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Early in the epidemic, Chinese researchers (Jian Lu, et al,) reported in the National Science Review earlier this month that there was an aggressive more virulent L strain compared to the older S strain of the virus. Of the 103 viral genomes they scoured, 70% were of the L-type variant using phylodynamic analysis of samples taken during the earliest phase of the outbreak that began in Wuhan late last year. But subsequent later samples taken later in the course of the epidemic were mostly of the S strain. Peer review by researchers at other institutions have recently called this study into question.

Does anyone know where this stands currently? Has an aggressive L strain been confirmed? Do current rRT-PCR tests make any distinctions between L and S strains?

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One and a half year later we see that the L strain (corresponding to Pango lineage B and all of its descendants, and to all Nextstrain clades except 19B) was winning the evolutionary race, mostly because of the emergence of Pango lineage B.1/Nextstrain clade 20A with mutations ORF1b:P314L and S:D614G that had a decisive advantage over the other virus variants. The S strain is still extant in form of Pango lineage A/Nextstrain clade 19B and its descendants, but marginalised numerically.

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  • $\begingroup$ S/L refers to the amino-acid at ORF8:84. Also this split is more interesting than it seems because this mutation ORF8:S84L plus the other one C8782T it comes with are found in bat viruses, so it is believed that the ORF8:S84L lineage (or A or 19B) is ancestral. The problem is that all the market samples were from the S84 lineage (or B or 19A). $\endgroup$
    – reuns
    Sep 24 at 14:49
  • $\begingroup$ @reuns Indeed the split is interesting, as there are no published sequences with just one of the two differentiating mutations, which suggests a double introduction to Wuhan city from a yet unknown source. $\endgroup$ Oct 26 at 9:25

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