CDC SARS-CoV-2 variant proportions: JN.1 emergence (US, 2023-2024)
Source:R/data.R
cdc_sarscov2_jn1.RdReal surveillance data from the CDC's national genomic surveillance program covering the emergence and dominance of the SARS-CoV-2 JN.1 lineage in the United States, October 2023 through June 2024.
Format
A data frame with 171 rows and 4 columns:
- date
Biweek ending date (Date).
- lineage
Lineage name (character): JN.1, XBB.1.5, EG.5.1, HV.1, HK.3, BA.2.86, KP.2, KP.3, JN.1.11.1, Other.
- count
Approximate sequence count per biweek (integer).
- proportion
CDC weighted proportion estimate (numeric).
Source
CDC COVID Data Tracker, SARS-CoV-2 Variant Proportions. Dataset ID: jr58-6ysp. https://data.cdc.gov/Laboratory-Surveillance/SARS-CoV-2-Variant-Proportions/jr58-6ysp
Public domain (U.S. Government Work, 17 USC 105).
Details
Derived from CDC's published weighted variant proportion estimates.
Approximate biweekly sequence counts were reconstructed from
proportions using a reference total of 8,000 sequences per period.
The original proportions are retained in the proportion column.
References
Ma KC, et al. (2024). Genomic Surveillance for SARS-CoV-2 Variants. MMWR, 73(42):941–948. doi:10.15585/mmwr.mm7342a1
Examples
data(cdc_sarscov2_jn1)
vd <- lfq_data(cdc_sarscov2_jn1,
date = date, lineage = lineage, count = count)
fit <- fit_model(vd, engine = "mlr")
growth_advantage(fit, type = "relative_Rt", generation_time = 5)
#> # A tibble: 9 × 6
#> lineage estimate lower upper type pivot
#> <chr> <dbl> <dbl> <dbl> <chr> <chr>
#> 1 BA.2.86 0.961 0.957 0.965 relative_Rt Other
#> 2 HK.3 0.900 0.896 0.904 relative_Rt Other
#> 3 HV.1 0.898 0.896 0.900 relative_Rt Other
#> 4 JN.1 1.01 1.01 1.01 relative_Rt Other
#> 5 JN.1.11.1 1.11 1.10 1.12 relative_Rt Other
#> 6 KP.2 1.16 1.15 1.16 relative_Rt Other
#> 7 KP.3 1.26 1.25 1.27 relative_Rt Other
#> 8 Other 1 1 1 relative_Rt Other
#> 9 XBB.1.5 0.860 0.850 0.870 relative_Rt Other