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The manuscript has been published on a peer-reviewed journal. It can be accessed freely via http://dx.doi.org/10.24272/j.issn.2095-8137.2022.238 The COVID-19 pandemic caused by SARS-CoV-2 poses a tremendous threat to human society. SARS-CoV-2 is airborne and mainly transmitted through social contact; however, it is highly debated whether cold-chain related transmission has occurred. Here, we present a new method and distinguish two transmission routes by detecting a lineage-specific reduction of SARS-CoV-2 evolutionary rate. After analyzing 1,610,125 SARS-CoV-2 genomic sequences, we found that two outbreaks in Xinfadi-Beijing and Auckland may be cold-chain related and respectively caused by two mutation-dormant variants. A Dalian outbreak in July 2020 and a Yingkou outbreak ten months later were epidemiologically connected and derived from a cold-chain related variant. Mutation-dormant variants were detected during the spread of spike D614G variant and the Delta Variant of Concern. Moreover, the earliest SARS-CoV-2 variant (i.e., the most recent common ancestor of SARS-CoV-2) was found to be a mutation-dormant variant. Its repeated spillover events were observed during the last two years, indicating that the COVID-19 outbreak in Wuhan could be associated with spillover events from cold-chains. In all the observed cases, the virus re-started mutating after the spillover events from cold-chains. A systematic identification of spillover events revealed that the frequency of cold-chain related transmission is in the order of magnitude of 0.1-10%. Our results indicate that that cold-chain related transmission should be rare but may have happened globally., DATA AND SOFTWARE AVAILABILITY The data was downloaded from https://ngdc.cncb.ac.cn/ncov/apis/, and the Coronavirus GenBrowser (CGB) is freely available from http://www.egps-software.net/egpscloud/eGPS_Desktop.html, as a plug-in of the eGPS Desktop. The algorithm developed in this study was integrated into the CGB, to search for mutation-dormant variants. It is available in the version 1.13, or the latest version of the eGPS Desktop.