Thanks for the post! I wanted to add a clarification regarding the discussion of metagenomic sequencing,
The first is metagenomic sequencing. This is technology that can take a sample from a patient or the environment and sequence all DNA and RNA in it, matching them against databases of known organisms. An example of a practical deployment would be to use it for diagnostic conundrums — if a doctor can’t work out why a patient is so sick, they can take a sample and send it to a central lab for metagenomic sequencing. If China had had this technology, they would have known in 2019 that there was a novel pathogen whose closest match was SARS, but which had substantial changes. Given China’s history with SARS they would likely have acted quickly to stop it. There are also potential use-cases where a sample is taken from the environment, such as waste water or an airport air conditioner. Novel pandemics could potentially be detected even before symptoms manifest by the signature of exponential growth over time of a novel sequence.
China does have metagenomic sequencing. In fact, metagenomic sequencing was used in China to help identify the presence of a new coronavirus in the early Covid patient samples (https://www.nature.com/articles/s41586-020-2008-3),
Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’)
Thanks Mike — a very useful correction. I’m genuinely puzzled as to why this didn’t lead to a more severe early response given China’s history with SARS. That said, I can’t tell from the article how soon the sample from this patient was sequenced/analysed.
Thanks for the post! I wanted to add a clarification regarding the discussion of metagenomic sequencing,
China does have metagenomic sequencing. In fact, metagenomic sequencing was used in China to help identify the presence of a new coronavirus in the early Covid patient samples (https://www.nature.com/articles/s41586-020-2008-3),
Thanks Mike — a very useful correction. I’m genuinely puzzled as to why this didn’t lead to a more severe early response given China’s history with SARS. That said, I can’t tell from the article how soon the sample from this patient was sequenced/analysed.