Abstract
Context The emergence of new methods for the analysis of environmental samples, such as massive parallel sequencing, creates a unique opportunity for studying the spread of viral nucleic acids in the environment. Aims The purpose of the article was to evaluate the diversity of ribonucleic acid (RNA) sequences of coronaviruses in the sample of water collected in the Small Aral Sea. Methods Nucleic acid sequencing of water samples collected from the Small Aral Sea was performed to assess diversity and spread of viruses. Key results A surprisingly high content of RNA fragments from coronaviruses was shown in aqueous samples. The presence of a wide variety of virus hosts from rodents and bats to mammals and humans was detected. Taxonomic classification of metagenomic data obtained after sequencing of nucleic acids of the Small Aral Sea samples showed the presence of coronaviruses RNA fragments of different genera. Conclusions This study showed that water samples from environmental sites can be used to assess the distribution and diversity of RNA fragments of coronaviruses. Continued monitoring of water samples could help establish a surveillance system for the early detection and monitoring of coronaviruses. Implications On the basis of the obtained results, it is hypothesised that the analysis of viromes and microbiomes creates new opportunities for studying the spread of viruses in the environment, which is a necessary fact for the development of possible anti-epidemic measures.