Spread of endemic SARS-CoV-2 lineages in Russia before April 2021

Abstract

In 2021, the COVID-19 pandemic was characterized by global spread of several lineages with evidence for increased transmissibility. Throughout the pandemic, Russia has remained among the countries with the highest number of confirmed COVID-19 cases, making it a potential hotspot for emergence of novel variants. Here, we show that among the globally significant variants of concern that have spread globally by late 2020, alpha (B.1.1.7), beta (B.1.351) or gamma (P.1), none have been sampled in Russia before the end of 2020. Instead, between summer 2020 and spring 2021, the epidemic in Russia has been characterized by the spread of two lineages that were rare in most other countries: B.1.1.317 and a sublineage of B.1.1 including B.1.1.397 (hereafter, B.1.1.397+). Their frequency has increased concordantly in different parts of Russia. On top of these lineages, in late December 2020, alpha (B.1.1.7) emerged in Russia, reaching a frequency of 17.4% (95% C.I.: 12.0%-24.4%) in March 2021. Additionally, we identify three novel distinct lineages, AT.1, B.1.1.524 and B.1.1.525, that have started to spread, together reaching the frequency of 11.8% (95% C.I.: 7.5%-18.1%) in March 2021. These lineages carry combinations of several notable mutations, including the S:E484K mutation of concern, deletions at a recurrent deletion region of the spike glycoprotein (S:Δ140–142, S:Δ144 or S:Δ136–144), and nsp6:Δ106–108 (also known as ORF1a:Δ3675–3677). Community-based PCR testing indicates that these variants have continued to spread in April 2021, with the frequency of B.1.1.7 reaching 21.7% (95% C.I.: 12.3%-35.6%), and the joint frequency of B.1.1.524 and B.1.1.525, 15.2% (95% C.I.: 7.6%-28.2%). Although these variants have been displaced by the onset of delta variant in May-June 2021, lineages B.1.1.317, B.1.1.397+, AT.1, B.1.1.524 and B.1.1.525 and the combinations of mutations comprising them that are found in other lineages merit monitoring.

Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike

“…Cys136 is removed only via direct mutation and occurs less often. Approximately half of the lineages with ΔDS 15-136 have both cysteines removed as in the Russian AT.1 lineage [ 39 ] or the C.1.2 lineage [ 28 ]. The distribution of the ΔDS 15-136 variants on the phylogenetic tree of SARS-CoV-2 S ( Fig 4C ) and the different paths leading to the disulfide loss ( S3 Table ) suggest that ΔDS 15-136 could have evolved in multiple lineages independently, and in several cases became dominant within the lineages.…”

Molecular epidemiology of SARS‐CoV‐2 in Mongolia, first experience with nanopore sequencing in lower‐ and middle‐income countries setting

“…In July 2021, first cases of the delta variant were detected in our study. Meanwhile across the globe, the proportion of delta variant had been dominated in neighboring and regional countries 12 including the Russian Federation, 21 South Korea, 22 and Vietnam 23 . In Mongolia, the Delta variant had apparently become dominant by September 2021, following the loosening of restrictive measures, including the resumption of commercial flights and presidential election campaigns.…”

Parametric analysis of the transmission dynamics during indigenous aggregated outbreaks caused by five SARS-CoV-2 strains in Nanjing, China

“…Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), first identified in December 2019, is constantly changing throughout the global pandemic of coronavirus disease 2019 (COVID-19) (1). SARS-CoV-2 has evolved from the original strain of the first epidemic to the Beta, Delta, and now the predominantly endemic Omicron strains, which are of great concern due to the increasing transmission and immune escape ability (2).…”