Understanding Zoonotic Transmission of SARS-CoV-2 using RNA Sequencing

The COVID-19 pandemic has now reached every corner of the world and is due to the zoonotic transmission of the SARS-CoV-2 virus from wild animals to humans. As human population increases, greater contact with wildlife may occur and result in the increasing probability of novel diseases introduced to humans that our immune system cannot defend against. Identifying possible zoonotic source of the disease is important to understand how to fight current outbreaks such as COVID-19, and prevent future outbreaks.

While bats are thought to be the source for the SARS-CoV-2 virus, the actual transmission is unknown and there may even be an intermediate species that was part of the transfer. In a recent study, researchers performed RNA sequencing using the Ion Torrent S5 sequencer to help them identify SARS-CoV-2 related coronaviruses in Malayan pangolins, which are the most illegally trafficked mammal in China. With the streamlined workflow of the Ion Torrent Total RNA-Seq Kit, RNA reads can be quickly aligned to known viral sequences to identify known pathogens or characterize ones not yet discovered. In this case, two sub-lineages were discovered, including one that exhibits strong similarity to the SARS-CoV-2 receptor binding domain, critical for viral infection.

This study highlights the potential risk of different coronaviruses in wild animals and the use of next-generation sequencing (NGS) to enable rapid pathogen identification. Targeted sequencing can further simplify the study of zoonotic transmission and pathogen detection. With the Ion AmpliSeq SARS-CoV-2 Research Panel, researchers now have access to a simple targeted sequencing assay with high sensitivity to detect SARS-CoV-2 from samples with very low viral load. With sequencing data in as little as 2.5 hours, the rapid turnaround time of the assay enables researchers to make faster decision under this urgent situation.

Learn more at www.thermofisher.com/ngscoronavirus

Explore Ion Torrent targeted NGS solutions for SARS-CoV-2 research

Read the paper: Lam, T.T., Shum, M.H., Zhu, H. et al. Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins. Nature (2020).

For Research Use Only. Not for use in diagnostic procedures.