Intra- vs. inter-host evolution of SARS-CoV-2 driven by uncorrelated selection - The evolution thwarted (preprint)

In viral evolution, a new mutation has to proliferate within the host (Stage I) in order to be transmitted and then compete in the host population (Stage II). We now analyze the intra-host single nucleotide variants (iSNVs) in a set of 79 SARS-CoV-2 infected patients with most transmissions tracked. Here, every mutation has two measures: i) iSNV frequency within each individual host in Stage I; ii) occurrence among individuals ranging from 1 (private), 2-78 (public) to 79 (global) occurrences in Stage II. In Stage I, a small fraction of non-synonymous iSNVs are sufficiently advantageous to rise to a high frequency, often 100%. However, such iSNVs usually fail to become public mutations. Thus, the selective forces in the two stages of evolution are uncorrelated and, possibly, antagonistic. For that reason, successful mutants, including many VOCs (variants of concern), have to avoid being eliminated in Stage I when they first emerge. As a result, they may not have the transmission advantage to outcompete the dominant strains and, hence, are rare in the host population. Few of them could manage to slowly accumulate advantageous mutations to compete in Stage II. When they do, they would appear suddenly as in each of the 6 successive waves of SARS-CoV-2 strains. In conclusion, Stage I evolution, the gate-keeper, may contravene the long-term viral evolution and should be heeded in viral studies.

Determination of the minimum detection limit of the new coronavirus 2019-nCoV nucleic acid detection kit (fluorescence PCR method)

Objective To determine the minimum detection limit of the novel coronavirus 2019-nCoV nucleic acid detection kit (fluorescent PCR method) developed and produced by Shanghai Jienuo Biotechnology Co., Ltd., and to verify whether it can effectively detect the novel coronavirus at the minimum detection limit level. Methods 20 different clinical positive samples were diluted to 5 concentration gradients of 62 500, 12 500, 2 500, 500, and 100 copies/mL, and the new coronavirus 2019-nCoV nucleic acid detection kit (fluorescent PCR method) was used for 3 repetitions Test, initially determine the minimum detection limit range;use 3 batches of kits to perform 20 repeated tests on 20 different clinical positive samples diluted to 5 concentration gradients of 1,500, 700, 500, 300, and 150 copies/mL, and further Determine the minimum detection limit;another 25 different clinical positive samples were diluted to the minimum detection limit level, and 20 repeated tests were performed with 3 consecutive batches of kits to verify the minimum detection limit. Results The positive detection rate of samples was 100% at the 4 concentration levels of 62 500, 12 500, 2 500, and 500 copies/mL. At the concentration level of 100 copies/mL, the positive detection rate of samples was =55%. The minimum detection limit is between 500 and 100 copies/mL;after 20 repeated determinations, the positive detection rate of the sample at the 3 concentration levels of 1, 500, 700, and 500 copies/mL is =95%, and the positive detection rate of the sample is =95%, and the positive detection rate of 300 and 150 copies/mL 2 The positive detection rate of the samples at each concentration level is less than 95%, and the minimum detection limit is determined to be 500 copies/mL;25 positive samples diluted to the minimum detection limit concentration level, the positive detection rate is more than 95%. Conclusion The minimum detection limit of the new coronavirus 2019-nCoV nucleic acid detection kit (fluorescent PCR method) developed and produced by Shanghai Genuo Biotechnology Co., Ltd. is determined to be 500 copies/mL. The sample can effectively detect viral nucleic acid and meets my country's relevant requirements for the minimum detection limit of detection reagents.