SARS-CoV-2-N1 and SARS-CoV2-N2

SARS CoV-2-N1 and -N2. These are the virus forms associated to COVID-19 outbreaks, deaths, and the pandemic sweeping the globe.  These are also the type mRNA used for determining exposure to the virus in test kits* used worldwide.  *[Biosynthesis]

The N1 and N2 designate the type of neuraminidase protein characterizing the virion surface of SARS CoV-2. Both are also present on some strains of Influenza A.  In the past, it was thought important to inoculate humans with both the Hx- and the Nx-type protein in order to stimulate an immune response.

However, a 1994 paper from the National Academy of Sciences, seems to indicate that a pure N1 and N2 inoculation may also be effective without cross-competition for viral antigens lowering its effectiveness.  Current vaccine strategies necessitate the use of annual multi-valent vaccines. Conventional influenza vaccines contain major antigens from the three major currently circulating strains of virus. A trivalent preparation would also be required for a NA-type vaccine. However, questions remain as to the potential for intermolecular antigenic competition between the N1NA and N2NA sub-types found in human viruses and the efficacy of such a bivalent preparation.  (This paper reported a preliminary study of a bivalent NA-specific vaccine, demonstrating that, (a) the absence of inter-NA antigenic competition, and (b) evidence of positive N1/N2 antigenic cross-reactivity.)

We make this paper from the March, 1994 issue of the PNAS available here at the link above.  We thought it was interesting enough, and helps put our present pandemic virus into the context of the “common flu”, pandemic Influenza A, and SARS.  It is under open-license restrains, however.

Again, the SARS CoV-2 virus can be characterized as follows…

Structure of Coronavirus nCoV 2019/2020

Coronaviruses (CoVs) are enveloped positive-sense mRNA viruses. ‘Positive-sense’ here refers to the ‘sugar-structure’ of the RNA and where the phosphate group is located – on the 5th carbon or 5′ upstream in the sugar-ring.

The designation “mRNA”  stands for “messenger RNA” that normal cells use as an intermediary to transcribe from RNA or DNA in the nucleus to directly produce proteins the cell needs.  Since the RNA of SARS-CoV-2 is positive-sense it can transcribe protein immediately for its purposes, and thus is designated an mRNA virus.

The club-like spikes (S-protein) projecting out from their surface gave them the name.  Coronaviruses possess an unusually large RNA genome as well as a unique replication strategy.  (Of these, there are “alpha-” and “beta-” types.  Beta-types contain an OC3 gene as part of the genome that evolves rapidly, while the alpha-type does not.  Essentially, the alpha-type is self limiting and can be fought by the human immune response rapidly.  Beta-type was unknown in humans until now.  More on types, below.)

There are already 20+ evolutions or mutations of the virus, according to  Coronaviruses cause a variety of diseases in animals ranging from cows, pigs, horses, and dogs to chicken, and other birds.  In humans, coronaviruses can cause potentially lethal respiratory infections.

Coronaviruses belong to the largest group of viruses called the Nidovirales order. Members of this order include the Coronaviridae, Arteriviridae, and Roniviridae families. The Coronvirinae are one of two subfamilies in the Coronaviridae family. Coronavirinae are further subdivided into for groups, the alpha-, beta-, gamma-, and delta- coronaviruses.  Nowadays, these viruses are divided using phylogenetic clustering. These virus families have animal and human hosts. The Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV) and Severe Acute Respiratory Coronavirus (SARS-CoV) are examples.

Nidoviruses contain an infectious, linear, positive-sense RNA genome that is capped and polyadenylated. Based on their genome size, nidoviruses are divided into two groups large and small nidoviruses.  All Nidovirales viruses are enveloped, non-segmented positive-sense RNA viruses containing very huge genomes.

Common features:

(i) a highly conserved genomic organization with a large replicase gene preceding structural and accessory genes,

(ii) expression of many non-structural genes by ribosomal frame-shifting,

(iii) several unique of unusual enzymatic activities encoded within the large replicase-transcriptase polyprotein, and

(iv) expression of downstream genes by synthesis of 3’-nested sub-genomic mRNAs.”




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