Thursday, February 10, 2022

It's In The GenBank - 3

Fig. 1 Banks R Banks
What should be in the GenBank (What is GenBank)?

In the previous post of this series I utilized a GenBank GBFF file concerning the genome of "the mother of all SARS-CoV-2 viruses" for comparisons:

"When scientists and researchers inform us that a particular SARS-CoV-2 virus 'is different now', i.e. that its genetic makeup is not what it once was, how do they determine that?

Obviously they compare one SARS-CoV-2 virus to another SARS-CoV-2 virus.

But which ones?

One way is to compare the Wuhan, China version of the virus discovered on December 30, 2019, to subsequent SARS-CoV-2 viruses discovered later around the world:

"In addition to understanding the transmissibility and pathogenicity of these emerging variants, it is crucially important to characterize their antigenicity and the level of cross-protection provided by infection by earlier viruses that are genetically and antigenically similar to the virus that first emerged in December 2019 and which is used in all of the current vaccine preparations."

(SARS-CoV-2 variants, emphasis added). That method is used in many published papers."

(It's In The GenBank - 2). I recently posed/posited the question: should that RNA virus nucleotide list be presented using DNA nomenclature (format), or instead, in RNA nomenclature (format) (Some Of My Best Friends Are Germs)?

Fig. 2 DNA Transcription
Some virologists would consider this issue to be an important one because the use of Uracil ('U') in DNA can be problematic (see link @ Fig. 2; cf. Uracil in DNA – occurrence, consequences and repair; cf. here; cf. here).

Before you form a conclusion to answer the question, take a look at today's appendices (SARS-CoV-2 RNA with DNA nucleotide nomenclature; SARS-CoV-2 RNA with RNA nucleotide nomenclature) to see that a significant change should take place in nucleotide print outs.

Those two appendices detail the differences that would exist if DNA "thymine (T) [C5H6N2O2]" nomenclature was replaced with RNA "uracil (U) [C4H4N2O2]" nomenclature in the GenBank RNA virus records of the database.

Nomenclature matters (Good Nomenclature: A Matter of Life and Death).

The next post in this series is here, the previous post in this series is here.

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