Sars-2 proteiinin EFR (156-158) Deltoille tyypillinen mutaatiokohta . Vert. omikronin deletiosubstituutioalueita.

Tämän EFR alueen substituutioilla tai deletioilla on merkitystä viruksen infektiossa. Parent- delta substituoi E156G  ja deletoi F ja R ( 157, 158). Jokin   virus  substituoi taas R158G  ja deletoi  E ja F (156, 157).    Yleensä vaikutaa läpi  AY-linjojen olevan E157G ja deletio FR157/158.  Tämä on  deltoille tyypillistä mutaatiokohtaa jatehokasta  konservoitumista työkaluna..  On havaittu muutama AY-variantti, joiden replikoitumistahti ja kasvutahti on suurempi kuin parent-deltan. Näitä on   AY43, AY120 ja jokin AY9? linjainen.  Vertailtaessa niiden rakenteita, eroa  parent-deltaan on vain  pari kappaletta . Toinen on se, että nopeat eivät substituoi  deltatunnuksella G142D ja  käyttävät mielellään T95I substituutiota.  Lisäksi  ne tekevät  pikkudeleetion M-proteiiniin, jollaista  deleetiota ei ole parent-deltassa. Delta-variantit tehostuessaan  ikäänkuin minimalisoivat  muutoksiaan, mikä onkin  omikronin suhteen suurinta eroa mielestäni, se kun taas  on oikein superheppu tuossa rönsyilevässä substituutioinnossaan  ja muutteluissaan, mutta moni muutos pielii tyypilliset  entiset  VOC-mutaatiopisteet.  Ehkä  rakennetta vahvistavat glykosylaatiot ja  sinkkisidokset ja -S-S- sidokset  ovat olleet  estämässä ja siksi se ilmeisesti tulee  heikentämään glykosylaatioita ja  sinkkisidosten  muodostumiskohtia taja  muuntelee   sekundääri ja tertiäärimuotoaan . Sinkkisidoksia  voi muodostaa C- motiivit ja niihin voi kuulua H ja D aminohappojakin. pinnimäisissä  kohdissa. C- proteiineja tosin harvemmin  näyttää muuttuvan pois tai tulevan uusia. Mutta  D ja Y ja H vaihtelevat.  Pitää ainakin pitää silmällä  C, H ja D muutoksia sinkin suhteen. Virus tarvitsee  sinkkiä myös virionin pakkaukseen. intravirioniseen tilaan.  vVirus stabiloi itseään  ja  kohtdeproteiinejaan   luhistaa.   Huom tässä on minun omia ajatuksiani eikä niin mitään artikkelin suomennosta. Virus on sinkkiproteiiniensa avulla  tehokas ja pysyy hyvin koossa. Kuten ihminenkin ja ihmisgenomi, joten  suosittelen vain sinkkilisää näinä päivinä kun virukset  kehräävät rakenteita virioneilleen ihmiskunnan kehoissa. D-vitamiininkin annosta olen nostanut,  samoin B-vitamiineja, C-vitamiinin  annosta  monipuolisen ravinnon ohella. 

 EFR- kohdan  deltetiosubstituutiot ovat DELTAN  merkkejä: Sekvenssi:  EFR( 156, 157, 158).

Omikron puolestaan  omaa  useita deletiosubstituutiotaipumuksia:

  Sekvenssissä  LPPA (24, 25, 26, 27) 

Linja  BA.2   tekee tähän  muutokset: L24S, deleetio 25/27(-PPA).   

LPPA-kohdasta jää jäljelle: S. 

Toinen altis  kohta on sekvenssi ATHV (67, 68, 69, 70). 

Tässä omikron  BA.1, BA.1.1 ja BA.3 tekevät substituution  A67V ja  deleetion  69/70 (-HV).    

ATHV-kohdasta jää jäljelle: VT. 

(Myös Sars-2 ETA-variantti teki substituution A67V. Sars-2  ALFA variantti taas  teki  deleetiota 67/70.(-HV).

Seuraava omikronin muutama kohta on   sekvenssissä LGVYY  ( 141,142, 143, 144, 145).

BA.1, BA.1.1 ja BA2 tekevät  substituution G142D.  BA.3 ei tehne tätä  substituutiota.

BA.1 ja BA.1.1 tekevät  deleetiot -VYY (del 143/145).

(Sars-2 THETA teki deleetion  -LGV (del 141/143).

 (Sars-2 KAPPA teki substituution G142D. ja tätä esiintyy  joissain  delta-varianteissa AY myös)

(Sars-2 ALFA teki deletion -YY (del 144/145).  

´(sars-2 MU variantti taas substituoi tässä Y144S ja Y145N). 

(Eräs deltavariantti AY.42 teki myös tuohon alueeseen   substituution Y145H).

Seuraava mutaatioalue, deleetio-substituutio ja insertio kohta on alueella  ( tässä otan vähän laajemman pätkän):

 INLVRDLPQGFSA ( 210, 211, 212, 213, 214, 215,216, 217, 218,219,220,221,222) :

Omicron modifioi  tätä aluetta.  Välillä  julkaistiin   deleetiomuoto ennenkuin  listoihin kirjoitettiin  substituutiomuoto N211I. Se esiintyy BA.1, BA.1.1. ja BA.3 varianteissa. 

 Niissä ilmaistaan olevan jokin deleetio 212/212 ja mahdollinen  insertio (EPE) on  havaittu  kohtaan 215. . 

 Sensijaan  BA.2 omikronvariantti ei omaa  ehkä  samanlaista  konformaatiota, sillä se  substituoi alueesta   kohdan V213G.   En tiedä jos sillä on sitä EPE-insertiota. En ole varma olisiko se mahdollinen.

Itseasiassa en oikein tiedä miltä tuo  alue näyttää sekvenssinä  näillä  eri omikron varianteilla  kokonaisuudessaan.  Olen katsonut miltä tämä ryväs näyttää Sveitsin mallin Spike-rakenteessa. Niitä EPE-kulman ryväksiähän on trimeerissä kolme uloketta tosiaan kuin rypälekimppuja ulkonevana, jotta periaatteessa  kaikki insertiot mahtuvat hyvin  tuohon ulkonevaan lenkiin ja onhan siellä matematiikan mukaan  jaksossa paikkaakin. EPE tarkoittaa kolmea aminohappoa glutamiinihappo (E)- proliini(P)- glutamiinihappo (E).

 BA,2  teki aivan peptidin  alkupäässä ne kolme deletiota, joita muut BA-variantit eivät tehneet.

 

(sars-2 BETA-variantti substituoi D215G. samoin C.1.2 virus, jota tarkkaillaan. . 

 (VUM-joukkoon kuuluva Congo-variantti B.1.640 tekee substituution I210T).

Deltalinjan AY.22  substituoi Q218H.

Deltalinjan  varianteissa on useassa A222V,

https://www.frontiersin.org/articles/10.3389/fimmu.2021.751778/full 

Tässä artikkelissa (20.11.2021) kuvataan Deltavariantin tyyppimutaatioita 

REVIEW article

Front. Immunol., 30 November 2021 | https://doi.org/10.3389/fimmu.2021.751778

The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape

Dandan Tian, Yanhong Sun, Jianming Zhou and Qing Ye^*

• National Clinical Research Center for Child Health, National Children’s Regional Medical Center, The Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, China

During the COVID-19 pandemic, SARS-CoV-2 variants have emerged and spread worldwide. The Delta (B.1.617.2) variant was first reported in India in October 2020 and was classified as a “variant of concern (VOC)” by the WHO on 11 May, 2021. Compared to the wild-type strain, several studies have shown that the Delta variant is more transmissible and has higher viral loads in infected samples. COVID-19 patients infected with the Delta variant have a higher risk of hospitalization, intensive care unit (ICU) admission, and mortality. The Delta variant is becoming the dominant strain in many countries around the world. This review summarizes and analyses the biological characteristics of key amino acid mutations, the epidemic characteristics, and the immune escape of the Delta variant. We hope to provide scientific reference for the monitoring and prevention measures of the SARS-CoV-2 Delta variant and the development strategy of a second-generation vaccine.

1 Introduction

Over the last two decades, SARS -CoV-2 has been the third coronavirus known to cause severe acute respiratory disease in humans, following SARS-CoV in 2003 and MERS-CoV in 2012 (1–3). Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a deleterious impact on health services and the global economy (4–6). As of 8 October 2021, COVID-19 has spread rapidly to more than 200 countries, and there have been 236,599,025 confirmed cases of COVID-19, including 4,831,486 deaths (www.who.int).

At the end of January 2020, the D614G mutation, which turns aspartic acid (Asp) into glycine (Gly) at site 614 of the spike protein, was first discovered in the UK and quickly became the dominant epidemic strain in the world, attracting widespread attention (7, 8). The established nomenclature systems for naming and tracking SARS-CoV-2 genetic lineages by Nextstrain, GISAID (https://www.gisaid.org/), and Pango are currently in use by scientists. The SARS-CoV-2 variants were classified as “variant of concern (VOCs)” and “Variant of Interest, VOI)” by the WHO. At present, Alpha B.1.1.7 (known as 20I/501Y.V1, VOC 202012/01) (9), Beta B.1.351 (known as 501Y.V2) (10), Gamma P.1 (known as 501Y.V3) (11) and Delta B.1.617.2 (known as 478K.V1) (12) are defined as “variants of concern (VOCs)” by the WHO. Several studies have indicated that the Delta variant has higher transmissibility (13–15) and immune evasion than the early original virus strain and the other three VOCs. COVID-19 patients infected with Delta have a higher risk of hospitalization, ICU admission, and mortality (16–18). The Delta is becoming a prominent global strain globally, which has brought new challenges to the prevention and control of the COVID-19 pandemic.

1.1 The Biological Characteristics of Key Amino Acid Mutations in the Spike Protein of the SARS-CoV-2 Delta Variant

SARS-CoV-2 invades host cells by binding the spike protein to angiotensin-converting enzyme-2 (ACE2) (19–21). The SARS‐CoV‐2 spike protein is cleaved by furin into the S1 subunit and S2 subunit. The S1 subunit consists of an N-terminal domain (NTD) and a receptor-binding domain (RBD) and is responsible for binding to the host-cell ACE2 receptor. In comparison, the S2 subunit includes the trimeric core of the protein and is responsible for membrane fusion. The spike protein is the dominant neutralization target of monoclonal antibodies (mAbs), convalescent plasma, and vaccines (22–24). Therefore, mutations in the S protein affect the transmissibility, pathogenicity, and immune escape of SARS-CoV-2 variants. The Delta variant has accumulated nine amino acid mutations (T19R, G142D, FR156⁃157del, R158G, L452R, T478K, D614G, P681R, D950N) in the spike protein (25).

1.1.1 L452R   ( Finnish comment: Tätä DELTA-tunnusta  ei ole  omikronilla!)

The L452R mutation is located in the receptor-binding motif (RBM) region in the RBD region, containing residues that bind to ACE2 (26–28). Analysis of the SARS-CoV-2 spike protein revealed that the L452 residue does not directly contact the ACE2 receptor (29). Instead, L452, together with F490 and L492, forms a hydrophobic patch on the surface of the spike RBD. The L452R mutation may cause structural changes in this region that stabilize the interaction between the spike protein and the host cell’s ACE2 receptor, leading to increasing infectivity (26, 30). Deng X et al. observed that the entry efficiency into host cells of stable pseudoviruses carrying the L452R mutation was 6.7-22.5-fold higher in 293T cells and 5.8-14.7-fold higher in human airway lung organoids (HAOs) compared to D614G alone (293T cells and HAOs can stably express ACE2) (26). These results indicated that L452R mutation could increase the binding affinity of the spike protein to the host-cell receptor ACE2.

Wilhelm A et al. (31) found that authentic SARS-CoV-2 variants harboring L452R had reduced susceptibility to convalescent and vaccine-elicited sera and mAbs. Compared to B.1, the neutralization activity of convalescent sera against Delta was reduced by 5.33-fold. The neutralization activity of sera elicited by the mRNA vaccine against Delta was 2-fold weaker than B.1. In contrast to Kappa, authentic SARS-CoV-2 variants harboring L452R have a substantial resistance against imdevimab and bamlanivimab. Even at high concentrations, imdevimab was not effective against Delta, indicating high resistance. However, neutralization of Delta was moderately reduced with the clinically approved combination of casirivimab/imdevimab (31). In addition, another pseudovirus simulation showed that the L452R mutation could enhance the immune escape ability of the virus against convalescent plasma (32) and monoclonal antibodies (SARS2-01, SARS2-02, LY-CoV555, SARS2-32, X593, P2B2F6) (33).

1.1.2 T478K  ((Finnish comment: Tämä  BETA- tunnus  on omikronvarianteilla BA.1, BA.1.1 ja BA.2, mutta ei  BA.3:ssa)

Compared with the other two B.1.617 lineages (B.1.617.1 and B.1.617.3), Delta (B.1.617.2) does not have the E484Q mutation but has a unique T478K mutation (25). An in silico molecular dynamics study on the protein structure of spike has predicted that the T478K mutation, substituting a non‐charged amino acid (threonine) with a positive one (lysine), may significantly alter the electrostatic surface of the protein and increase steric hindrance of the spike protein. These factors could enhance the binding affinity of RBD to ACE2 and enhance the ability of the virus to invade the host cell (34). Similarly, in vitro cell culture studies have shown that the Delta variant carrying T478K is more likely to undergo secondary mutation in a low titer antibody environment, leading to the failure of host antibody immunization (34).

1.1.3 P681R   ( Finnish comment: Tätä DELTA-tunnsuta ei ole tässä muodossa omikronissa. Omikronilla on P681H, kuten  ALFA, THETA ja MU-varianteillakin)

Interestingly, the P681R mutation in the S protein of the B.1.617 lineage is unique and newly identified in VOCs. The P681R mutation is located at the furin cleavage site (FCS; residues RRAR positioned between 682-5), and the cleavage of this region is the key to host cell entry (35). Several analyses have found that the P681R mutation affects viral replication dynamics and potentially determines the B.1.617 variants (36–38). Pseudoviruses carrying the P681R mutation showed that this mutation significantly increased the level of the cleaved S2 subunit and the level of the cleaved S2 subunit of the D614G/P681R mutation was significantly higher than that of D614G alone. In vitro, cell culture experiments revealed that the size of floating syncytia in the D614G/P681R mutant-infected culture was significantly larger than that in the D614G mutant-infected cell culture (39). These data suggested that the P681R mutation facilitates furin-mediated cleavage of the SARS-CoV-2 S protein, accelerates viral fusion, and promotes cell-cell infection.

In addition, the neutralization analyses of pseudoviruses showed that three monoclonal antibodies against RBD had 1.5-fold (1.2 ~2.65) decreased neutralization activity by against pseudoviruses with the D614G/P681R mutation. The neutralizing activity assay using the 19 sera elicited by the BNT162b2 vaccine (two doses) showed that pseudoviruses carrying the D614G/P681R mutation are significantly resistant to the vaccine-induced NAbs compared to the D614G pseudoviruses (39). These results suggested that the P681R mutation generated resistance to some mAbs and sera elicited by mRNA vaccines.

Stefano Pascarella et al. (40) reported that the surface electrostatic potential (EP) of the RBD of the spike protein is markedly increased. This is particularly noticeable in the Delta variant, which shows multiple replacements from neutral or negatively charged amino acids to positively charged amino acids. The EP in the spike protein of the Delta variant includes the uncharged and hydrophobic residue of Leu452 changing to the positively charged residue Arg and the neutral residue Thr changing to the positively charged Lys at position 478. The positive electrostatic potential can favor the interaction between the B.1.617.2+ RBD and the negatively charged ACE2, increasing the binding affinity of RBD to ACE2 receptor, thus conferring a potential increase in the virus transmission.

The above studies suggested that L452R, T478K, and P681R are the three key mutations of the SARS-CoV-2 Delta variant. These mutations increased transmissibility and generated immune escape of the Delta variant, as shown in Figure 1.