Haogao Gu, Samuel S.M. Cheng, Pavithra Krishnan, Daisy Y.M. Ng, Lydia D.J Chang, Gigi Y.Z. Liu, Sammi S.Y. Cheuk, Mani M.Y. Hui, Mathew C.Y. Fan, Jacob H.L. Wan, Leo H.K. Lau, Daniel K.W. Chu, Vijaykrishna Dhanasekaran, Malik Peiris, and Leo L.M. Poon
The paper is now available on the EID journal.
We sequenced 50% of COVID-19 cases recently imported to Hong Kong (N=212) and identified 70 cases infected by the Delta variants. The phylogeny of our Delta variant sequences is similar to the one built by using the global dataset, suggesting travel hubs can be used to monitor SARS-CoV-2 sequence diversity.
The source codes for different analyses were stored in different sub-directories under the scripts directory. The results generated by the scripts can be found in the results directory.
r$> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] gdtools_0.2.3 officer_0.3.19 ggnewscale_0.4.5 colorspace_2.0-2 ggrepel_0.9.1
[6] ggtree_3.0.2 lubridate_1.7.10 Biostrings_2.60.1 GenomeInfoDb_1.28.1 XVector_0.32.0
[11] IRanges_2.26.0 S4Vectors_0.30.0 BiocGenerics_0.38.0 forcats_0.5.1 stringr_1.4.0
[16] dplyr_1.0.7 purrr_0.3.4 readr_1.4.0 tidyr_1.1.3 tibble_3.1.2
[21] ggplot2_3.3.5 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] nlme_3.1-152 bitops_1.0-7 fs_1.5.0 httr_1.4.2
[5] rprojroot_2.0.2 tools_4.1.0 backports_1.2.1 utf8_1.2.1
[9] R6_2.5.0 DBI_1.1.1 lazyeval_0.2.2 withr_2.4.2
[13] tidyselect_1.1.1 phangorn_2.7.1 compiler_4.1.0 cli_3.0.0
[17] rvest_1.0.0 xml2_1.3.2 labeling_0.4.2 scales_1.1.1
[21] quadprog_1.5-8 systemfonts_1.0.2 httpgd_1.1.1 digest_0.6.27
[25] pkgconfig_2.0.3 dbplyr_2.1.1 rvg_0.2.5 rlang_0.4.11
[29] readxl_1.3.1 rstudioapi_0.13 farver_2.1.0 generics_0.1.0
[33] jsonlite_1.7.2 zip_2.2.0 RCurl_1.98-1.3 magrittr_2.0.1
[37] GenomeInfoDbData_1.2.6 patchwork_1.1.1 Matrix_1.3-4 Rcpp_1.0.7
[41] munsell_0.5.0 fansi_0.5.0 ape_5.5 lifecycle_1.0.0
[45] stringi_1.7.2 zlibbioc_1.38.0 grid_4.1.0 crayon_1.4.1
[49] lattice_0.20-44 haven_2.4.1 hms_1.1.0 pillar_1.6.1
[53] uuid_0.1-4 igraph_1.2.6 codetools_0.2-18 fastmatch_1.1-0
[57] reprex_2.0.0 glue_1.4.2 BiocManager_1.30.16 modelr_0.1.8
[61] vctrs_0.3.8 treeio_1.16.1 cellranger_1.1.0 gtable_0.3.0
[65] assertthat_0.2.1 broom_0.7.8 tidytree_0.3.4 later_1.2.0
[69] aplot_0.0.6 rvcheck_0.1.8 ellipsis_0.3.2 here_1.0.1