Experiment 4: Validation on the GISAID dataset

AL Alejandro Lopez-Rincon
AT Alberto Tonda
LM Lucero Mendoza-Maldonado
DM Daphne G. J. C. Mulders
RM Richard Molenkamp
CP Carmina A. Perez-Romero
EC Eric Claassen
JG Johan Garssen
AK Aletta D. Kraneveld
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From the GISAID repository31, we downloaded 53,183 sequences available on August 10th, for SARS-CoV-2, from different countries, from there 52,645 have as <1% Ns, high coverage and host = “homo sapiens”. Then, we calculated the frequency table of the 21-bps sequences obtained from experiments 2 and 3, to verify which sequences remain and could be used for detection. The appearance frequency of the target sequences among the samples in the GISAID dataset is reported in Table 1, second column. In addition, we downloaded 26 sequences from GISAID repository of other hosts (manis javanica, rhinolophus affinis, canine and felis catus) to make a comparison in the sequences from experiment 2 and 3.

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