Despite of the fast development of highly effective vaccines to control the current COVID$-$19 pandemic, the unequal distribution and availability of these vaccines worldwide and the number of people infected in the world lead to the continuous emergence of SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2) variants of concern. It is likely that real-time genomic surveillance will be continuously needed as an unceasing monitoring tool, necessary to follow the spillover of the disease spread and the evolution of the virus. In this context, new genomic variants of SARS-CoV-2 that may emerge as a response to selective pressure, including variants refractory to current vaccines, makes genomic surveillance programs tools of utmost importance. Here propose a statistical model for the estimation of the relative frequencies of SARS-CoV-2 variants in pooled samples. This model is built by considering a previously defined selection of genomic polymorphisms that characterize SARS-CoV-2 variants. The methods described here support both raw sequencing reads for polymorphisms-based markers calling and predefined markers in the VCF format. Results obtained by using simulated data show that our method is quite effective in recovering the correct variant proportions. Further, results obtained by considering longitudinal data from wastewater samples of two locations in Switzerland agree well with those describing the epidemiological evolution of COVID-19 variants in clinical samples of these locations. Our results show that the described method can be a valuable tool for tracking the proportions of SARS-CoV-2 variants.
翻译:尽管为控制目前的COVID19美元大流行病而迅速开发了高效疫苗,但在全世界,这些疫苗的分布和供应不均,而且全世界受感染人数众多,这导致人们关注的变异性不断出现,尽管迅速发展了控制目前COVID19美元大流行病的高效疫苗,这些疫苗在全世界的分布和供应不均,而且全世界受感染者人数众多,这导致SAS-COV-2(严重急性呼吸综合综合症冠状冠状病毒病毒2)变异体的不断出现,因此,可能继续需要实时基因组监测,作为不间断的监测工具,这是跟踪SARS-COV-2变异体蔓延和病毒演变情况所必需的。在这方面,SARS-COV-2的新基因组变异体可能出现新的基因变异体,作为对选择性压力的反应,包括变异体与目前疫苗相相相相抗异变异的变种,使得基因组监测程序工具具有极其重要的意义。这里提出一个统计模型模型,用来选择SIS-CF2的变异体变异性变异体的变种。这里描述基于多形态的多形态标记的标志的标志,在SRC-SVCFS-23变异体变体的变体的变异体的变体的模型中,通过这些变体的变体的变体的变体的变体的变体的变体的变体的变体的变种,用模型的变体的变种,可以进一步显示的变体的变体的变体的变体的变体的变体的变体,用数据,用模型显示的变体的变体的变体的变体的变体的变体的变体的变体的变体的变体的变体的变体的变体的变体的变体的变体的变体的变体。