The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia

Abstract

Delta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution has led to the emergence of multiple sublineages, most of which are well-mixed between countries. By contrast, here we show that nearly the entire Delta epidemic in Russia has probably descended from a single import event, or from multiple closely timed imports from a single poorly sampled geographic location. Indeed, over 90 per cent of Delta samples in Russia are characterized by the nsp2:K81N + ORF7a:P45L pair of mutations which is rare outside Russia, putting them in the AY.122 sublineage. The AY.122 lineage was frequent in Russia among Delta samples from the start, and has not increased in frequency in other countries where it has been observed, suggesting that its high prevalence in Russia has probably resulted from a random founder effect rather than a transmission advantage. The apartness of the genetic composition of the Delta epidemic in Russia makes Russia somewhat unusual, although not exceptional, among other countries.

Keywords: AY.122; Delta lineage; ORF7a:P45L; SARS-CoV2 in Russia; cross-border transmission of SARS-CoV2; genomic epidemiology of SARS-CoV2.

Figure 1.

Frequencies of Delta variants (B.1.617.2 + AY.*) in Russia measured for 15-day sliding windows of 7 days around each day, and logistic growth estimates with 95 per cent confidence intervals.

Figure 2.

Mutations in the Delta lineage observed in >5 per cent of Russian Delta samples. The following mutations that characterize the major sublineage of B.1.617.2 (‘21J’ in Nextstrain nomenclature) and occur in >85 per cent of Delta samples both in Russia and globally are not shown: RdRp:G671S, exonuclease:A394V, nsp6:T77A, nsp3:A488S, nsp3:P1228L, nsp6:V120V, ORF7b:T40I, nsp3:P1469S, N:G215C, nsp4:D144D, nsp4:V167L, and nsp4:T492I.

Figure 3.

Dynamics of Delta sublineages in Russia. A) The fraction of the nsp2:K81N + ORF7a:P45L combination among all Delta samples from Russia in 15-day sliding window. The confidence band is the 95 per cent binomial confidence interval. B) Timeline for phylogenetically inferred imports (PIIs) of Delta subclades into Russia. Each horizontal line represents a Russian subclade descendant from a single PII, ordered by the date of the earliest sample. Circles represent samples obtained on a particular date; circle size reflects the number of samples; circle color indicates the region of sampling. The AY.122 + ORF7a:P45L sublineage is marked by an arrow. The two PIIs with known travel history for the earliest samples are marked with asterisks. C, D) UShER tree of Delta (C) and its AY.122 + ORF7a:P45L sublineage (D). For visualization purposes, 95 per cent of Russian and 99.8 per cent of non-Russian tips were pruned randomly, so some of the PIIs are not shown. The internal node corresponding to the main PII and which defines the AY.122 + ORF7a:P45L sublineage is marked by a red circle; branches leading to the Russian descendants of the main PII are colored in red; to other Russian sequences, in purple; to non-Russian sequences, in blue; internal branches, in gray. Branch lengths are measured in the number of mutations.

Figure 4.

The dynamics of the effective reproduction number R_e for the main PII of the Delta clade in Moscow inferred by BDSKY (black line; shaded red bars show 50 per cent and 95 per cent posterior credible intervals); and for all (blue line) or for Delta (red line) SARS-CoV-2 cases in Moscow inferred by EpiEstim. The gray line shows the 7-day rolling average of the daily number of new cases in Moscow independent of the genotype.

Figure 5.

Fraction of Delta samples in the largest PII and (A) inferred number of PIIs or (B) relatedness of Delta samples, for countries with at least 50 Delta samples in each of the 10 ML trials (Table S3). In (B), the horizontal axis indicates the normalized relatedness of samples from the same country, compared with randomly picked samples; lower values correspond to increased relatedness (see Methods). Dots correspond to the mean (centroid) across the 10 ML trees for 29,964 non-Russian samples with added Russian sequences, with standard deviations shown as error bars. Colors indicate the date when the Delta lineage reached 1 per cent frequency in this country.