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

Abstract

Background: Delta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution has led to emergence of multiple sublineages, many of which are well-mixed between countries.

Aim: Here, we aim to study the emergence and spread of the Delta lineage in Russia.

Methods: We use a phylogeographic approach to infer imports of Delta sublineages into Russia, and phylodynamic models to assess the rate of their spread.

Results: We show that nearly the entire Delta epidemic in Russia has probably descended from a single import event despite genetic evidence of multiple Delta imports. Indeed, over 90% 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.

Conclusion: The apartness of the genetic composition of the Delta epidemic in Russia makes Russia somewhat unusual, although not exceptional, among other countries.

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% confidence intervals.

Figure 2.

Mutations in the Delta lineage observed in >5% 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% 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% binomial confidence interval. B) Timeline for imports of Delta subclades into Russia. Each horizontal line represents a Russian subclade descendant from one import, ordered by the date of the earliest sample. Circles represent samples taken 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 imports with known travel history are shown as asterisks. C) AY.122+ORF7a:P45L sublineage on the UShER tree of Delta. For visualization purposes, 90% of Russian and 99% of non-russian tips were pruned randomly. An internal node that was defined as the main import and which defines the AY.122+ORF7a:P45L sublineage is marked by an orange circle; Russian samples are colored in red; non-Russian samples are colored in blue; internal branches are colored in grey. Branch lengths are measured in the number of mutations.

Figure 4.

The estimated trajectory of the effective reproduction number R_e for the main import Delta clade in Moscow. The gray line shows the 7-day rolling average of the daily number of new cases (independent of genotype) in Moscow.

Figure 5.

Fraction of Delta samples in the largest import and 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 50,000 non-Russian samples with added Russian sequences, with standard deviations shown as error bars. Colors indicate the date when the Delta lineage reached 1% frequency in this country.