Sars-2 viruksen S-proteinin fuusiopeptidi (FP) kohta ja siihen liittyvä alue (Connecting region)

 https://pubs.acs.org/doi/10.1021/acs.jpcb.1c04176

 

Fuusiopeptidikohta sijaitsee  S-proteiinissa aminohpoissa  816-911.

Mitä vaikuttaa mutaatiot tässä jaksossa viruksen luonteenpiirteisiin ja onko niitä?

Löytyy ainakin K854N eräässä deltavriantissa AY.49 USA  lineage (Connecting region alueeksi nimitetty kohta). Sen kumulatiivisenprevalenssin käyrä onmilteiolematon matomainen: https://outbreak.info/situation-reports?pango=AY.49

Myös AY.86 omaa mutaation A845S (42.5%:ssa)  Canada &USA lineage. Tämä variantti  aiheutti pienen aallon heiäkuussa, muta kumulatiivinen prevalenssi on alle 0%. Variantti ei aikuta olevan  sen jälkeen nousuun päin menossa, päin vastoin.  

Koetan pitää silmäll, jos löytyy muitkin fuusiopeptidialueen tai sen liitännäisalueen  mutaatioita. Niistä kai mikään ei paranna deltan itsensä  kykyjä. 

Delta S proteiinin  fuusiopeptidin (FP) rakenne on seuraava 

:816 -SFIEDLLFNKVTLADAGF-833

Fuusiopeptidiin liittyvä alue  jatkossaa: 834-IKQYGC-840

841-   LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG  TITSGWTFGA -890 

891-GAALQIPFAM-  900

991-QMAYRFNGIG VTQNLVY -917

 Sitten ttulee HR alue1. 

Katson minkä  Sars-2 variantin alueella on vaarallinen fuusiopeptidimutaatio: Olen etsinyt vain deltavarianteista tähän asti.

Löytyi artikkeli:

 

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. 2020 Dec;9(1):2488-2496.

doi: 10.1080/22221751.2020.1844552.

Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal

Vítor Borges  ¹ , Joana Isidro  ¹ , Helena Cortes-Martins  ² , Sílvia Duarte  ³ , Luís Vieira  ^{3   4} , Ricardo Leite  ⁵ , Isabel Gordo  ⁵ , Constantino P Caetano  ⁶ , Baltazar Nunes  ^{6   7} , Regina Sá  ⁸ , Ana Oliveira  ⁸ , Raquel Guiomar  ⁹ , Portuguese network for SARS-CoV-2 genomics  ¹ ; João Paulo Gomes  ¹

Affiliations

• PMID: 33131453
• PMCID: PMC7717510
• DOI: 10.1080/22221751.2020.1844552

Free PMC article

Abstract

Genomic surveillance of SARS-CoV-2 was rapidly implemented in Portugal by the National Institute of Health in collaboration with a nationwide consortium of >50 hospitals/laboratories. Here, we track the geotemporal spread of a SARS-CoV-2 variant with a mutation (D839Y) in a potential host-interacting region involving the Spike fusion peptide, which is a target motif of anti-viral drugs that plays a key role in SARS-CoV-2 infectivity. The Spike Y839 variant was most likely imported from Italy in mid-late February and massively disseminated in Portugal during the early epidemic, becoming prevalent in the Northern and Central regions of Portugal where it represented 22% and 59% of the sampled genomes, respectively, by 30 April. Based on our high sequencing sampling during the early epidemics [15.5% (1275/8251) and 6.0% (1500/24987) of all confirmed cases until the end of March and April, respectively], we estimate that, between 14 March and 9 April (covering the epidemic exponential phase) the relative frequency of the Spike Y839 variant increased at a rate of 12.1% (6.1%-18.2%, CI 95%) every three days, being potentially associated with 24.8% (20.8-29.7%, CI 95%; 3177-4542 cases, CI 95%) of all COVID-19 cases in Portugal during this period. Our data supports population/epidemiological (founder) effects contributing to the Y839 variant superspread. The potential existence of selective advantage is also discussed, although experimental validation is required. Despite huge differences in genome sampling worldwide, SARS-CoV-2 Spike D839Y has been detected in 13 countries in four continents, supporting the need for close surveillance and functional assays of Spike variants.

Keywords: COVID-19; D839Y; SARS-CoV-2; Spike; fusion peptide; genetic variant; genomic epidemiology; mutation.

Conflict of interest statement

No potential conflict of interest was reported by the author(s).