library_construction_protocol: Viral RNA was isolated from serum samples using the QIAamp MinElute Virus Spin Kit or QIAamp Viral RNA mini (Qiagen), following the manufacturer's protocol. Reverse transcription of purified RNA was performed using the SuperScript IV First-Strand Synthesis System (Thermo Fisher Scientific) and the reverse primer 5'-CTC TCT CTT CAG CTG GGT-3' with additional adaptor sequence and a 4-nucleotide index sequence for multiplexing. Residual primers and dNTPs were removed using ExoSAP-IT PCR Product Cleanup Reagent (Applied Biosystems). The resulting complementary DNA (cDNA) was amplified by PCR using the KAPA HiFi HotStart ReadyMix PCR Kit (Roche), forward primer 5'-GTA GAT GTC TAG GGG AAG GAC-3' and reverse primer targeting the adaptor sequence. PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter), and excess primers and dNTPs were again removed with ExoSAP-IT. DNA quality and fragment size distribution were evaluated using the Agilent Genomic DNA ScreenTape System, and concentrations were determined via Qubit fluorometric quantification (Thermo Fisher). Purified amplicons were submitted to Quintara for long-read sequencing.