Challenges in diagnosing Wuhan Coronavirus (2019nCov)(translated excerpt from this article mp.weixin.qq.com/s/Jazc0sbrp8oz…)
US will face exactly the same problem when the outbreak starts here (I hope I am wrong)
US will face exactly the same problem when the outbreak starts here (I hope I am wrong)
1. Diagnoses require rtPCR test kits (PCR primer and reporter probes) tailor-made for 2019nCov. Each kind of virus require its own PCR primer & report probes
This was done in record speed: Shanghai PHCC got the first sample on 12/26, completed RNA sequencing on 1/6.
This was done in record speed: Shanghai PHCC got the first sample on 12/26, completed RNA sequencing on 1/6.
3 biotech companies in Shanghai got certification to make PCR primers and reporter probes right away: 上海辉睿生物、上海捷诺生物和上海伯杰公司. And they have already manufactured 100,000 test kits by Jan 16th. 
However, they have to supply the kits to the entire country of China, and test kits go to provincial-level CDC lab and some hospitals directly. The kit supply is being strained right now because reagents needed to make the kits are in shortage (suppliers on vacation due to CNY
The rate-limiting step of diagnosis is currently at provincial CDC labs (it takes 30+ mins to run 1 test on 1 PCR machine)
PCR machines & technician are running at capacity limit --> huge backlog of patient samples --> huge number of suspected but unconfirmed cases.
PCR machines & technician are running at capacity limit --> huge backlog of patient samples --> huge number of suspected but unconfirmed cases.
3A hospitals are certified to run rtPCR tests since Jan 23rd, but availability of PCR machines is limited. Also risk of contamination from viral samples in 3A hospital labs has not been 100% addressed. so limit capacity is available via hospital labs.
2. Protocol requires the first positive case of nCov2019 in each province to be confirmed by China CDC in Beijing.
For example, the first confirmed patient in Jiangsu province has been in isolation ward since Jan 10th, but it took 12 days for his Jan10 sample to be tested....
For example, the first confirmed patient in Jiangsu province has been in isolation ward since Jan 10th, but it took 12 days for his Jan10 sample to be tested....
.. because of the validation test needed to be done by China CDC.
Most urgent issue at hospitals right now:
1. Too many fevered patients to be treated promptly. Typical wait time from check-in to discharge in a fever clinic is *5 hours*.
1. Too many fevered patients to be treated promptly. Typical wait time from check-in to discharge in a fever clinic is *5 hours*.
2. real-time diagnosis not available (samples needed to be sent to provincial CDC in batches), causing cross-infection among fever patients in waiting rooms.
3. hospital staff do not have onsite lodging, requiring them to commute and exposing them to infection risks.
3. hospital staff do not have onsite lodging, requiring them to commute and exposing them to infection risks.
4. in-patient care capacity << # of severe cases
--> highly suspected patients (not diagnosed, not in isolation) still roaming around, and potentially spreading the virus.
--> highly suspected patients (not diagnosed, not in isolation) still roaming around, and potentially spreading the virus.
My personal take for a potential US outbreak: situation will be quite similar to China, except for issue #1. only Atlanta CDC has the capacity to do rtPCR on nCov2019 at the moment.
Thus, expect some initial chaos when the outbreak starts in the US as well.
Thus, expect some initial chaos when the outbreak starts in the US as well.
