Metagenomic detection and reconstruction of Lake Sinai Virus from honey bee sequence data

A survey of public honey bee sequence data was performed to detect infections by Lake Sinai Virus (LSV). The Sequence Read Archive of the National Center for Biotechnology Information (NCBI) was queried to identify accessions of RNA sequence data derived from honey bee. These were filtered as described below and then up to 50 million reads or read pairs were downloaded and searched against a reference database of conserved LSV sequence. Accessions with matches above a specified threshold were downloaded in their entirety and assembled into longer contiguous sequences (contigs). The result contigs were searched against each open reading frame (ORF) of the reference LSV genome present in the NCBI database (accession NC_032433.1) and matching regions from each contig. These ORF sequences were aligned with additional sequences identified in NCBI databases through the BLAST web service. These alignments provide the basis for computing phylogenetic trees, rates of nucleotide substitution, codon usage bias, and other evolutionary parameters.

本研究针对公开的蜜蜂序列数据集开展调查，旨在检测莱克西尼病毒（Lake Sinai Virus, LSV）的感染情况。我们检索了美国国家生物技术信息中心（National Center for Biotechnology Information, NCBI）的序列读取存档（Sequence Read Archive, SRA）数据库，以筛选源自蜜蜂的RNA序列登录号。随后按照既定流程对这些登录号进行过滤，进而下载至多5000万条读段或读段对，并针对保守的LSV序列参考数据库进行序列比对筛查。将比对结果达到指定阈值的登录号完整下载，并组装为更长的重叠群（contigs）。将所得重叠群与NCBI数据库中参考LSV基因组（登录号NC_032433.1）的各开放阅读框（open reading frame, ORF）进行比对，提取每个重叠群的匹配区域序列。通过BLAST在线服务，将这些开放阅读框序列与NCBI数据库中鉴定得到的其他序列进行多序列比对。上述比对结果为构建系统发育树、计算核苷酸替换速率、密码子使用偏好性及其他进化参数提供了坚实基础。