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I read an interesting article about two strains of the coronavirus: https://www.newscientist.com/article/2236544-coronavirus-are-there-two-strains-and-is-one-more-deadly/

I would like to know how the scientists used to classify a coronavirus as l-strain and s-strain. And more specifically I would like to have the genome(The DNA) for a l-strain and a s-strain.

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    $\begingroup$ “Two of the key claims made by this paper appear to have been reached by misunderstanding and over-interpretation of the SARS-CoV-2 data, with an additional analysis suffering from methodological limitations ... Given these flaws, we believe that Tang et al. should retract their paper, as the claims made in it are clearly unfounded and risk spreading dangerous misinformation at a crucial time in the outbreak." —Response to “On the origin and continuing evolution of SARS-CoV-2” $\endgroup$
    – iayork
    Commented Mar 19, 2020 at 21:12

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Article links to this publication which has all the information needed: https://academic.oup.com/nsr/advance-article/doi/10.1093/nsr/nwaa036/5775463

It is mentioned in the paper that:

Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated.

Their results highlight evolutionary changes in the development of new variations in functional sites in the receptor-binding domain (RBD). These developmental variations have a spike in changes to the RBD of SARS-CoV-2 and viruses from pangolin SARSr-CoVs

How do they define S and L variations?

They did population genetics on 103 available SARS-CoV-2 genomes. These two major types are well defined by two SNPs which show complete linkage across the viral strains.

It also important to mention that SARS-CoV-2 was found to have 96.2% similairty to a bat SARS-related coronavirus (SARSr-CoV; RaTG13) but not very similar to SARS-CoV (79%) or MERS-CoV (50%).

How do we know that there's two type?

We know there's two types because from the 103 sequenced genomes two SNP locations show significant linkage. These are SNPs at location 8,782 (orf1ab: T8517C, synoniumous) and 28,144 (ORF8: C251T, S84L).

If you have a "CT" (as in base pairs) haplotype SARS-CoV-2 you've got the L-type ("L" type because T28,144 is in the codon of Leucine). Otherwise, if you've got a "TC" haplotype you have the S-type (C28,144 is in the codon of Serine).

They found that S-type is the ancient (less aggressive version) by aligning it with other older viruses. In fact for each variant of the virus the ancestral state was inferred by alignments of SARS-CoV-2 (NC_045512), RaTG13, and GD Pangolin-Cov.

So to be more precise on my answer for finding S and L types. You sequence the genome of an infected individual (you can find these online on NCBI) align it with the current reference sequence (MN908947, NC_045512), look at the SNPs and figure if they have a "CT" or "TC" haplotype to determine S or L type.

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  • $\begingroup$ I downloaded the complete genome of MN908947 and NC_045512. They are both identitical. Aren't they supposed to be different? $\endgroup$
    – yuval
    Commented Mar 19, 2020 at 14:03
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    $\begingroup$ The paper was a little confusing on that. I aligned them and you're right. I changed my answer to reflect your question better. $\endgroup$
    – m4rio
    Commented Mar 19, 2020 at 18:09
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    $\begingroup$ I downvoted this answer because it doesn’t point out that the notion of two biologically significant strains is nonsense, the product of incompetent researchers messing with things they don’t understand. See genuine experts’ opinion in Response to “On the origin and continuing evolution of SARS-CoV-2” $\endgroup$
    – iayork
    Commented Mar 19, 2020 at 21:14
  • $\begingroup$ Understandable, I'll read the linked page and see if I can add more clarity to the answer with more correct research. Feel free to edit/modify my response or add a new one. $\endgroup$
    – m4rio
    Commented Mar 19, 2020 at 21:37
  • $\begingroup$ Hey you were really useful in answering this question. Could you help me with another similar question? I would really appreciate it! biology.stackexchange.com/questions/92383/… $\endgroup$
    – yuval
    Commented Apr 5, 2020 at 11:49
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I know it's been a while, but in case anyone comes back to this: since the beginning of the pandemic, many tools have been developed to help identifying lineages and clades.

L-Strain corresponds to Pango lineage B and descendants including all VOCs like Alpha, Delta and Omicron.

S-Strain corresponds to Pango lineage A and descendants (and Nextstrain clade 19B).

To find out if something is A/B, just drop them into Nextclade and check the Clade column. Everything is L, unless it says 19B: enter image description here

In this example, the sequences with id #2, #3, and #4 are S, everything else shown is L.

Disclosure: I'm a Nextstrain/Nextclade developer.

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