Genomic epidemiology as a tool for understanding drivers of hepatitis A community outbreaks in Massachusetts and New Hampshire
Krasilnikova, L. A.; Bouton, L.; Brock-Fisher, T. M.; Decker, E.; Godec, M.; Thompson, Z.; Dart, E.; Gao, F.; Gladden-Young, A.; Messer, K. S.; Norville, J.; Specht, I.; Osinski, A.; Li, J.; Lones, C.; DeRuff, K. C.; Siddle, K. J.; Church, D.; Benton, C.; Hansen, K.; Bowen, H.; Bhattacharyya, S.; Epie, N.; Brown, C. M.; Madoff, L. C.; MacInnis, B. L.; Gallagher, G. R.; Smole, S.; Bean, C.; Talbot, E. A.; Burns, M.; Doucette, M.; Fortes, E.; Park, D. J.; Sabeti, P. C.; Wohl, S.
Show abstract
Despite the existence of an effective vaccine, the United States continues to experience outbreaks of hepatitis A, including in Massachusetts (MA) and New Hampshire (NH) in 2018 and again in MA in 2023. To clarify the relationship between these outbreaks and better understand their drivers, we generated hepatitis A virus whole genome sequences from reported cases and analyzed them using open-source genotyping tools developed and released as part of this study. We found that the 2018 and 2023 outbreaks were caused by distinct viral strains, despite affecting individuals with similar demographic characteristics and reported risk factors. Detailed analysis of genomic and epidemiologic data further resolved transmission patterns within and across outbreaks, showing that experiencing homelessness and prior use of drugs were associated with increased transmission while also revealing transmission between individuals with and without these risk factors, as well as spread across state borders. Together, these findings demonstrate the value of broadly accessible genomic tools for understanding hepatitis A outbreaks and illustrate how whole genome analysis can complement epidemiological investigation by resolving transmission patterns and outbreak drivers that can inform public health interventions.
Matching journals
The top 9 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Mapping the emergence of SARS-CoV-2 Omicron variants on a university campus 94%
- SARS-CoV-2 within-host population expansion, diversification and adaptation in zoo tigers, lions and hyenas 93%
- Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions 92%
Similar papers in this journal
- Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons 93%
- Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination 92%
- Immunogenicity of convalescent and vaccinated sera against clinical isolates of ancestral SARS-CoV-2, beta, delta, and omicron variants 92%
Similar papers in this journal
- Respiratory virus detection and sequencing from negative SARS-CoV-2 rapid antigen tests 92%
- Large-scale genomic analysis of SARS-CoV-2 Omicron BA.5 emergence in the United States 91%
- Serial interval and incubation period estimates of monkeypox virus infection in 12 U.S. jurisdictions, May – August 2022 91%
Similar papers in this journal
- In depth sequencing of a serially sampled household cohort reveals the within-host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants 93%
- SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to mass gathering events 93%
- West Nile Virus spread in Europe - phylogeographic pattern analysis and key drivers 92%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.