Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.
Áine Niamh O'TooleVerity HillOliver G PybusAlexander WattsIssac I BogochKamran KhanJane P Messinanull nullnull nullnull nullHouriiyah TegallyRichard J LessellsJennifer GiandhariSureshnee PillayKefentse Arnold TumediGape NyepetsiMalebogo KebabonyeMaitshwarelo I MatshekaMadisa MineSima TokajianHamad HassanTamara SalloumGeorgi MerhiJad KoweyesJemma L GeogheganJoep de LigtXiaoyun RenMatthew StoreyNikki E FreedChitra PattabiramanPramada PrasadAnita S DesaiRavi VasanthapuramThomas F SchulzLars SteinbrückTanja Stadlernull nullAntonio ParisiAngelica BiancoDarío García de ViedmaSergio Buenestado-SerranoVítor BorgesJoana IsidroSílvia DuarteJoão Paulo GomesNeta S ZuckermanMichal MandelboimOrna MorTorsten SeemannAlicia ArnottJenny DraperMailie L GallWilliam RawlinsonIra W DevesonSanmarié SchlebuschJamie McMahonLex LeongChuan Kok LimMaria ChironnaDaniela LoconsoleAntonin BalLaurence JossetEdward HolmesKirsten St GeorgeErica Lasek-NesselquistReina S SikkemaBas Oude MunninkMarion KoopmansMia BryttingV Sudha RaniS PavaniTeemu SmuraAlbert HeimSatu KurkelaMassab UmairMuhammad SalmanBarbara BartoliniMartina RuecaChristian DrostenThorsten WolffOlin SilanderDirk EgginkChantal ReuskenHarry VennemaAekyung ParkChristine V F CarringtonNikita SahadeoMichael CarrGabo Gonzaleznull nullnull nullnull nullnull nullnull nullnull nullnull nullTulio de OliveiraNuno Rodrigues FariaAndrew RambautMoritz U G KraemerPublished in: Wellcome open research (2021)
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
Keyphrases
- sars cov
- respiratory syndrome coronavirus
- south africa
- coronavirus disease
- public health
- physical activity
- hiv positive
- single cell
- copy number
- emergency department
- machine learning
- deep learning
- electronic health record
- clinical practice
- gene expression
- quality improvement
- climate change
- adverse drug
- men who have sex with men
- artificial intelligence