Protocol for amplification of RSV and for whole-genome sequencing. This protocol can amplify the whole genome in two parallel RT-PCR reactions in order to make RSV sequencing accessible and affordable. This protocol does not require prior subtyping as it covers RSV-A and RSV-B in the same reaction. The primer panel is an optimisation of a previously published panel by Wang et al.
Our optimisation from the original panel allows for multiplex PCR, so the whole genome can be amplified in just two PCR reactions. In addition to this, primers have been modified to account for commonly-occurring mutations that affect primer-binding areas and were causing suboptimal amplification. These primers were used to cover the complete hRSV genome (both A and B) by splitting them into two pools of non-consecutive amplicons (odd-numbered amplicon primers in one pool, even-numbered amplicon primers in other).
This protocol has been tested for RSV RNA amplification from RSV-positive nasopharyngeal swabs of CT value up to 26 using Seegene Allplex Respiratory Panel (Seegene Inc, Seoul, South Korea). However, it provides best results with CT values below 21. For samples of low viral load, an alternative primer panel is provided only with the amplicons sufficient to sequence the G and F genes. This alternative panel has succesfully sequenced samples of CT values up to 30, albeit with higher amount of total reads required in the case of very high CT value.
Illumina CovidSeq (Illumina Inc, San Diego, USA) reagents were used for the RT-PCR, with a mix previously published for amplification of Influenza RNA and a thermocycling program optimised in our lab. Library preparation was performed according to the Illumina CovidSeq protocol.
1. Primer A10f has been replaced to solve the amplicon dropout for Nextclade variant A.D.5.2 (mutation G13793A).
2. The relative concentration of primers has been modified to improve amplicon homogeneity.
3. An alternative panel has been added to amplify the G and F genes suitable for low viral load samples.
4. A bioinformatic analysis section has been added with a link to a custom pipeline for this protocol.