Brief remarks on a sensational study from Lombardy, which finds conclusive evidence of SARS-2 infection in a patient sample from 12 September 2019.
Sep 15
The black line represents the percentage of suspected measles and rubella cases that tested negative for these viruses at a reference laboratory in Lombardy. The spike after July 2019 reflects the growing portion of patients whose rashes were caused instead by SARS-2. I finally got to read that new Italian study on pre-pandemic SARS-2 infections in Lombardy that has been making the rounds. It comes out of an Italian reference laboratory for measles and rubella surveillance, where scientists noticed an increase in the portion of suspected measles cases that were testing negative, all the way back in August 2019. Since skin rashes are a well-documented Corona symptom, they recently decided to test old archival samples for SARS-2, to see if they couldn’t solve this small mystery. They looked at samples going back to 2018, and their tests came up positive for SARS-2 RNA in thirteen cases. Eleven of these samples were collected before anybody declared a pandemic. Four of the eleven also had anti-SARS-2 antibodies – including the earliest sample, taken from an eight-month-old infant on 12 September 2019. None of these patients had any relevant travel history.
What’s most interesting, is the genetic sequences of these early samples from Fall 2019:
In total, we obtained 15 sequences, including 12 from pre-pandemic cases. All three major mutations (C3037T, C14408T, and A23403G), which had first been detected weeks after the outbreak in China, were observed whenever these regions were sequenced, indicating that sequences from October 2019 already carried mutations that had been absent in the first sampled strains (e.g., Wuhan-Hu-1) reported from China …
It’s like this: By comparing early SARS-2 sequences with closely related pangolin and bat viruses, we can infer that the progenitor of SARS-CoV-2 lacked a series of so-called alpha mutations, seen in the earliest sequences from Wuhan. By late January 2020, these alpha mutations were increasingly joined by a series of beta mutations in the sequenced Wuhan viruses. There is a good relative chronology here: Viruses with alpha and beta mutations probably postdate viruses with alpha mutations alone.
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