Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is focused on a single isolate of bat coronaviruses (bat CoVs) which does not adequately represent genetically related coronaviruses (CoVs). The unique bat CoV RaTG13 is the only identified sequence genetically associated with SARS-CoV-2. Data scarcity of bat CoV sequences raises concerns over several fundamental experimental and biostatistical aspects, e.g., repeatability of sequences and intraspecies variations in critical gene regions, such as the receptor-binding domain of the spike protein. The Sunda pangolin has been proposed as the intermediate host and source of SARS-CoV-2, but no pangolin CoV isolates have been reported in its habitats in Southeast Asia. Most pangolin CoVs were isolated from pangolins captured during illegal animal trafficking, raising questions about such isolates’ reliability and quality. Problems with pangolin CoV sampling are also related to the substandard quality of deposited sequences. There is an urgent need for field surveys of bat CoVs and possible intermediate hosts, such as pangolins, ferrets, and civets, in Southeast Asia to investigate the genomic source of SARS-CoV-2 and assess possible future risks for new outbreaks.