Wastewater dataset on the SARS-CoV-2 sublineages circulating in Central Arkansas, USA, post-COVID-19 pandemic

Data File 1. NCBI Sequence Read Archive accession numbers and metadata of wastewater samples collected in four wastewater treatment facilities in Central Arkansas, USA (Little Rock’s Adams Field, Fourche Creek, and Little Maumelle and Pine Bluff) between 08 February 2022 and 16 April 2024.Data File 2. Mean Ct values of SARS-CoV-2 genes (Orf1ab, S-protein, and N-protein) and endogenous control (PMMoV) in wastewater samples collected in four wastewater treatment facilities in Central Arkansas, USA (Little Rock’s Adams Field, Fourche Creek, and Little Maumelle and Pine Bluff) between 08 February 2022 and 16 April 2024. Undetermined values were Ct > 40.Data File 3. Lineage analysis of SARS-CoV-2 and consensus sequences (FASTA format) detected through RNA sequencing in wastewater samples collected in four wastewater treatment facilities in Central Arkansas, USA (Little Rock’s Adams Field, Fourche Creek, and Little Maumelle and Pine Bluff) between 08 February 2022 and 19 March 2024. The data were generated using Illumina DRAGEN COVID Lineage software, and the most abundant variants detected in each sample are shown. This software aligns SARS-CoV-2 sequence reads to a reference genome to generate a consensus genome sequence and identify mutations, including amino acid substitutions and deletions. It then performs lineage/clade classification using Pangolin and/or NextClade. ^aWorld Health Organization’s terminology used to classify SARS-CoV-2 variants. ^bPercentage of base calls in the consensus SARS-CoV-2 sequence that are not ambiguous, i.e., the software could confidently assign a specific nucleotide (A, T, C, or G).Data File 4. Relative abundance of SARS-CoV-2 lineages based on amino acid changes in wastewater samples in Central Arkansas (Little Rock’s Adams Field, Fourche Creek, and Little Maumelle and Pine Bluff) from 02 November 2021 to 19 March 2024. The data was obtained by using the bioinformatic package Freyja (https://github.com/andersen-lab/Freyja)¹³.

数据集1：2022年2月8日至2024年4月16日期间，采集自美国阿肯色州中部四座污水处理厂（小石城亚当斯菲尔德、富什溪、小马默雷及派恩布拉夫污水处理厂）的废水样本对应的NCBI序列读取存档（NCBI Sequence Read Archive）编号及元数据。数据集2：2022年2月8日至2024年4月16日期间，采集自美国阿肯色州中部上述四座污水处理厂的废水样本中，严重急性呼吸综合征冠状病毒2（SARS-CoV-2）基因（Orf1ab、S蛋白、N蛋白）及内参（PMMoV）的平均循环阈值（Ct值）。未检出样本的Ct值大于40（Ct > 40）。数据集3：2022年2月8日至2024年3月19日期间，采集自美国阿肯色州中部上述四座污水处理厂的废水样本中，通过RNA测序检测到的SARS-CoV-2谱系分析结果及共识序列（FASTA格式）。该数据通过Illumina DRAGEN COVID Lineage软件生成，且展示了各样本中检测到的丰度最高的变异株；该软件将SARS-CoV-2序列读段比对至参考基因组，以生成共识基因组序列并识别突变（包括氨基酸替换与缺失），随后利用Pangolin和/或NextClade进行谱系/进化枝分类。^a采用世界卫生组织的命名体系对SARS-CoV-2变异株进行分类。^b指共识SARS-CoV-2序列中非歧义碱基调用的占比，即软件可明确指定特定核苷酸（A、T、C或G）。数据集4：2021年11月2日至2024年3月19日期间，美国阿肯色州中部上述四座污水处理厂的废水样本中，基于氨基酸变化的SARS-CoV-2谱系相对丰度。该数据通过生物信息学工具包Freyja（https://github.com/andersen-lab/Freyja）¹³获取。