The Omicron version of COVID has caused a great deal of concern around the world, including confirmation of infection in some people in Europe, but if you want to know more about what this new strain means, then CNCAV presents below a number of important details. .
“OMICRON. In any case, we have a new option. Nasoală. All the more disgusting as the levels of competence of the respondents are the ones we know. The only consolation should be that, given the skill levels of the answers, we can expect the virus to stop evolving sooner or later. On the same principle of the Red Queen that I have repeatedly referred to in relation to viral evolutionism: .
The omicron variant appeared sometime in October in the Republic of South Africa. Most likely, as a result of infection of a severely immunocompromised patient (probably untreated HIV-HIV infection has a prevalence of more than 30% in the South African population), which produced suboptimal immune responses. Which answers forced the virus to evolve to evade them, but on the other hand they were not able to eliminate it. And in this way a persistent SARS-CoV-2 infection occurred.
I've seen cases like this before, one of them in a transplant patient in Pittsburgh.
Good. What came out? That's it. A variant that has a total of 50 mutations, more than 30 of them in the structure of the spike protein and 10 in the RBD (receptor binding domain), the structure that binds to receptors and to which neutralizing antibodies are directed, including those in the vaccine.
Mutations in spike protein structure - A67V, Δ69-70, T95I, G142D / Δ143-145, Δ211 / L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478, T478 Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F.
Mutations other than spike protein - NSP3 - K38R, V1069I, Δ1265 / L1266I, A1892T; NSP4-T492I; NSP5 - P132H; NSP6 - Δ105-107, A189V; NSP12 - P323L; NSP14 - I42V; E - T9I; M-D3G, Q19E, A63T; N - P13L, Δ31-33, R203K, G204R.
How do we read mutations? The initials are amino acids.
• D614G. It means that in position 614 of the glycoprotein aspartic acid (D) was replaced by glycine (G). This is a well-known mutation, which occurred in the Wuhan strain when it first entered Europe last year and made a decisive contribution to the SARS-CoV-2 pandemic.
• L452R. Replacement, in position 452, of leucine with arginine: provides a better binding of spike protein to the receptor and reduces the ability of the immune system to recognize.
• P681R. Replacement, in position 681, of proline with arginine. It is considered to increase the cellular infectivity of the virus by cleaving the S precursor in the active S1 / S2 configuration.
Not good.
The bad news:
• The omicron variant is spreading rapidly. In a graph of the initial spread of viral variants, it beats everything that moves. See chart.
• Cases have so far been identified in South Africa, Lesotho, Botswana, Zimbabwe, Mozambique, Namibia and Eswatini, Hong Kong and Belgium. Maybe there will be more, but I haven't watched in a few hours.
• Numerous mutations in RBD (and NTD) associate resistance to neutralizing antibodies (including monoclonal antibodies used in therapy).
• The mutation cluster in the vicinity of the furin cleavage site (H655Y + N679K + P681H) increases the efficiency of virus entry into the cell and therefore the transmissibility of the virus.
• Deletion nsp106 (△ 105-107) which is not new to omicron, can generate antagonism of antiphenones, ie resistance to innate immunity, thus increasing the transmissibility.
• R203K + G204R are mutations that occur outside the spike domain, in the nucleocapsid (they were in the Alpha, Gamma and Lambda variants) and are associated with increased infectivity.
• In Hong Kong, the two patients tested had extremely high viral loads (positive at 17-18 realtime cycles), which suggests a very high virus production. It can lead to both serious illness and increased transmissibility.
• Hong Kong patients were in different rooms, and the virus was found widespread in both rooms - meaning that the virus is transmissible through aerosols. It is transmitted very easily (and high viral loads do not help us at all).
The good news:
• deletion △ 69-70 in the S gene allows very easy identification of the omicron variant - hence its immediate traceability.
• Most regions of the N and RdRp genes that are used for diagnosis by real-time PCR tests are preserved. This means that the tests will work to monitor patients infected with the omicron variant.
• Similarly, the regions of the nucleocapsid structure recognized by rapid antigen tests are not substantially altered and may be recognized. So the tests still work.
• One of the experts in structural biology of coronaviruses suggested that the combined P681H and N679K mutations are extremely rare precisely because they are not stable. He mentioned, however, that it is not known how these mutations are affected by the rest of the mutations in the omicron structure.
What do we not know?
• the extent to which the virus has the ability to spread massively around the world replacing the delta variant. What is the transmissibility of this virus (ie, is R0 higher, the series of increases being continued with each new variant)?
• the extent to which omicron infection has greater pathogenicity (ie, higher lethality and sequelae). It is already known that some patients may remain asymptomatic.
What do we know?
-that we need to protect ourselves. Wear a mask whenever you are indoors with other people.
-Don't leave the house if you have a fever. Do not allow your classmates / employees / pupils / students to come to school if they have a fever.
Unfortunately, we did not leave the forest, and we will probably continue to do so until we learn what we need to do and what we need to do, not just what we want.
In the picture, the way viral variants were initially spread in the Republic of South Africa. "
Dr. Cristian Apetrei, Romanian professor in the Department of Microbiology and Molecular Genetics, is a member of the Center for Vaccine Research and the Postgraduate Program in Microbiology and Immunology (PMI) at the University of Pittsburgh, USA. ”