G-quadruplexes in viral genomes can be applied as the targets of antiviral therapies, which has attracted
wide interest. However, it is still not clear whether the pervasive number of such elements in the viral world
is the result of natural selection for functionality. In this study, we identified putative quadruplex-forming
sequences (PQSs) across the known viral genomes and analyzed the abundance, structural stability, and
conservation of viral PQSs. A Viral Putative G-quadruplex Database (http://jsjds.hzau.edu.cn/MBPC/
ViPGD/index.php/home/index) was constructed to collect the details of each viral PQS, which provides
guidance for selecting the desirable PQS. The PQS with two putative G-tetrads (G2-PQS) was significantly
enriched in both eukaryotic viruses and prokaryotic viruses, whereas the PQSs with three putative G-tetrads
(G3-PQS) were only enriched in eukaryotic viruses and depleted in prokaryotic viruses. The structural
stability of PQSs in prokaryotic viruses was significantly lower than that in eukaryotic viruses. Conservation
analysis showed that the G2-PQS, instead of G3-PQS, was highly conserved within the genus. This suggested
that the G2-quadruplex might play an important role in viral biology, and the difference in the
occurrence of G-quadruplex between eukaryotic viruses and prokaryotic viruses may result from the
different selection pressures from hosts.