US CDC officially launched the National SARS-CoV-2 Strain Surveillance (NS3) program in November 2020 “to increase the number and representativeness of viruses undergoing characterization”. [1, 2, 3, 4]
The Association of Public Health Laboratories (APHL) recieved a letter from the CDC on October 1, 2020 requesting laboratories provide specimens on a biweekly basis for whole genome sequencing by the CDC, and that they be confirmed specimens with Ct values less than 28. [5] The CDC wrote:
“We are requesting that you provide real time reverse transcription-polymerase chain reaction (real time RT-PCR)-confirmed diagnostic specimens…for whole genome sequencing by CDC, to begin establishing a set of viral sequences to be made available in the public space” specifically “provide SARS-CoV-2-positive (based on molecular test) deidentified, specimens (with Ct values less than 28 and not previously sequenced) and corresponding standardized metadata from 5 COVID-19 cases every 2 weeks, representing a variety of demographic and clinical characteristics, and geographic locations”…”for national virologic monitoring of the virus. This activity will be conducted as part of routine public health surveillance [as defined in 45 CFR 46.102(1)(2)]
It’s as if the CDC knew that after the mass vaccination campaign rolled ahead, that SARS-CoV-2 variants would rapidly emerge and they needed to gear up the labs in preparation, but that whole genome sequencing required the virus to be present, thus the Ct<28 stipulation!