COVID-19 cryptic transmission and genetic information blackouts: Need for effective surveillance policy to better understand disease burden

Abstract

h 2 We read with interest on the case of SARS-CoV-2 re-infection n the importance of genomic information in understanding the rue burden of COVID-19 [1] . After the emergence of SARS-CoV-2 n China, initial cases in Japan were travel-associated cases from ffected areas, as determined by the viral sequence analyses. In oncordance with global COVID-19 epidemic, the Asian SARS-CoVclades were dominant until the beginning of March, 2020 [2] . owever, as of April, with the emergence of European clades (20A, 0B, 20C) as the dominant clade in Japan, there were no reorts on local transmission of the Asian clades (19A and 19B) ithin the following weeks (figure). Our analysis however indiates the Asian clade remains in circulation, with at least two trains confirmed locally. Both strains (Japan/Nagasaki-24_7-1/2020 nd Japan/Nagasaki-24_7-2/2020), isolated in July 2020, belonged o the “diminished” Asian clade, 19B (figure). In addition to the 28 isolates from Japan, and the 4981 globally isolated strains, we bserved that both of the sampled strains were of an orphaned onophyletic clade, in which the next closest strain of this clade as a locally strain that was isolated in January (Japan/TY-WK21/2020) ( Fig. 1 ). While there may be limited sampling in cerain geographical areas, we are confident that this distinct clade epresents initial introduction from China, followed by basal amlification and persistent community maintenance of transmission ycle. While outbreaks may derive from local spread after introuction events, these events can generally be traced by using phyogenetically ancestral viruses of outbreak clades. In this context, he detection of persistent transmission of an orphan clade that is nique to Japan indicates local transmission that may remain un-