2285. Using Genomic Sequencing to Describe SARS-CoV-2 Transmission Dynamics in U.S. Major League Soccer Clubs
Notice bibliographique
Résumé
Abstract Background In 2020–2022, U.S. Major League Soccer (MLS) used SARS-CoV-2 mitigation protocols that included masking, social distancing, avoiding contact with others outside of training and games, testing, quarantine, and isolation. In addition to isolation for those who tested positive, a SARS-CoV-2 genomic sequencing strategy was developed to identify whether infections were associated with intra-league transmission. Methods Nasopharyngeal swabs were collected by MLS club medical staff from players and staff from February 2021 through September 2022. During this time, surveillance testing changed from daily to weekly to testing only symptomatic players and staff. SARS-CoV-2 positive samples were analyzed using amplicon-based whole genome sequencing. A phylogenetic tree was constructed using Nextstrain to visualize genomes from infected players and staff in the context of genomes available on GISAID circulating in the United States during corresponding time periods. To identify transmission links, all genomes were compared in a pairwise fashion. Genomes that were 0–2 nucleotides different were considered part of direct transmission clusters. Results Of 250 samples that were rtPCR positive for SARS-CoV-2, 215 (86%) were sequenced. Phylogenetic analysis showed a broad diversity of lineages, including some predominant overseas (e.g., AY.98.1). Pairwise comparison revealed SARS-CoV-2 sequences from 7 individuals appeared to be linked. These individuals were on 2 different MLS teams; there was an off-field exposure (dinner). Five (71%) had identical SARS-CoV-2 sequences; 2 had sequences that were 1 nucleotide different at the consensus level. Subconsensus genome analysis revealed that differences of 1 nucleotide were due to subconsensus mutations fluctuating below and above 50%, suggesting all 7 individuals were part of a transmission cluster. Phylogenetic analysis revealed that the sequences from the cluster were distinct from reference sequences and were likely a unique transmission chain. Conclusion SARS-CoV-2 transmission may occur within, and even between, professional sports teams. Pairwise comparison of individual genomes can provide improved granularity to identify clusters and understand SARS-CoV-2 transmission. Disclosures Davidson H. Hamer, MD, Kephera Diagnostics: Grant/Research Support|Takeda: Advisor/Consultant|Takeda: Grant/Research Support|Trinity Biotech, LLC: Advisor/Consultant|Valneva: Advisor/Consultant|Valneva: Grant/Research Support Daniel Bourque, MD, Kephera Diagnostics: Grant/Research Support
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,002 | 0,001 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».