of vaccines or antiviral-based therapeutics. In conclusion, the tiled-PCR amplification assays described offer a more streamlined approach to facilitate high-throughput, high sensitivity of RSV WGS, which is capable of supporting enhanced genomic surveillance initiatives, as well as the more comprehensive genomic analyses required to inform public health strategies for the development and usage of vaccines and antiviral drugs. IMPORTANCE We present assays to efficiently sequence genomes of the RSVA and RSVB. This enables researchers and public health agencies to acquire high-quality genomic data using rapid and cost-effective approaches. Genomic data based comparative analysis can be used to conduct surveillance and monitor circulating isolates for efficacy of vaccines and antiviral therapeutics.
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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 | 0.002 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.002 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".