IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 27 boulevard Jean Moulin, 13005, Marseille, France.
Virus Genes. 2022 Feb;58(1):53-58. doi: 10.1007/s11262-021-01877-2. Epub 2021 Nov 27.
Great concerns have been raised about SARS-CoV-2 variants over the past six months. At the end of 2020, an increasing incidence of spike substitutions Q677H/P was described in the USA, which involved six independent lineages. We searched for changes to this amino acid in the sequence database of SARS-CoV-2 genomes obtained at the IHU Méditerranée Infection (Marseille, France) from 3634 patients sampled between February 2020 and April 2021. In seven genomes (0.2%), we found a deletion of five amino acids at spike positions 675-679 (QTQTN) including Q677, and in 76 genomes (2.3%) we found a Q677H substitution. The 83 genomes were classified in ten different Pangolin lineages. Genomes with a spike Q677 deletion were obtained from respiratory samples collected in six cases between 28 March 2020 and 12 October 2020 and in one case on 1 February 2021. The Q677H substitution was found in genomes all obtained from respiratory samples collected from 19 January 2021 and were classified in seven different lineages. Most of these genomes (41 cases) were of UK variant. Two others were classified in the B.1.160 Pangolin lineage (Marseille-4 variant) which was first detected in July 2020 in our institute but was devoid of this substitution until 19 January 2021. Also, eight genomes were classified in the A.27/Marseille-501 lineage which was first detected in our institute in January 2021 and which either harboured or did not harbour the Q677H substitution. Thus, the spike Q677H substitution should be considered as another example of convergent evolution, as it is the case of spike substitutions L18F, E484K, L452R, and N501Y which also independently appeared in various lineages.
过去六个月来，人们对 SARS-CoV-2 变体产生了极大的关注。2020 年底，在美国，人们发现 Spike 氨基酸 Q677H/P 取代的发生率不断增加，涉及六个独立的谱系。我们在 IHU Méditerranée Infection（马赛，法国）从 2020 年 2 月至 2021 年 4 月期间采集的 3634 名患者的 SARS-CoV-2 基因组序列数据库中搜索了该氨基酸的变化。在七个基因组（0.2%）中，我们发现 Spike 位置 675-679（QTQTN）的五个氨基酸缺失，包括 Q677，在 76 个基因组（2.3%）中发现了 Q677H 取代。这 83 个基因组被分类为十个不同的穿山甲谱系。具有 Spike Q677 缺失的基因组是从 2020 年 3 月 28 日至 10 月 12 日采集的 6 例呼吸道样本和 2021 年 2 月 1 日采集的 1 例样本中获得的。Q677H 取代是在 2021 年 1 月 19 日采集的呼吸道样本获得的基因组中发现的，这些基因组被分类为七个不同的谱系。这些基因组中大多数（41 例）是英国变体。另外两个被分类为 B.1.160 穿山甲谱系（马赛-4 变体），该变体于 2020 年 7 月首次在我们研究所检测到，但直到 2021 年 1 月 19 日才出现这种取代。此外，还有 8 个基因组被分类为 A.27/马赛-501 谱系，该谱系于 2021 年 1 月首次在我们研究所检测到，这些基因组携带或不携带 Q677H 取代。因此，Spike Q677H 取代应该被视为另一个趋同进化的例子，就像 Spike 氨基酸 L18F、E484K、L452R 和 N501Y 的情况一样，它们也独立出现在不同的谱系中。
