*2.5. Viral Genome Sequencing*

Viral genome was sequenced using the Sanger (population) method. Viral RNA was isolated from 140 μL of viral suspension with the QIAamp Viral RNA Mini Kit (Qiagen, Courtaboeuf, France) following the manufacturer's instructions. The whole 2C region (from nt 4039 to nt 5025) was amplified

using the Superscript III One-step reverse transcription-polymerase chain reaction (RT-PCR) system with Platinum Taq DNA polymerase kit (Thermo Fischer Scientific). The amplicons were checked on a 2% agarose gel, purified on Nucleoseq columns (Machery-Nagel, Hœrdt, France), and sequenced using the BigDye Terminator v3.1 Cycle Sequencing Kit (Thermo Fischer Scientific, Les Ulis, France). The sequences were purified with the BigDye XTerminator Purification Kit. Sequenced products were analyzed on a 3500Dx genetic analyzer (Thermo Fischer Scientific). Electrophoregrams were manually edited with Seqscape software v3 (Thermo Fischer Scientific). The sequences of primers are shown in Table 1.


**Table 1.** Primers used for sequencing.
