PDF(Pubmed)
Abstract：
A total of 14 973 alleles in 29 661 sequenced samples collected between March 2021 and January 2023 by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex) and collaborators were used to construct a thorough map of mutations of the Mexican SARS-CoV-2 genomic landscape containing Intra-Patient Minor Allelic Variants (IPMAVs), which are low-frequency alleles not ordinarily present in a genomic consensus sequence. This additional information proved critical in identifying putative coinfecting variants included alongside the most common variants, B.1.1.222, B.1.1.519, and variants of concern (VOCs) Alpha, Gamma, Delta, and Omicron. A total of 379 coinfection events were recorded in the dataset (a rate of 1.28 %), resulting in the first such catalogue in Mexico. The most common putative coinfections occurred during the spread of Delta or after the introduction of Omicron BA.2 and its descendants. Coinfections occurred constantly during periods of variant turnover when more than one variant shared the same niche and high infection rate was observed, which was dependent on the local variants and time. Coinfections might occur at a higher frequency than customarily reported, but they are often ignored as only the consensus sequence is reported for lineage identification.
摘要：
在2021年3月至2023年1月之间，由墨西哥基因组监测联盟（CoViGen-Mex）和合作者收集的29661个测序样品中，共有14973个等位基因用于构建墨西哥SARS-CoV-2基因组景观突变的完整图谱，其中包含患者内部次要等位基因变体（IPMAV）。它们是通常不存在于基因组共有序列中的低频率等位基因。这些额外的信息被证明对于识别推定的共感染变异以及最常见的变异至关重要，B.1.1.222、B.1.1.519和相关变体(VOCs)Alpha,Gamma,Delta,还有Omicron.数据集中共记录了379例合并感染事件（发生率为1.28%），导致墨西哥第一个这样的目录。最常见的推定共感染发生在Delta传播期间或引入OmicronBA.2及其后代之后。当多个变异体共享相同的生态位并且观察到高感染率时，在变异体周转期间不断发生共感染。这取决于局部变异和时间。共感染的发生频率可能高于习惯报告，但它们经常被忽略，因为只有共有序列被报告用于谱系鉴定。
