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lördag 31 december 2022

GITHUB aiheita uusimmista GISAID-tietueen kautta tulleista kiinalaisista varianteista

uusimmat GITHUB asiat: 

 https://www.who.int/news/item/30-12-2022-who-meets-with-chinese-officials-on-current-covid-19-situation

https://github.com/cov-lineages/pango-designation/issues

 

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Hevosen koronaviruksen taxonominen sijainti: Betakoronavirus 1, Embecovirus


 https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=694003&lvl=3&keep=1&srchmode=1&unlock

Lineage (full): 

Lisäys: Coronaviridae ryhmässä  Luokittelemattomissa koronaviruksissa UNCLASSIFIED CORONAVIRINAE  löytyy myös hevosen koronaviruslajia:

Equine coronavirus CH21

Taxonomy ID: 2861865 (for references in articles please use NCBI:txid2861865)
current name
Equine coronavirus CH21
NCBI BLAST name: viruses
Rank: species
Genetic code: Translation table 1 (Standard)
Lineage( full )
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Nidovirales; Cornidovirineae; Coronaviridae; Coronavirinae; unclassified Coronavirinae

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fredag 30 december 2022

Tampereen Aamulehti mainitsee tänään hevosten koronaviruksesta (ECoV)

 Kangasalalainen ratsastus­koulu painii tunnistamattoman tauti­aallon kanssa – yrittäjä epäilee syyksi hevosten koronavirusta, josta on tullut Suomessa yleinen riesa Juttua täydennetty lisätiedoilla 30.12. klo 16.41 Lue lisää kirjoittajalta Juha Karilainen, Emma Heikkilä Seuraa ja lue artikkeliin liittyviä aiheita

Viite 1. Equine coronavirus: An emerging enteric virus of adult horses.
Pusterla N, Vin R, Leutenegger C, Mittel LD, Divers TJ. Equine Vet Educ. 2016 Apr;28(4):216-223. doi: 10.1111/eve.12453. Epub 2015 Oct 25. PMID: 32313392 Free PMC article. Review.  Abstract

Equine coronavirus (ECoV) is an emerging virus associated clinically and epidemiologically with fever, depression, anorexia and less frequently colic and diarrhoea in adult horses. Sporadic cases and outbreaks have been reported with increased frequency since 2010 from Japan, the USA and more recently from Europe. A faeco-oral transmission route is suspected and clinical or asymptomatic infected horses appear to be responsible for direct and indirect transmission of ECoV. A presumptive clinical diagnosis of ECoV infection may be suggested by clinical presentation, haematological abnormalities such as leucopenia due to lymphopenia and/or neutropenia. Confirmation of ECoV infection is provided by specific ECoV nucleic acid detection in faeces by quantitative PCR (qPCR) or demonstration of coronavirus antigen by immunohistochemistry or electron microscopy in intestinal biopsy material obtained ante or post mortem. The disease is generally self-limiting and horses typically recover with symptomatic supportive care. Complications associated with disruption of the gastrointestinal barrier have been reported in some infected horses and include endotoxaemia, septicaemia and hyperammonaemia-associated encephalopathy. Although specific immunoprophylactic measures have been shown to be effective in disease prevention for closely-related coronaviruses such as bovine coronavirus (BCoV), such strategies have yet not been investigated for horses and disease prevention is limited to basic biosecurity protocols. This article reviews current knowledge concerning the aetiology, epidemiology, clinical signs, diagnosis, pathology, treatment and prevention of ECoV infection in adult horses. 

Viite 2.

Outbreak of equine coronavirus infection among riding horses in Tokyo, Japan
https://doi.org/10.1016/j.cimid.2021.101668
 
Viite 3.
 
The First Detection of Equine Coronavirus in Adult Horses and Foals in Ireland.
Nemoto M, Schofield W, Cullinane A. Viruses. 2019 Oct 14;11(10):946. doi: 10.3390/v11100946. PMID: 31615132 Free PMC article.
The objective of this study was to investigate the presence of equine coronavirus (ECoV) in clinical samples submitted to a diagnostic laboratory in Ireland. ...Nucleocapsid, spike and the region from the p4.7 to p12.7 genes of positive samples were sequenced, and s … the Irish viruses were distinguishable from those circulating in other countries. This is the first report of ECoV detected in both foals and adult horses in Ireland.

Viite 2.
Identification of a recombinant equine coronavirus in donkey, China.
Qi PF, Gao XY, Ji JK, Zhang Y, Yang SH, Cheng KH, Cui N, Zhu ML, Hu T, Dong X, Yan B, Wang CF, Yang HJ, Shi WF, Zhang W. Emerg Microbes Infect. 2022 Dec;11(1):1010-1013. doi: 10.1080/22221751.2022.2056522. PMID: 35311478 Free PMC article.
Equine coronavirus (ECoV) was first identified in the USA and has been previously described in several countries. In order to test the presence of ECoV in China, we collected 51 small intestinal samples from donkey foals with diarrhoea from a donkey farm in Shandong Province, China between August 2020 and April 2021. Two samples tested positive for ECoV and full-length genome sequences were successfully obtained using next-generation sequencing, one of which was further confirmed by Sanger sequencing. The two strains shared 100% sequence identity at the scale of whole genome. Bioinformatics analyses further showed that the two Chinese strains represent a novel genetic variant of ECoV and shared the highest sequence identity of 97.05% with the first identified ECoV strain - NC99. In addition, it may be a recombinant, with the recombination region around the NS2 gene. To our knowledge, this is the first documented report of ECoV in China, highlighting its risk to horse/donkey breeding. In addition, its potential risk to public health also warrants further investigation.

 

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Tampereen Aamulehti tänään 30.12.2022 puluissa esiityvästä NewCastle-tautia aiheuttavasta viruksesta AOAV-1 , orthoavulavirus 1, Paramyxoviridae

Tampere Tampereella todettu herkästi tarttuvaa lintuvirusta keskustan puluissa – Toimi näin, jos kohtaat kuolleen linnun Ihmiselle virus voi aiheuttaa silmän sidekalvon tulehdusta. Sairasta kesykyyhkyä ei kannata ottaa hoitoon, vaan siitä tulee ilmoittaa paikalliselle virkaeläinlääkärille. Juha Karilainen, Emma Heikkilä 15:28 | Päivitetty 16:41 Aamulehti Tampereen keskustasta joulukuun puolivälissä kuolleena löydetyistä neljästä kesykyyhkystä eli pulusta on todettu lintujen ortoavulavirus 1, kertoo Ruokavirasto perjantaina. Ruokaviraston mukaan Tampereen keskustassa on joulukuun lopun aikana havaittu useita kuolleita puluja, ja myös havaintoja sairaista puluista on ilmoitettu alueen virkaeläinlääkäreille. Tutkimuksiin lähetetyissä puluissa todettu virus on virulenttia eli voimakkaasti tautia aiheuttavaa virustyyppiä. Samaa virusta todettiin joulukuun alkupuolella kesykyyhkyssä Lempäälässä. Myös syyskuussa 2022 todettiin viruksen aiheuttamaa kesykyyhkyjen kuolleisuutta, Ruokavirasto kertoo. Virus aiheuttaa siipikarjassa Newcastlen tautia, joka on vakava eläintauti. Oireina voi olla lentokyvyttömyyttä, apaattisuutta ja hermostollisia oireita, kuten esimerkiksi kävely pää vinossa sekä lintujen kuolemia. Ihmiselle virus voi aiheuttaa silmän sidekalvon tulehdusta, mutta tartunnat ovat Ruokaviraston mukaan harvinaisia, ja vaativat yleensä läheistä kontaktia tartuntaa kantavaan lintuun. Sairaasta linnusta pitää ilmoittaa Jos kaupunkialueelta löytää kuolleen linnun, voi sen poimia muovipussiin ja laittaa sekajätesäiliöön. Ruokavirasto kehottaa ottamaan yhteyttä paikalliseen virkaeläinlääkäriin, jos maastosta löytyy useita kuolleita tai sairaita lintuja. Virkaeläinlääkäri huolehtii tarvittaessa näytteenotosta ja ohjeistaa jatkotoimenpiteistä. Sairaita kesykyyhkyjä ei kannata ottaa hoitoon tartunnan leviämisvaaran vuoksi. Ruokavirasto suosittelee, että luonnonvaraisia lintuja hoidetaan sellaisessa paikassa, jossa ei ole lintuja kotieläimenä. Ortolavirustartunnan voi ehkäistä huolehtimalla hyvästä tautisuojauksesta lintujen pitopaikoissa. Ruokaviraston mukaan siipikarjan ja muiden lintujen pitäjien pitäisi huolehtia siitä, että linnut eivät pääse tekemisiin luonnonvaraisten lintujen kanssa. Myös lintujen rehut ja juomavesi täytyy suojata luonnonvaraisilta linnuilta. Lintujen pitopaikkaan kuljettaessa täytyy vaihtaa suojavaatteet ja jalkineet sekä pestä kädet. Ruokavirasto kehottaa ilmoittamaan kunnaneläinlääkärille, jos lintujen pitopaikassa havaitaan Newcastlen taudin oireita. Tartunnan saaneen pitopaikan linnut joudutaan Ruokaviraston mukaan lopettamaan. Ruokavirastosta muistutetaan, että kuolleita ja sairaita lintuja on syytä aina käsitellä hansikkaat kädessä. Kädet täytyy pestä lintujen käsittelyn jälkeen huolellisesti. Lue lisää: Kangasalalainen ratsastus­koulu painii tunnistamattoman tauti­aallon kanssa – yrittäjä epäilee syyksi hevosten koronavirusta, josta on tullut Suomessa yleinen riesa Juttua täydennetty lisätiedoilla 30.12. klo 16.41 Lue lisää kirjoittajalta Juha Karilainen, Emma Heikkilä Seuraa ja lue artikkeliin liittyviä aiheita

 

PubMed tietoa:eläinteiteellisestä tutkimuksesta  vuosilta 2015-2019

 https://bmcvetres.biomedcentral.com/articles/10.1186/s12917-020-02470-9

Newcastle disease (ND) causes severe economic losses in poultry industry worldwide. Egyptian poultry industry suffered from severe economic losses since the isolation of Velogenic Newcastle disease virus (vNDV) genotype VIId in 2011 and up till now despite the use of different vaccination programs. So, this study aimed to isolate and characterize the vNDV from a total of 120 poultry flocks from ten provinces in the Egyptian Delta region with a history of respiratory manifestation, high mortalities or a decrease in egg production between 2015 and 2019.

Newcastle disease (ND) encompasses a critical impact amongst the most economically viral poultry diseases leading to high mortality and morbidity rates in the susceptible poultry. It still causing a drop in egg production even in vaccinated layers [1]. Besides the economic impact through the loss of productive assets, trade restrictions are of significant concern for exporting countries. Within the last 5 years, 109 of 200 member countries have reported the disease to the OIE [2].

Newcastle disease virus (NDV) or Avian paramyxoviruses 1 (APMV-1) was recently classified to Genus Avian Orthoavulavirus, family Paramyxoviridae and common NDV is recently known as Avian Orthoavulavirus-1 (AOAV-1) [3, 4]. Full fusion (F) gene nucleotide sequencing classified all AOAV-1 into two classes; class I and class II. AOAV-1 class II contains virulent, and non-virulent viruses, with 21 identified genotypes (I to XXI Genotype). Updated classification criteria of AOAV-1 genotype VII viruses merged all the subgenotypes into only 3, VII.1.1 including previous subgenotypes (b, d, e, j, l), VII.1.2 included previous subgenotypes (f), and VII.2 included the previous subgenotypes (h, i, k) [5].

AOAV-1 (genotype VII) causes fatal infections in poultry and other susceptible birds as they are responsible for the fourth major panzootic of ND worldwide which caused by viruses of genotype VII.1.1 [6]. Similarly, in the Egyptian poultry industry, AOAV-1 is specially subgenotypes VIId and VIIb are incriminated in significant economic losses. The partial sequence of the F gene and phylogenetic analysis of AOAV-1 isolated from different outbreaks in Egypt from 2011 to 2017 belonged to genotype VIId [7,8,9,10].

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onsdag 28 december 2022

Omicronlinjasta BA.5.3 muodostuu runsashaarainen BQ.1* ryhmä jota seurataan.

https://github.com/cov-lineages/pango-designation/blob/master/lineage_notes.txt#L1125 

 

Omicronin linja BA.5.3 on tuottanut alalinjan BA.5.3.1, jota merkataan BE koodilla.

BE.1.1.1 taas merkataan koodilla BQ.

BQ.1 taas on tuottanut runsaasti vaarallisia ja runsaita  alalinjoja ja siksi kaikkia BQ.1* linjoja seurataan. Sen alalinjoille on tarvittaessa annettu lyhennyskoodi alalinjan alalinjaa varten.

BQ.1.1.1 = CZ

BQ.1.1.5 = DN

BQ.1.1.7 = DK

BQ.1.1.8= DP

BQ.1.1.14=CW

BQ.1.1.15=DM

Mitä taas tulee BQ.1 linjan jälkeisiin linjoihin BA.5.3 alalinjavarianttien joukossa, niistä en tässä mainitse enempää; ne näkyvät viimeisen BQ.1 - linjalaisen (BQ.1.27) alapuolella




BA.5.3 Alias of B.1.1.529.5.3, mainly found in Germany and South Africa, from pango-designation issue #550


BA.5.3.1 Alias of B.1.1.529.5.3.1, mainly found in South Africa, Austria, and England, from pango-designation issue #625

BE.1 Alias of B.1.1.529.5.3.1.1, mainly found in South Africa, Austria and England, from pango-designation issue #625

BE.1.1 Alias of B.1.1.529.5.3.1.1.1, Germany lineage

BE.1.1.1 Alias of B.1.1.529.5.3.1.1.1.1, found globally, from pango-designation issue #931

 

BQ.1 Alias of B.1.1.529.5.3.1.1.1.1.1, Nigeria lineage, from pango-designation issue #993

BQ.1.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1, found globally, defining mutations ORF1b:N1191S and S:R346T, from issue #993

BQ.1.1.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.1, Europe, ORF1b:V1639A

 

CZ.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.1.1, England/SouthKorea/Romania, S:F490I

 

BQ.1.1.2 Alias of B.1.1.529.5.3.1.1.1.1.1.1.2, England, S:D253G, from issue #1209

BQ.1.1.3 Alias of B.1.1.529.5.3.1.1.1.1.1.1.3, England, A15111G

BQ.1.1.4 Alias of B.1.1.529.5.3.1.1.1.1.1.1.4, T29173C

BQ.1.1.5 Alias of B.1.1.529.5.3.1.1.1.1.1.1.5, ORF1b:P2313L, ORF1a:V3855I

 

DN.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.5.1, S:K147N

DN.1.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.5.1.1 found mainly in UK and Denmark, from pango-designation issue #1463

 

BQ.1.1.6 Alias of B.1.1.529.5.3.1.1.1.1.1.1.6, ORF1a:L681F

BQ.1.1.7 Alias of B.1.1.529.5.3.1.1.1.1.1.1.7, ORF1a:S216Y

 

DK.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.7.1, S:339N, ORF1a:A1809T

 

BQ.1.1.8 Alias of B.1.1.529.5.3.1.1.1.1.1.1.8, ORF1a:H374Y, ORF1a:L969F

 

DP.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.8.1, S:A352S, England/Belgium

 

BQ.1.1.9 Alias of B.1.1.529.5.3.1.1.1.1.1.1.9, S:S151I

BQ.1.1.10 Alias of B.1.1.529.5.3.1.1.1.1.1.1.10, S:Y144-, T16413C, Denmark/Germany

BQ.1.1.11 Alias of B.1.1.529.5.3.1.1.1.1.1.1.11, S:S494P

BQ.1.1.12 Alias of B.1.1.529.5.3.1.1.1.1.1.1.12, France/US, S:S494P, on ORF1a:T4368I branch

BQ.1.1.13 Alias of B.1.1.529.5.3.1.1.1.1.1.1.13, Denmark/Israel/Switzerland/France, E:V62F and S:Y144-

BQ.1.1.14 Alias of B.1.1.529.5.3.1.1.1.1.1.1.14, England, G23608T

 

CW.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.14.1, England, S:G446S

 

BQ.1.1.15 Alias of B.1.1.529.5.3.1.1.1.1.1.1.15, Spain, T18897C

 

DM.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.15.1, Spain/Europe/US, S:A348S

 

BQ.1.1.16 Alias of B.1.1.529.5.3.1.1.1.1.1.1.16, England, S:Q607H

BQ.1.1.17 Alias of B.1.1.529.5.3.1.1.1.1.1.1.17, France, ORF1a:S2273F

BQ.1.1.18 Alias of B.1.1.529.5.3.1.1.1.1.1.1.18, France, C6541T

BQ.1.1.19 Alias of B.1.1.529.5.3.1.1.1.1.1.1.19, England, N:Q380H

BQ.1.1.20 Alias of B.1.1.529.5.3.1.1.1.1.1.1.20, Denmark, S:144- and ORF3a:H204Y

BQ.1.1.21 Alias of B.1.1.529.5.3.1.1.1.1.1.1.21, Switzerland/France, S:144- and A17946G

BQ.1.1.22 Alias of B.1.1.529.5.3.1.1.1.1.1.1.22, Australia/England/Denmark, S:144- and C913A

BQ.1.1.23 Alias of B.1.1.529.5.3.1.1.1.1.1.1.23, France, ORF3a:V97I, S:Y144-, on G6421T branch

BQ.1.1.24 Alias of B.1.1.529.5.3.1.1.1.1.1.1.24, England, 11941T, S:Y144-

BQ.1.1.25 Alias of B.1.1.529.5.3.1.1.1.1.1.1.25, USA/Canada, S:F490S and S:Y144-, from issue #1350

BQ.1.1.26 Alias of B.1.1.529.5.3.1.1.1.1.1.1.26, S:E471Q

BQ.1.1.27 Alias of B.1.1.529.5.3.1.1.1.1.1.1.27, France/USA, S:G181R, ORF1a:F2864L, on G6421T branch

BQ.1.1.28 Alias of B.1.1.529.5.3.1.1.1.1.1.1.28, S:P251L, ORF1b:P976S, on C18828T branch

BQ.1.1.29 Alias of B.1.1.529.5.3.1.1.1.1.1.1.29, S:Q613H

BQ.1.1.30 Alias of B.1.1.529.5.3.1.1.1.1.1.1.30, Canada, S:V445A

BQ.1.1.31 Alias of B.1.1.529.5.3.1.1.1.1.1.1.31, Indonesia/global, S:S256L

 

BQ.1.2 Alias of B.1.1.529.5.3.1.1.1.1.1.2, found globally, defined by S:I666V, from issue #1082

BQ.1.3 Alias of B.1.1.529.5.3.1.1.1.1.1.3, found globally, defined by S:E619Q, from issue #1082

BQ.1.4 Alias of B.1.1.529.5.3.1.1.1.1.1.4, England and Denmark, defined by S:R190T

BQ.1.5 Alias of B.1.1.529.5.3.1.1.1.1.1.5, defined by ORF1b:T1076I

BQ.1.6 Alias of B.1.1.529.5.3.1.1.1.1.1.6, US lineage, defined by ORF1a:G94C

BQ.1.7 Alias of B.1.1.529.5.3.1.1.1.1.1.7, defined by S:L54F

BQ.1.8 Alias of B.1.1.529.5.3.1.1.1.1.1.8, defined by ORF1a:S505F and S:Y144-, issue #1202

BQ.1.8.1 Alias of B.1.1.529.5.3.1.1.1.1.1.8.1, England/Australia, S:256L

BQ.1.8.2 Alias of B.1.1.529.5.3.1.1.1.1.1.8.2, England/Scotland, S:A688V

BQ.1.9 Alias of B.1.1.529.5.3.1.1.1.1.1.9, US lineage, defined by ORF1a:V2604I followed by S:346T (independent from BQ.1.1)

BQ.1.10 Alias of B.1.1.529.5.3.1.1.1.1.1.10, international lineage, 27600T

BQ.1.10.1 Alias of B.1.1.529.5.3.1.1.1.1.1.10.1, Italy/England/Denmark, S:H146L, issue #1189

BQ.1.11 Alias of B.1.1.529.5.3.1.1.1.1.1.11, international lineage, 29541T

BQ.1.12 Alias of B.1.1.529.5.3.1.1.1.1.1.12, international lineage, 28849T

BQ.1.13 Alias of B.1.1.529.5.3.1.1.1.1.1.13, international lineage, ORF1a:V627I

BQ.1.13.1 Alias of B.1.1.529.5.3.1.1.1.1.1.13.1 found mainly in USA and Europe, from pango-designation issue #1400

BQ.1.14 Alias of B.1.1.529.5.3.1.1.1.1.1.14, international lineage, 18570A

BQ.1.15 Alias of B.1.1.529.5.3.1.1.1.1.1.15, international lineage, ORF1a:L3116F

BQ.1.16 Alias of B.1.1.529.5.3.1.1.1.1.1.16, international lineage, ORF1a:A540V

BQ.1.17 Alias of B.1.1.529.5.3.1.1.1.1.1.17, Denmark/Germany, S:K444T mutated further to S:444M

BQ.1.18 Alias of B.1.1.529.5.3.1.1.1.1.1.18, Denmark/Austria, E:P71S, then S:R346T and S:Y144-

BQ.1.19 Alias of B.1.1.529.5.3.1.1.1.1.1.19, S:S494P

BQ.1.20 Alias of B.1.1.529.5.3.1.1.1.1.1.20, S:A348S

BQ.1.21 Alias of B.1.1.529.5.3.1.1.1.1.1.21, England/France, S:R346S, S:Y144-

BQ.1.22 Alias of B.1.1.529.5.3.1.1.1.1.1.22, Canada, S:R346T after C26681T

BQ.1.23 Alias of B.1.1.529.5.3.1.1.1.1.1.23, Singapore/Indonesia/Australia, A2653G and S:Y144-

BQ.1.24 Alias of B.1.1.529.5.3.1.1.1.1.1.24, South Africa, S:T240I, S:R346T, #1240

BQ.1.25 Alias of B.1.1.529.5.3.1.1.1.1.1.25, S:R346T, T8038C, T25569C, G26031A

BQ.1.25.1 Alias of B.1.1.529.5.3.1.1.1.1.1.25.1, found mainly in USA, from pango-designation issue #1451

BQ.1.26 Alias of B.1.1.529.5.3.1.1.1.1.1.26, found mainly in Denmark, from pango-designation issue #1315

BQ.1.26.1 Alias of B.1.1.529.5.3.1.1.1.1.1.26.1, found mainly in Denmark, from pango-designation issue #1369

BQ.1.27 Alias of B.1.1.529.5.3.1.1.1.1.1.27, USA/England, S:V445A

 

BQ.2 Alias of B.1.1.529.5.3.1.1.1.1.2, international, S:A522P

 

BE.1.2 Alias of B.1.1.529.5.3.1.1.2, mainly found in Costa Rica and USA, from pango-designation issue #923

BE.1.1.2 Alias of B.1.1.529.5.3.1.1.1.2, Germany lineage, defined by ORF9b:S50L

 

CC.1 Alias of B.1.1.529.5.3.1.1.1.2.1, Germany lineage, defined by S:N450D

 

BE.1.2.1 Alias of B.1.1.529.5.3.1.1.2.1, Panama, Canada, USA, defined by S:V445A, from issue #1095

BE.1.3 Alias of B.1.1.529.5.3.1.1.3, Finland and Estonia lineage

BE.1.4 Alias of B.1.1.529.5.3.1.1.4, America lineage, ORF1b:V1787I

BE.1.4.1 Alias of B.1.1.529.5.3.1.1.4.1, S:A701V

BE.1.4.2 Alias of B.1.1.529.5.3.1.1.4.2, S:R346T

BE.1.4.3 Alias of B.1.1.529.5.3.1.1.4.3, Mexico, S:V445A

BE.1.4.4 Alias of B.1.1.529.5.3.1.1.4.4, S:L176F

 

BE.2 Alias of B.1.1.529.5.3.1.2, Belgium lineage

BE.3 Alias of B.1.1.529.5.3.1.3, USA lineage

BE.4 Alias of B.1.1.529.5.3.1.4, Bangladesh, defined by ORF1a:T3308N, from issue #1115

BE.4.1 Alias of B.1.1.529.5.3.1.4.1, Bangladesh, defined by S:P209L, S:R346T, from issue #1115

BE.4.1.1 Alias of B.1.1.529.5.3.1.4.1.1, Bangladesh, defined by S:K444R, from issue #1115

 

CQ.1 Alias of B.1.1.529.5.3.1.4.1.1.1, Bangladesh, defined by S:Y144- and 11866T

CQ.1.1 Alias of B.1.1.529.5.3.1.4.1.1.1.1, Canada/England, S:A262S

CQ.2 Alias of B.1.1.529.5.3.1.4.1.1.2, Japan/US, defined by S:V445A

 

BE.4.2 Alias of B.1.1.529.5.3.1.4.2, Bangladesh, defined by S:K444N & S:N460K, from issue #1114

BE.5 Alias of B.1.1.529.5.3.1.5, South Africa, S:R346T, #1281

BE.6 Alias of B.1.1.529.5.3.1.6, France, S:R346S

BE.7 Alias of B.1.1.529.5.3.1.7, South Africa, S:R346T, #1280

BE.8 Alias of B.1.1.529.5.3.1.8, South Africa, S:R346T, #1278

BE.9 Alias of B.1.1.529.5.3.1.9, found mainly in Brazil, from pango-designation issue #1302

BE.10 Alias of B.1.1.529.5.3.1.10, S:K444T, S:N460K, mainly Brazil, from issue #1411

 

BA.5.3.2 Alias of B.1.1.529.5.3.2, mainly found in Germany, from pango-designation issue #697

BA.5.3.3 Alias of B.1.1.529.5.3.3, UK lineage

BA.5.3.4 Alias of B.1.1.529.5.3.4, Germany lineage

BA.5.3.5 Alias of B.1.1.529.5.3.5, mainly found in South Africa, from pango-designation issue #1042

BA.5.5 Alias of B.1.1.529.5.5, mainly found in USA, from pango-designation issue #656

BA.5.5.1 Alias of B.1.1.529.5.5.1, mainly found in USA, from pango-designation issue #873

BA.5.5.2 Alias of B.1.1.529.5.5.2, mainly found in USA, Canada, England and Ireland, from pango-designation issue #938

BA.5.5.3 Alias of B.1.1.529.5.5.3, USA lineage, from pango-designation issue #1015

BA.5.6 Alias of B.1.1.529.5.6, USA lineage

BA.5.6.1 Alias of B.1.1.529.5.6.1, Peru lineage

BA.5.6.2 Alias of B.1.1.529.5.6.2, mainly found in USA, Belgium and Mexico, from pango-designation issue #903

BA.5.6.3 Alias of B.1.1.529.5.6.3, mainly found in England, from pango-designation issue #1118

BA.5.6.4 Alias of B.1.1.529.5.6.4, found in USA and Europe, from pango-designation issue #1191

 

BW.1 Alias of B.1.1.529.5.6.2.1, Mexico lineage, from pango-designation issue #1059, defined by S:460K

BW.1.1 Alias of B.1.1.529.5.6.2.1.1, Mexico lineage, defined by S:V486A, issue #1341

 

BA.5.7 Alias of B.1.1.529.5.7, Australia lineage

BA.5.8 Alias of B.1.1.529.5.8, mainly found in England, USA, Denmark and Scotland, from pango-designation issue #743

BA.5.9 Alias of B.1.1.529.5.9, mainly found in Germany, Switzerland and Denmark, from pango-designation issue #753

BA.5.10 Alias of B.1.1.529.5.10, mainly found in Philippines, Canada, and USA, from pango-designation issue #936

BA.5.10.1 Alias of B.1.1.529.5.10.1, mainly from Philippines, defined by S:346T, from pango-designation issue #1031

 

DF.1 Alias of B.1.1.529.5.10.1.1, found mainly in UK, from pango-designation issue #1270

BA.5.11 Alias of B.1.1.529.5.11, South Africa, C1627T, S:R346T, #1277

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Sars-Cov-2 rekombinaatioista luetteloa. Rekombinantit XA- XBK


 

https://github.com/cov-lineages/pango-designation/blob/master/lineage_notes.txt

Rekombinantit päivitetty 27.12.2022

Ne ovat juoksevalla numerolla merkattuja.Juokseva numero ei näy tässä kopiossa kuten netissä. Kirjoitan tähän numerot, koska lista alkaa  Wuhanin A.sta ja rekombinantit tulevat vasta X-kirjaimen kohdalta esiin.

Rekombinanttisarja XA-XZ on välillä 2261-2283.

Rekombinanttisarja XAA-XAZ on välillä 2284-2309.

Rekombinanttisarja XBA-XBK, (joka viimeksimainittu on viimeisin käytetty koodinimi) on välillä2310-2340. Oin tiedot omalle tietokoneelle eilen ja nyt on jo kulunut yksi vuorokausi, mutta asetan eiliset päivitykset tähän.


Sitaatti  GITHUBin Sars-Cov-2 varianttien   rekombinanttien päivityslistasta. Omikronin rekombinantit tulevat kuvioihin vasta  XD:stä alkaen.



XA Recombinant lineage with parental lineages B.1.1.7 and B.1.177, UK lineage

XB Recombinant lineage with parental lineages B.1.634 and B.1.631, Central and North America lineage, discussed in pango-designation issue #189. Formally B.1.628

XC Recombinant lineage with parental lineages AY.29 and B.1.1.7, Japan lineage, from pango-designation issue #263

XD Recombinant lineage of Delta and BA.1, France and Denmark lineage, from pango-designation issue #444

XE Recombinant lineage of BA.1 and BA.2, UK lineage, from pango-designation issue #454

XF Recombinant lineage of Delta and BA.1, UK lineage, from pango-designation issue #445

XG Recombinant lineage of BA.1 and BA.2, Denmark lineage, from pango-designation issue #447

XH Recombinant lineage of BA.1 and BA.2, Denmark lineage, from pango-designation issue #448

XJ Recombinant lineage of BA.1 and BA.2, Finland lineage, from pango-designation issue #449

XK Recombinant lineage of BA.1 and BA.2, Belgium lineage, from pango-designation issue #460

XL Recombinant lineage of BA.1 and BA.2, UK lineage, from pango-designation issue #464

XM Recombinant lineage of BA.1.1 and BA.2, European lineage, from pango-designation issue #472

XN Recombinant lineage of BA.1 and BA.2, UK lineage, from pango-designation issue #480

XP Recombinant lineage of BA.1.1 and BA.2, UK lineage, from pango-designation issue #481

XQ Recombinant lineage of BA.1.1 and BA.2, UK lineage, from pango-designation issue #468

XR Recombinant lineage of BA.1.1 and BA.2, UK lineage, from pango-designation issue #469

XS Recombinant lineage of Delta and BA.1.1, USA lineage, from pango-designation issue #471

XT Recombinant lineage of BA.1 and BA.2, South Africa lineage, from pango-designation issue #478

XU Recombinant lineage of BA.1 and BA.2, lineage in India and other countries, from pango-designation issue #522

XV Recombinant lineage of BA.1 and BA.2, lineage in Denmark and Italy, from pango-designation issue #463

XW Recombinant lineage of BA.1 and BA.2, USA, Germany, England lineage, from pango-designation issue #591

XY Recombinant lineage of BA.1 and BA.2, predominantly in USA, from pango-designation issue #606

XZ Recombinant lineage of BA.2 and BA.1, USA lineage, from pango-designation issue #636

XAA Recombinant lineage of BA.1 and BA.2, USA lineage, from pango-designation issue #664

XAB Recombinant lineage of BA.1 and BA.2, Germany lineage, from pango-designation issue #665

XAC Recombinant lineage of BA.1 and BA.2, Canada and USA lineage, from pango-designation issue #590

XAD Recombinant lineage of BA.2 and BA.1, Germany lineage, from pango-designation issue #607

XAE Recombinant lineage of BA.2 and BA.1, USA and Chile lineage, from pango-designation issue #637

XAF Recombinant lineage of BA.1 and BA.2, Costa Rica lineage, from pango-designation issue #676

XAG Recombinant lineage of BA.1 and BA.2, lineage in Brazil and other countries, from pango-designation issue #709

XAH Recombinant lineage of BA.2 and BA.1, lineage in Slovenia and other countries, from pango-designation issue #755

XAJ Recombinant lineage of BA.2.12.1 and BA.4, predominantly in England, from pango-designation issue #826

XAK Recombinant lineage of BA.1 and BA.2, Germany lineage, from pango-designation issue #823

XAL Recombinant lineage of BA.1 and BA.2, Germany lineage, from pango-designation issue #757

XAM Recombinant lineage of BA.1.1 and BA.2.9, lineage mainly found in Panama and USA, from pango-designation issue #759

XAN Recombinant lineage of BA.2 and BA.5.1, lineage found most often in Spain and Denmark, from pango-designation issue #771

XAP Recombinant lineage of BA.2* and BA.1*, USA lineage, from pango-designation issue #789

XAQ Recombinant lineage of BA.1* and BA.2*, lineage mainly found in Canada, from pango-designation issue #798

XAR Recombinant lineage of BA.1* and BA.2*, Reunion lineage, from pango-designation issue #860

XAS Recombinant lineage of BA.5* and BA.2*, USA lineage, from pango-designation issue #882

XAT Recombinant lineage of BA.2.3.13 and BA.1*, Japan lineage, from pango-designation issue #885

XAU Recombinant lineage of BA.1.1* and BA.2.9*, predominantly in Spain, England and France, from pango-designation issue #894

XAV Recombinant lineage of BA.2* and BA.5*, mainly France, USA, and Scotland lineage, from pango-designation issue #911

XAW Recombinant lineage of BA.2* and AY.122, Russia lineage, from pango-designation issue #895

XAY Recombinant lineage of BA.2 and AY.45, South Africa lineage, from pango-designation issue #844

XAY.1 South Africa/US lineage with 4 AA substitutions including S:D253G

XAY.1.1 South Africa with S:R346T and ORF1a:K2108N, from issue #1255

XAY.2 South Africa/Denmark/Israel lineage with ORF1a:Y3765C

XAZ Recombinant lineage of BA.2.5, BA.5. and BA.2.5, predominantly found in France, Germany, Croatia, Denmark and USA, from pango-designation issue #797

XBA Recombinant lineage of perhaps AY.45 and perhaps BA.2 (with perhaps 5 breakpoints), South_Africa lineage, constellation 2 from pango-designation issue #844

XBB Recombinant lineage of BJ.1 and BA.2.75 with breakpoint in S1, found in USA and Singapore, from issue #1058

XBB.1 Mostly Bangladesh and Singapore, defined by S:G252V, from issue #1088

XBB.1.1 Singapore/Denmark, defined by ORF1a:P309L

XBB.1.2 Singapore, defined by S:S640F

XBB.1.3 Singapore, India/Italy, defined by S:A484T

XBB.1.4 Europe, S:T883I

XBB.1.4.1 Mainly Denmark, Norway and Sweden, defined by S:S673G, from pango-designation issue #1352

XBB.1.5 USA, S:F486P

XBB.1.6 USA, S:L216F, S:H146K, from issue #1428

XBB.1.7 USA-NY, S:V608I

XBB.2 Defined by S:D253G, from issue #1173

XBB.2.1 Defined by S:N764S

XBB.2.2 Defined by S:Q613H

XBB.3 Defined by ORF1b:I1988V on ORF1a:D82G branch

XBB.3.1 Defined by S:Q677R, India-TN/Singapore, from issue #1241

XBB.3.2 Defined by S:M177T

XBB.3.3 Defined by S:V1122L, USA

XBB.4 Defined by S:K444R on ORF1a:D82G branch, from issue #1239

XBB.4.1 England/Austria, S:L5F, S:T470N

XBB.5 Defined by S:A653V on ORF1a:D82G branch, India-TN, Singapore, Australia

XBC Recombinant lineage of BA.2 and B.1.617.2*, predominantly in Philippines, from pango-designation issue #1100

XBC.1 Mostly Philippines, South Korea, US, Singapore, defined by S:L452M, from issue #1130

XBC.2 Mostly Philippines, defined by S:K97R

XBD Recombinant lineage of BA.2.75.2 and BF.5, India and world, from pango-designation issue #1137

XBE Recombinant lineage of BA.5.2 and BE.4.1, predominantly in USA and England, from pango-designation issue #1246

XBF Recombinant lineage of BA.5.2.3 and CJ.1, Australia, from pango-designation issue #1259

XBG Recombinant lineage of BA.2.76 and BA.5.2, predominantly in UK, from pango-designation issue #896

XBH Recombinant lineage of BA.2.3.17 and BA.2.75.2, predominantly in Brunei, from pango-designation issue #1229

XBJ Recombinant lineage of BA.2.3.20 and BA.5.2, possibly Philippines, from pango-designation issue #1268

XBK Recombinant lineage of BA.5.2 and CJ.1, Denmark/Europe, from pango-designation issue #1418


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