COVID-19: New Delta AY.122 variant causes more disease severity and deaths in Russia

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In the last 24 hours, Russia registered a total of 32,136 new COVID-19 infections and 1,184 deaths and local physicians are saying the actual cases could be far more higher as there is now limited testing capabilities due to a shortage of testing reagents and kits in the country over the last few weeks.

To date, the country has confirmed 9,833,749 cases of COVID-19 and 282,462 COVID-19 deaths, according to the national coronavirus information center. Russia’s total excess fatality count since the start of the coronavirus pandemic is at least 810,000.

In the last few weeks, local scientists and researchers were baffled by a sudden surge in cases that affected many that were fully vaccinated along with a higher prevalence of disease severity and the occurrence of viral loads upon hospital admission.

This propelled a team of researchers from Russian Academy of Sciences, the Skolkovo Institute of Science and Technology, National Research University Higher School of Economics, Smorodintsev Research Institute of Influenza, the Ministry of Health of the Russian Federation and the Lomonosov Moscow State University to further investigate.

Their study findings revealed that a new Delta variant named AY.122 was behind the new surges.

Russian scientists believe that the new AY.122 Delta subvariant has enhanced transmissibility, enhanced immune evasiveness and better replication potential hence resulting in rapid disease severity and higher mortality risk.

The study team used a phylogeographic approach to infer imports of Delta sublineages into Russia, and phylodynamic models to assess the rate of their spread showing that nearly the entire Delta epidemic in Russia has probably descended from a single import event despite genetic evidence of multiple Delta imports.

Alarmingly 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.

Importantly the AY.122 lineage was frequent in Russia among Delta samples from the start of these new surges, 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.

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

Their study findings were published on a preprint server and is currently being peer reviewed. 

https://www.medrxiv.org/content/10.1101/2021.12.02.21267168v1

The Delta (B.1.617.2 + AY.*) variant of SARS-CoV-2 that was first detected in India in late 2020 [6] is, as of November 2021, the prevalent lineage in most countries including Russia [7]. It was shown to be more infectious but also to cause higher mortality than earlier variants of concern [8,9].

The fast spread of Delta may be associated with its reduced sensitivity to neutralization by antibodies [10] as well as increased efficiency of fusion with human cells [11]. Delta has spread rapidly in Russia, increasing in frequency from 1% in April to over 90% in June [12,13].

The phylogeny of Delta is more structured than that of other variants of concern, and its characteristic mutations have accumulated gradually [14]. While Delta clearly has increased fitness compared to ancestral strains, whether its sublineages change its properties further is less clear [15–17]. Still, adaptive evolution of SARS-CoV-2 in the human genome continues [18], highlighting the need for surveillance of novel variants.

Thanks to extensive efforts of many countries in sampling and sequencing SARS- CoV-2 genomes from patients, it is possible to track the spread of different viral variants across the world. Here, we analyze the emergence and spread of the Delta variant in Russia between April-October 2021 and compare it to other countries.

We show that the majority of Russian samples carry the same set of mutations, strongly suggesting that they have descended from a single import event.

Delta has spread in Russia rapidly in spring 2021

Among the 4,639 high-quality Russian samples that were available in GISAID on October 21, 2021, 1,439 are Delta samples, i.e., belong to pango lineage B.1.617.2 or derived lineages (AY.*).

The earliest high-quality Delta sample was collected on April 7, 2021 in Moscow; two lower-quality Delta samples date to February 28 and March 26, 2021.

Since April, the frequency of Delta among the Russian samples has been growing, reaching 98% by early July 2021, with the estimated daily logistic growth rate of 9.74% (95% C.I.: 9.28%-10.2%). This growth rate is comparable with that observed in other countries [33,34].

The timing of this growth was similar between Russia’s regions (Fig. 1).

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.

LineageWHO LabelCountryPercentLineage CountTotal Count
AY.122DeltaRussia87%1,6531,904
AY.4.5DeltaLithuania68%2,5463,762
AY.43DeltaBosnia and Herzegovina62%198319
AY.4DeltaUnited Kingdom61%253,324418,353
AY.4DeltaIreland60%3,8226,419

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