A pre-built named list containing curated biological and epidemiological metadata for 12 SARS-CoV-2 Variants of Concern (VOC) and Variants of Interest (VOI): Alpha, Beta, Delta, Epsilon, Eta, Gamma, Iota, Kappa, Lambda, Omicron, Theta, Zeta. Includes mutation profiles, nomenclature, temporal detection records, defining SNPs, and a fully citable reference table with 21 verified references.
Usage
data(sarscov2_variants)Format
A named list of 13 elements (12 metadata fields plus a structured References object). See Details for per-element descriptions.
Source
Compiled from 21 peer-reviewed and surveillance sources; see
sarscov2_variants$References$data for the full reference table
with DOIs and URLs. Built from SARS_CoV_2_VOC_VOI.xlsx via
get_variants.
Details
The object is available automatically after library(ViralEntropR)
via lazy loading. It is produced by get_variants from the
curated Excel workbook SARS_CoV_2_VOC_VOI.xlsx (not bundled with
the package; see data-raw/sarscov2_variants.R for the reproducible
build script).
List elements:
WHO_LabelList of 12. WHO variant label strings (e.g.
"Alpha","Omicron").Pango_LineageList of 12. Pango lineage designations (e.g.
"B.1.1.7").GISAID_CladeCharacter(12). GISAID clade strings (e.g.
"GRY","GR/484A").Nextstrain_CladeCharacter(12). Nextstrain clade strings (e.g.
"20I/501Y.V1").Country_First_DetectedList of 12. Country of first documented detection per variant.
Date_Earliest_SampleCharacter(12). Month-Year of earliest documented sample (e.g.
"Sep-2020").Date_First_DetectedCharacter(12). Month-Year of world-level first detection.
Date_First_Detected_USCharacter(12). Month-Year of first US detection.
Spike_MutationsList of 12. Character vectors of Spike protein mutations per variant, read from the Excel workbook.
Mutation_SitesList of 12. Integer vectors of amino acid positions extracted from
Spike_Mutations.Defining_SNPsList of 12. Canonical defining SNP strings (
NAfor variants not characterised in the reference set).Defining_SNP_SitesList of 12. Integer positions extracted from
Defining_SNPs.ReferencesNamed list with three elements:
$data– data frame of 21 verified references (columns: ID, Authors, Year, Title, Journal_Source, Volume_Issue_Pages, DOI, URL, Type, Variants_Covered, Data_Field, Citation);$display(variant = NULL)– renders an interactivedatatable, optionally filtered by WHO label (requires the DT package);$cite(variant)– returns formatted citation strings for a given WHO label, suitable for manuscript use.
References
The 21 curated references cover peer-reviewed articles, CDC MMWR government
reports, and outbreak.info surveillance database records. Full provenance
is available via sarscov2_variants$References$data or the
interactive display.
Examples
# Object is available immediately after library(ViralEntropR)
# --- Basic access ---------------------------------------------------------
# All 12 WHO labels
unlist(sarscov2_variants$WHO_Label)
#> [1] "Alpha" "Beta" "Delta" "Epsilon" "Eta" "Gamma" "Iota"
#> [8] "Kappa" "Lambda" "Omicron" "Theta" "Zeta"
# Pango lineage for Alpha
sarscov2_variants$Pango_Lineage[[
which(unlist(sarscov2_variants$WHO_Label) == "Alpha")
]]
#> [1] "B.1.1.7"
# World detection dates for all variants
data.frame(
Variant = unlist(sarscov2_variants$WHO_Label),
Detected = sarscov2_variants$Date_First_Detected,
Country = unlist(sarscov2_variants$Country_First_Detected)
)
#> Variant Detected Country
#> 1 Alpha Dec-2020 United Kingdom
#> 2 Beta Oct-2020 South Africa
#> 3 Delta Dec-2020 India
#> 4 Epsilon Jul-2020 USA
#> 5 Eta Nov-2020 Nigeria
#> 6 Gamma Dec-2020 Brazil
#> 7 Iota Nov-2020 USA
#> 8 Kappa Oct-2020 India
#> 9 Lambda Dec-2020 Peru
#> 10 Omicron Nov-2021 South Africa
#> 11 Theta Feb-2021 The Philippines
#> 12 Zeta Apr-2020 Brazil
# --- Mutation sites -------------------------------------------------------
# Defining SNPs and sites for Delta
idx <- which(unlist(sarscov2_variants$WHO_Label) == "Delta")
sarscov2_variants$Defining_SNPs[[idx]]
#> [1] "T19R" "L452R" "T478K" "P681R" "D950N"
sarscov2_variants$Defining_SNP_Sites[[idx]]
#> [1] 19 452 478 681 950
# All Spike mutation sites for Omicron
sarscov2_variants$Mutation_Sites[[
which(unlist(sarscov2_variants$WHO_Label) == "Omicron")
]]
#> [1] 67 95 142 145 211 212 339 346 371 373 375 417 440 446 477 478 484 493 496
#> [20] 498 501 505 547 614 655 679 681 764 796 856 954 969 981
# --- Nomenclature ---------------------------------------------------------
data.frame(
WHO = unlist(sarscov2_variants$WHO_Label),
PANGO = unlist(sarscov2_variants$Pango_Lineage),
GISAID = sarscov2_variants$GISAID_Clade,
Nextstrain = sarscov2_variants$Nextstrain_Clade
)
#> WHO PANGO GISAID Nextstrain
#> 1 Alpha B.1.1.7 GRY 20I/501Y.V1
#> 2 Beta B.1.351 GH/501Y.V2 20H/501Y.V2
#> 3 Delta B.1.617.2 G/478K.V1 21A/S:478K
#> 4 Epsilon B.1.427/B.1.429 GH/452R.V1 21C
#> 5 Eta B.1.525 G/484K.V3 21D/S:484K
#> 6 Gamma P.1 GR/501Y.V3 20J/501Y.V3
#> 7 Iota B.1.526 GH/253G.V1 21F
#> 8 Kappa B.1.617.1 G/452R.V3 21B/S:154K
#> 9 Lambda C.37 GR/452Q.V1 21G
#> 10 Omicron B.1.1.529 GR/484A 21K
#> 11 Theta P.3 GR/1092K.V1 20B/S:265C
#> 12 Zeta P.2 GR/484K.V2 20B/S:484K
# --- References -----------------------------------------------------------
# Full reference data frame (21 rows)
sarscov2_variants$References$data[,
c("ID", "Authors", "Year", "Journal_Source")
]
#> ID Authors Year
#> 1 1 Ghosh N, Nandi S, Saha I 2022
#> 2 2 Abulsoud AI, et al. 2023
#> 3 3 Aleem A, Akbar Samad AB, Vaqar S 2023
#> 4 4 Zella D, Giovanetti M, Benedetti F, et al. 2021
#> 5 5 Wink PL, Volpato FCZ, Monteiro FL, et al. 2022
#> 6 6 Chatterjee S, Bhattacharya M, et al. 2023
#> 7 7 Washington NL, Gangavarapu K, et al. 2021
#> 8 8 Long SW, Olsen RJ, Christensen PA, et al. 2021
#> 9 9 Zhang W, Davis BD, Chen SS, et al. 2021
#> 10 10 Gangavarapu K, Abdel Latif A, et al. 2023
#> 11 11 Chen C, Shi Q, Dong XP 2021
#> 12 12 Firestone MJ, Lorentz AJ, Meyer S, et al. 2021
#> 13 13 CDC COVID-19 Response Team 2021
#> 14 14 Gangavarapu K, Abdel Latif A, et al. 2023
#> 15 15 Gangavarapu K, Abdel Latif A, et al. 2023
#> 16 16 Gangavarapu K, Abdel Latif A, et al. 2023
#> 17 17 Kannan SR, Spratt AN, Sharma K, et al. 2022
#> 18 18 Dhawan M, Saied AA, Mitra S, et al. 2022
#> 19 19 Tao K, Tzou PL, Nouhin J, et al. 2021
#> 20 20 Brookes AJ 1999
#> 21 21 Salleh MZ, Derrick JP, Deris ZZ 2021
#> Journal_Source
#> 1 International Immunopharmacology
#> 2 Biomedicine & Pharmacotherapy
#> 3 StatPearls [Internet], StatPearls Publishing
#> 4 Journal of Medical Virology
#> 5 Infection Control & Hospital Epidemiology
#> 6 Viruses
#> 7 Cell
#> 8 The American Journal of Pathology
#> 9 JAMA
#> 10 outbreak.info
#> 11 Zoonoses
#> 12 MMWR Morb Mortal Wkly Rep
#> 13 MMWR Morb Mortal Wkly Rep
#> 14 outbreak.info
#> 15 outbreak.info
#> 16 outbreak.info
#> 17 Journal of Autoimmunity
#> 18 Biomedicine & Pharmacotherapy
#> 19 Nature Reviews Genetics
#> 20 Gene
#> 21 International Journal of Molecular Sciences
# Formatted citation strings for Gamma
sarscov2_variants$References$cite("Gamma")
#> [1] "Ghosh N, Nandi S, Saha I (2022). A review on evolution of emerging SARS-CoV-2 variants based on spike glycoprotein. International Immunopharmacology. 105:108565. doi:10.1016/j.intimp.2022.108565"
#> [2] "Abulsoud AI, et al. (2023). Mutations in SARS-CoV-2: Insights on structure, variants, vaccines, and biomedical interventions. Biomedicine & Pharmacotherapy. 157:113977. doi:10.1016/j.biopha.2022.113977"
#> [3] "Aleem A, Akbar Samad AB, Vaqar S (2023). Emerging Variants of SARS-CoV-2 and Novel Therapeutics Against Coronavirus (COVID-19). StatPearls [Internet], StatPearls Publishing."
#> [4] "Zella D, Giovanetti M, Benedetti F, et al. (2021). The variants question: What is the problem?. Journal of Medical Virology. 93(12):6479-6485. doi:10.1002/jmv.27196"
#> [5] "Long SW, Olsen RJ, Christensen PA, et al. (2021). Sequence Analysis of 20,453 Severe Acute Respiratory Syndrome Coronavirus 2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern. The American Journal of Pathology. 191(6):983-992. doi:10.1016/j.ajpath.2021.03.004"
#> [6] "Firestone MJ, Lorentz AJ, Meyer S, et al. (2021). First Identified Cases of SARS-CoV-2 Variant P.1 in the United States - Minnesota, January 2021. MMWR Morb Mortal Wkly Rep. 70(10):346-347. doi:10.15585/mmwr.mm7010e1"
#> [7] "Tao K, Tzou PL, Nouhin J, et al. (2021). The biological and clinical significance of emerging SARS-CoV-2 variants. Nature Reviews Genetics. 22(12):757-773. doi:10.1038/s41576-021-00408-x"
#> [8] "Salleh MZ, Derrick JP, Deris ZZ (2021). Structural Evaluation of the Spike Glycoprotein Variants on SARS-CoV-2 Transmission and Immune Evasion. International Journal of Molecular Sciences. 22(14):7425. doi:10.3390/ijms22147425"
if (interactive() && requireNamespace("DT", quietly = TRUE)) {
# Interactive DT table of all references
sarscov2_variants$References$display()
# Filtered to Omicron references only
sarscov2_variants$References$display(variant = "Omicron")
}