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onsdag 10 november 2021

Deltaviruksen (AY) alalinjat löytyvät seuraamalla Sars-2 viruksen varianttien puuta B.1.

11.11. 2021. Deltavirus B.1.617.2  on voittamassa  muidn VOC-virusten  aiemmin valloittamia  alueita kaikkine  alalinjoineen, joita on unsaasti.  B.1.617.2 merkataan lyhennyksenä AY. Alalinjoja siten merkataan AY.1:stä eteenpäin  ja niitä on noin 120. kaikilla on hieman toisesta poikkeava mutaatiokirjo ja myös kliininen merkityskin on ieman ehkä poikkeava, mutta  kaikenkaikkiaan  ne katsotaan lähinnä deltan itsensä kaltaiseksi toistaiseksi "nyrkkisääntönä". Mon niistä on uudehkoja, joten vakutuksiakin ja tieteellisiä johtopäätöksiä  saa jonkin aikaa odotella.  Viisainta on vain  vahvistaa  rokotuskattavuutta edelleen kautta maailman, koska rokottamattomien joukosta löytyy  vaikemmat sairastumiset toistaiseksi.  Asia on niin uutta m,onille, että  on vaikeaa motivoida koko maailaa rokottautumaan ja moni valiokaan ei ole motivoitunut kiirehtimään asiaa ja toisaalta ekonomiset asiatkin ja  esim. sotatilat  ym estävät  adekvaatit terveydenhoidolliset  funktiot.  Jopa rokottavat  vikamiehet ovat hengenvaarassa enemänkin  niistä syistä kuin itse viruksesta.

 https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/

B.1. linja ( parent lineage)

B.1.617    Tästä viruksesta on 1 sekvenssi olemassa. se löytyi Intiasta. 

B.1.617.1.  sai myöhemmin  nimen Kappa.

B.16.1.7.2. sai myöhemmin imen Delta ja  siitä tuli  juuri AY-linjaan.

AY tarkoittaa B.1.617.2.

B.1.617.3  lie sekin katsottu Kappa-nimiseksi. 

A-linjaa on  vähitellen  kaavoitettu ja siihen kuuluu nyt  runsas määrä  virusrakenteita AY.1 -  AY.121 asti ainakin. älla on  nimetty 119  viimeiseksi. Näistä löytyy useita deltavarianttien  S-mutaatioita, ainakin 27 kpl. joukosta.

01.11.21 | Lineage summaries

 

Summary of designated AY lineages

We’ve continued to incorporate new AY lineages in recent pangoLEARN models. As previously outlined, most of these lineages show significant geographical clustering and they have been designated to help researchers track the virus on a finer scale. Their designation does not imply any functional biological difference from B.1.617.2 and, like B.1.617.2, they correspond to the WHO-defined Delta variant (https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/)..

Below is a summary of the AY lineages that have been designated to date, including their dominant geographical locations and associated mutations. We expect that new AY lineages will continue to follow and will add any future AY lineages to this table.

Table of currently designated AY lineages, their predominant geographical location(s) and their associated mutation(s). Note that the listed mutations are those that occurred along the phylogenetic branch immediately preceding the common ancestor of the lineage. These mutations are therefore those that separate the AY lineage from closely related sequences but may not be all of the mutations that separate them from other AY lineages or more distant B.1.617.2 sequences.


LineagePredominant countriesAssociated mutation(s)
AY.1MultipleG22813T (S:K417N)
AY.2USAG22813T (S:K417N)
AY.3USAA11456G (Orf1ab:I3731V)
AY.3.1USAG3644T (Orf1ab:D1127Y), C18115T (Orf1ab:H5951Y)
AY.4UKC7851T (Orf1ab:A2529V)
AY.4.1UKA20374C (Orf1ab:I6704L),G22899T (S:G446V)
AY.4.2Europe, particularly UKT21995C (S:Y145H)
AY.4.3EuropeC21638T (S:S26P)
AY.4.4EuropeG24348C (S:S929T)
AY.4.5LithuaniaA14882C (Orf1ab:D4873A)
AY.5UKG24928T (synonymous)
AY.5.1PortugalC27143A (M:N207K)
AY.5.2PortugalC25572T (synonymous)
AY.5.3USAC7488T (Orf1ab:T2408I)
AY.5.4EuropeC1191T (Orf1ab:P309L)
AY.6UKG17331T (Orf1ab:E5689D)
AY.7UKG11365T (synonymous), G12718T (Orf1ab:Q4151H), C27629A (Orf7a:A79D)
AY.7.1DenmarkA18675G (synonymous)
AY.7.2EuropeG25445T (Orf3a:G18V)
AY.8UKA14170G (Orf1ab:I4636V)
AY.9UKC22792T (synonymous)
AY.9.1EuropeC4321T (synonymous)
AY.9.2EuropeG1729A (synonymous)
AY.9.2.1CanadaT6152C (synonymous),C16092T (synonymous)
AY.10UKC12756T (Orf1ab:T4164I), C13665T (synonymous)
AY.11UKC3486T (Orf1ab:A1074V), C18526T (Orf1ab:R6088C), C29509T (synonymous)
AY.12IsraelC23934T (S:T791I)
AY.13USAA17406G (synonymous)
AY.14USAG20718T (Orf1ab:M6818I)
AY.15CanadaA16872G (synonymous), G27382C (Orf6:D61H)
AY.16KenyaT26076A (synonymous)
AY.16.1FranceA12417G (Orf1ab:N4051S),G12911A (Orf1ab:V4216I)
AY.17Ireland, Northern IrelandC17436T (synonymous)
AY.18CanadaT23470C (synonymous), C27807T (synonymous)
AY.19South AfricaG25019T (S:D1153Y), G25947T (Orf3a:Q185H)
AY.20USA, MexicoC2061T (Orf1ab:A599V)
AY.21Italy, SwitzerlandG28195T (Orf8:R101L), T28897C (synonymous), C29167T (synonymous)
AY.22PortugalT12496C (synonymous), G26062T (Orf3a:G224C)
AY.23Indonesia, Singapore, Japan, South KoreaC1404T (Orf1ab:P380L), C4752T (Orf1ab:T1496I)
AY.23.1SingaporeC25262A (S:L1234I)
AY.24IndonesiaC25702T (Orf3a:P104S)
AY.25USAA27507C (synonymous)
AY.26USA, MexicoA27345T (Orf6:K48N)
AY.27CanadaG29422T (synonymous)
AY.28Sri LankaC8950T (synonymous), C9246T (Orf1ab:A2994V), G24794T (S:A1078S)
AY.29JapanT5514C (Orf1ab:V1750A)
AY.29.1JapanG22081T (S:Q173H)
AY.30Thailand, CambodiaA13482G (synonymous)
AY.31MyanmarT3306C (Orf1ab:M1014T), T23480C (S:S640P), G24872T (S:V1104L)
AY.32South AfricaC9286T (synonymous)
AY.33EuropeA21647G (S:T29A)
AY.34Europe, USAG23593C (S:Q677H)
AY.34.1Brazil, ChileG8017T (synonymous)
AY.35USAG23012C (S:E484Q)
AY.36Nigeria, UK, USAT15628C (Orf1ab:C5122R), G18079T (Orf1ab:V5939L)
AY.37Liberia, USA, FranceT20911C (synonymous)
AY.38South AfricaC2509T (synonymous)
AY.39USAG27604A (Orf7a:V71I)
AY.39.1Australia, USAA13482G (synonymous)
AY.39.1.1New ZealandG19563T (Orf1ab:L6433F)
AY.39.2PeruG5716T (Orf1ab:K1817N)
AY.40ReunionC28099T (Orf8:S69L)
AY.41EuropeG1820A (Orf1ab:G519S), G22992T (S:S477I)
AY.42EuropeC25872T (synonymous)
AY.43EuropeA28299T (N:Q9L)
AY.44USAC6040T (synonymous)
AY.45South AfricaG13812T (Orf1ab:M4516I)
AY.46AfricaC10977T (Orf1ab:A3571V)
AY.46.1USAT25673C (Orf3a:L94P)
AY.46.2Germany, TurkeyA17799G (synonymous)
AY.46.3BrazilG28378T (synonymous)
AY.46.4USAG23545T (S:E661D)
AY.46.5UKT16242G (synonymous)
AY.46.6EuropeC6310T (synonymous)
AY.47USAG22427A (S:V289I)
AY.48USAG27948T (Orf8:E19*)
AY.49USAT5773C (synonymous),C10834T (synonymous),C23039G (S:Q493E),G24124T (S:K854N),A27979T (Orf8:Q29L)
AY.50IrelandC19554T (synonymous),G22484C (S:V308L),G28809T (N:G179V)
AY.51EuropeG12223T,A25697T (Orf3a:E102V),G28248A (Orf8:D119N)
AY.52USAT25689C (synonymous)
AY.53EuropeG1738T (synonymous),C18348T (synonymous)
AY.54USAA25806G (synonymous)
AY.55Rwanda and other countriesA10978G (synonymous)
AY.56USAC25624T (Orf3a:H78Y)
AY.57VietnamC1403T (Orf1ab:P380S)
AY.58EuropeC5192T (synonymous)
AY.59MalaysiaT20391G (synonymous)
AY.60EuropeC2919T (Orf1ab:P885L),T8634C (Orf1ab:I2790T)
AY.61ItalyT25532C (Orf3a:I47T)
AY.62USA, MexicoA1045T (synonymous)
AY.63NorwayA19126G (Orf1ab:I6288V),C25710T (synonymous),G29616T (Orf10:R20I)
AY.64USAC5784T (Orf1ab:T1840I),C24130T (synonymous),G25691T (Orf3a:G100V)
AY.65Bahrain and other countriesG14028T (Orf1ab:M4588I)
AY.66EuropeT6496C (synonymous)
AY.67USAA27368G (Orf6:Q56R)
AY.68EuropeG105T (synonymous),C19524T (synonymous),T24499A (S:D979E)
AY.69South KoreaA4838G (Orf1ab:I1525V),G9431A (Orf1ab:V3056I),G16864A (Orf1ab:V5534I),C27559T (synonymous)
AY.70EuropeG28899T (N:R209I),G28903T (N:M210I)
AY.71EuropeC25317T (S:S1252F)
AY.72EuropeG6080T (Orf1ab:D1939Y),A25856G (Orf3a:D155G)
AY.73EuropeC6573T (Orf1ab:S2103F),C28409T (N:P46S),C28893T (N:P207L)
AY.74CanadaG3994A (synonymous),C25413T (synonymous)
AY.75USAC21622T (synonymous)
AY.75.1Multiple countries, non-USAG29744A (synonymous)
AY.76MalaysiaT7233C (Orf1ab:L2323S)
AY.77USAT27346C (Orf6:Y49H)
AY.78Germany, TurkeyG14874T (Orf1ab:K4870N),G29227A (synonymous)
AY.79MalaysiaT2125C (synonymous)
AY.80EuropeG5017A (synonymous),G19735T (Orf1ab:D6491Y)
AY.81USAG11358A (Orf1ab:R3698K),A28032G (Orf8:I47V)
AY.82FijiC9144T (Orf1ab:S2960F),C22783T (synonymous)
AY.83USAC5544T (Orf1ab:T1760I),A25491T (synonymous)
AY.84EuropeG28086T (Orf8:A65S)
AY.85ThailandC1825T (synonymous),G16914T (synonymous),T17748A (synonymous)
AY.86Canada, USAG24095T (S:A845S),C29445T (N:T391I)
AY.87UKC832T (synonymous),G27556T (Orf7a:A55S)
AY.88Ghana and other countriesG20709T (Orf1ab:M6815I)
AY.89UKC7851T (Orf1ab:A2529V)
AY.90UKG9251A (Orf1ab:V2996I)
AY.91South Africa, NamibiaC28236T (Orf8:R115C)
AY.91.1EuropeC15540T (synonymous),C17010T (synonymous),C28310T (N:P13S)
AY.92EuropeC28657T (synonymous)
AY.93CanadaC7262T (Orf1ab:L2333F)
AY.94EuropeC15924T (synonymous)
AY.95Maldives, EuropeT22293C (S:L244S)
AY.96BotswanaA28254C (Orf8:I121L)
AY.97EuropeC6840T (Orf1ab:A2192V)
AY.98UKG526T (Orf1ab:E87D)
AY.98.1EuropeC7768T (synonymous)
AY.99South Africa, NigeriaA3536G (Orf1ab:I1091V)
AY.99.1BrazilC8994T (Orf1ab:T2910I)
AY.99.2BrazilC4927T (synonymous),C12525T (Orf1ab:T4087I)
AY.100USAG17122T (Orf1ab:A5620S)
AY.101Brazil, ChileC9474T (Orf1ab:A3070V)
AY.102Peru, ChileA27690T (synonymous)
AY.103USAC24208T (synonymous)
AY.104Sri LankaT13048C (synonymous),C23277T (S:T572I)
AY.105USAC1063T (synonymous)
AY.106Jordan and other countriesC22326T (S:S255F)
AY.107USAA15012G (synonymous)
AY.108Pakistan and other countriesC745T (synonymous),C823T (synonymous),C6828T (Orf1ab:S2188F)
AY.109Nigeria and other countriesA14836G (Orf1ab:I4858V)
AY.110USAC912A (Orf1ab:S216Y)
AY.111UKC4456T (synonymous)
AY.112BahrainG28461A (N:G63D)
AY.113USA, MexicoA12772G (synonymous)
AY.114USAG19677T (Orf1ab:Q6471H)
AY.115BotswanaA10691G (Orf1ab:I3476V)
AY.116AfricaA10691G (Orf1ab:I3476V)
AY.116.1USAG12071A (Orf1ab:D3936N)
AY.117USAC15810T (synonymous)
AY.118USAT826C (synonymous)
AY.119USAG19006T (Orf1ab:A6248S)

 





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