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\begin{document}

\title{Novel and extendable genotyping system for Human Respiratory Syncytial
Virus based on whole-genome sequence analysis}



\author[1]{Jiani Chen}%
\author[2]{Xueting Qiu}%
\author[3]{Samuel Shepard}%
\author[4]{Do-Kyun Kim}%
\author[4]{James Hixson}%
\author[5]{Pedro Piedra}%
\author[5]{Vasanthi Avadhanula}%
\author[2]{Justin Bahl}%
\affil[1]{University of Georgia}%
\affil[2]{University of Georgia College of Veterinary Medicine}%
\affil[3]{Centers for Disease Control and Prevention}%
\affil[4]{The University of Texas Health Science Center at Houston}%
\affil[5]{Baylor College of Medicine}%


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  \date{May 27, 2024}


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\begin{abstract}
Background: Human respiratory syncytial virus (RSV) is one of the
leading causes of respiratory infections, especially in infants and
young children. Previous RSV sequencing studies have primarily focused
on partial sequencing of G gene (200-300 nucleotides) for genotype
characterization or diagnostics. However, the genotype assignment with G
gene has not recapitulated the phylogenetic signal of other genes and
there is no consensus on RSV genotype definition. Methods: We conducted
Maximum Likelihood phylogenetic analysis with 10 RSV individual genes
and whole-genome sequence (WGS) that are published in GenBank. RSV
genotypes were assigned by the statistical support monophyletic clusters
with at least 10-year detection time from the WGS phylogeny. Results: In
this study, we first statistically examined the phylogenetic
incongruence, rate variation for each RSV gene sequence and WGS. We then
proposed a new RSV genotyping system based on a comparative analysis of
WGS and the spatial and temporal distribution of each lineage. We also
provided an RSV classification tool to perform RSV genotype assignment.
Conclusions: This revised RSV genotyping system will provide important
information for disease surveillance, epidemiology, and vaccine
development.%
\end{abstract}%



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