A highly divergent SARS-CoV-2 lineage B.1.1 sample in a patient with long-term COVID-19 (preprint)

We report the genomic analysis of a highly divergent SARS-CoV-2 sample obtained in October 2022 from an HIV+ patient with presumably long-term COVID-19 infection. Phylogenetic analysis indicates that the sample is characterized by a gain of 89 mutations since divergence from its nearest sequenced neighbor, which had been collected in September 2020 and belongs to the B.1.1 lineage, largely extinct in 2022. 33 of these mutations were coding and occurred in the Spike protein. Of these, 17 are lineage-defining in some of the variants of concern (VOCs) or are in sites where another mutation is lineage-defining in a variant of concern, and/or shown to be involved in antibody evasion, and/or detected in other cases of persistent COVID-19; these include some "usual suspects," such as Spike:L452R, E484Q, K417T, Y453F, and N460K. Molecular clock analysis indicates that mutations in this lineage accumulated at an increased rate compared to the ancestral B.1.1 strain. This increase is driven by the accumulation of nonsynonymous mutations, for an average dN/dS value of 2.2, indicating strong positive selection during within-patient evolution. Additionally, there is reason to believe that the virus had persisted for at least some time in the gastrointestinal tract, as evidenced by the presence of mutations that are rare in the general population samples but common in samples from wastewater. Our analysis adds to the growing body of research on evolution of SARS-CoV-2 in chronically infected patients and its relationship to the emergence of variants of concern.

Pathogenicity of SARS-CoV-2 Omicron BA.5 and BE.1 Variants in Syrian Hamsters and hACE2-transgenic Mmice (preprint)

A new variant of the SARS-CoV-2 Omicron BA.5 virus has displaced all previous variants of the virus around the world. Preliminary assessment of the effectiveness of drugs for the prevention and treatment of COVID-19 requires the availability of infection models in animals. In this study, we characterize the infection model SARS-CoV-2 Omicron BA.5 and its progeny sublineage BE.1 in hACE2-transgenic mice and in Syrian hamsters. Both sublineages turned out to be pathogenic for animals – the challenged animals showed weight loss, a high level of viral load and acute inflammation in the lungs. Part of BA.5-infected mice died after virus challenge, indicating that this virus variant is more pathogenic than the previous BA.1 variant but less pathogenic than Wuhan variant.

An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint-Petersburg, Russia (preprint)

The Omicron variant of SARS-CoV-2 has rapidly spread globally in late 2021 - early 2022, displacing the previously prevalent Delta variant. Before December 16, 2021, community transmission had already been observed in tens of countries globally. However, in Russia, the majority of reported cases at that time had been sporadic and associated with travel. Here, we report an Omicron outbreak at a student dormitory in Saint Petersburg between December 16 - 29, 2021, which was the earliest known instance of large-scale community transmission in Russia. Out of the 465 sampled residents of the dormitory, 180 (38.7%) tested PCR positive. Among the 118 residents for whom the variant has been tested by whole-genome sequencing, 111 (94.1%) carried the Omicron variant. Among these 111 residents, 60 (54.1%) were vaccinated or had reported previous COVID-19. Phylogenetic analysis confirmed that the outbreak was caused by a single introduction of the BA.1.1 sublineage of Omicron. The dormitory-derived clade constituted a significant proportion of BA.1.1 samples in Saint-Petersburg and has spread to other regions of Russia and other countries. The rapid spread of Omicron in a population with preexisting immunity to previous variants underlines its propensity for immune evasion.

Immunogenicity and safety of a recombinant adenovirus type-5 COVID 19 vaccine in adults: data from a randomised, double-blind, placebo-controlled, single-dose, phase 3 trial in Russia (preprint)

BackgroundTo determine the immunogenicity, efficacy, reactogenicity, and safety of a single dose of recombinant adenovirus type-5 vectored COVID-19 vaccine (Ad5-nCoV, 5 x 1010 viral particles per 0.5 mL dose), we conducted a single-dose, randomised, double-blind, placebo-controlled, parallel group (3:1 Ad5-nCoV:placebo), phase 3 trial (Prometheus). MethodsFrom 11-September-2020 to 05-May-2021, across six sites in the Russian Federation, 496 participants were injected with either placebo or Ad5-nCoV expressing the full-length spike (S) protein from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). ResultsSeroconversion (the primary endpoint) rates of 78.5% (95% CI: 73.9; 82.6) against receptor binding domain (RBD), 90.6% (95% CI: 87.2; 93.4) against S protein and 59% (95% CI: 53.3; 64.6) against neutralising SARS-CoV2 antibodies 28 days post-vaccination. Geometric mean titres (GMTs) were also elevated for antibodies against the RBD (405.32 [95% CI: 361.58; 454.46]) and S protein (678.86 [95% CI: 607.44; 754.40]) compared to the GMT of neutralising antibodies against SARS-CoV-2 (16.73 [95% CI: 15.36; 18.22]). Using an IFN-{gamma} ELISpot assay after stimulating the cells with full-length S protein we showed that the Ad5-nCoV vaccine induced the most robust cellular immune response on Days 14 and 28. Up to Day 28, the primary and all secondary endpoints of the Ad5-nCoV vaccine were statistically superior to the placebo ([p] <0.001). Systemic reactions were reported in 113 of 496 (22.8%) participants (Ad5-nCoV, 26.9%; Placebo, 10.5%), and local reactions were reported in 108 (21.8%) participants (Ad5-nCoV, 28.5%; Placebo, 1.6%). These were generally mild and resolved within 7 days after vaccination. Of the six serious adverse events reported, none of the events were vaccine related. There were no deaths or premature withdrawals. ConclusionA single-dose of Ad5-nCoV vaccine induced a marked specific humoral and cellular immune response with a favourable safety profile. Trial RegistrationClinicalTrials.gov: NCT04540419

SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint-Petersburg, Russia (preprint)

The B.1.1.529 Omicron variant of SARS-CoV-2 is rapidly spreading, displacing the globally prevalent Delta variant. Before December 16, 2021, community transmission had already been observed in tens of countries globally. However, in Russia, all reported cases had been sporadic and associated with travel. Here, we report an Omicron outbreak at a students’ dormitory in Saint Petersburg, Russia. Out of the 462 sampled residents of the dormitory, 206 (44.6%) tested PCR positive, and 159 (77.1%) of these infections carried the S:ins214EPE insertion, indicating that they were of the Omicron strain. 104 (65%) of Omicron-positive patients have been vaccinated and/or reported previous covid-19. Whole genome sequencing confirmed that the outbreak is caused by the Omicron variant. Phylogenetic analysis showed that the outbreak has a single origin, and belongs to the S:346K sublineage of Omicron which may be characterized by an increased rate of spread, compared to other Omicron sublineages. The rapid spread of Omicron in a population with preexisting immunity to previous variants underlines its propensity for immune evasion.

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

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.

One-shot immunization with Sputnik Light (the first component of Sputnik V vaccine) is effective against SARS-CoV-2 Delta variant: efficacy data on the use of the vaccine in civil circulation in Moscow (preprint)

ObjectivesVaccination remains the most effective response to the COVID-19 pandemic. Most vaccines use two-dose regimens. In turn, single-dose vaccines also have high potential, since, on the one hand, they simplify the vaccination program, make it more accessible and convenient for more people around the world, and on the other hand, they are better suited for subsequent revaccination. However, there is not enough data on the effectiveness of single-dose vaccine variants against new genetic lines to assess their current potential. It is not clear how much a single dose of immunization protects against the globally dominant delta variant. In this work, we investigated the effectiveness of a single dose vaccine (Sputnik Light, the first component of Sputnik V vaccine) against the Delta variant in Moscow. MethodsTo assess the effectiveness of one dose of viral vector vaccine based on rAd26 against the delta variant in Moscow, we used data from the Moscow registries of vaccination against COVID-19 and the incidence of COVID-19. The availability of data on the number of seropositive residents of Moscow made it possible to consider the size of the immune layer formed because of a previous COVID-19 disease or vaccination. To calculate the effectiveness, the proportion of COVID-19 cases among those vaccinated with a single dose and the proportion of cases among those who were not vaccinated in July 2021. ResultsOur data indicate that throughout July 2021, the dominant variant of the coronavirus at the level of 99.5% in Moscow was the SARS-CoV-2 delta variant and its subsidiary lines. Considering the immune layer of 46% allowed us to calculate the effectiveness of a one-shot vaccine against the delta variant in Moscow during the first three months after vaccination at the level of 69.85% (95% confidence interval [CI], 64.08 to 74.70). In the 18-29-year-old group, the overall vaccine efficacy against the delta variant was 88.61%, in the 18-59 group - 75.28%. Sputnik Light demonstrates higher efficacy against Delta variant than many two-shot vaccines. ConclusionThe results indicate a high efficacy of a single immunization first component of Sputnik V vaccine against delta variant among young and middle-aged people, at least during the first 3 months after receiving the one-shot vaccine.

Spread of Endemic SARS-CoV-2 Lineages in Russia Before April 2021 (preprint)

In 2021, the COVID-19 pandemic is characterized by global spread of several lineages with evidence for increased transmissibility. Russia is 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, alpha (B.1.1.7), beta (B.1.351) or gamma (P.1), none have been sampled in Russia before January 2021. Instead, between summer 2020 and spring 2021, the epidemic in Russia has been characterized by the spread of two lineages that are rare elsewhere: 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 in different parts of Russia. Mutational composition and frequency dynamics suggest that B.1.1.317 and B.1.1.397+ may be more transmissible than the previously predominant B.1.1. On top of these lineages, in January 2021, B.1.1.7 emerged in Russia, reaching the 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, the frequency increase of lineages B.1.1.317, B.1.1.397+, AT.1, B.1.1.524 and B.1.1.525 suggest that the combinations of mutations observed in them could have increased the rate of their spread.

COVID-19 pandemic in Saint Petersburg, Russia: combining surveillance and population-based serological study data in May, 2020 - April, 2021 (preprint)

Background: The COVID-19 pandemic in Russia has already resulted in 500,000 excess deaths, with more than 5.6 million cases registered officially by July 2021. Surveillance based on case reporting has become the core pandemic monitoring method in the country and globally. However, population-based seroprevalence studies may provide an unbiased estimate of the actual disease spread and, in combination with multiple surveillance tools, help to define the pandemic course. This study summarises results from four consecutive serological surveys conducted between May 2020 and April 2021 at St.Petersburg, Russia and combines them with other SARS-CoV-2 surveillance data. Methods: We conducted four serological surveys of two random samples (May-June, July-August, October--December 2020, and February-April 2021) from adults residing in St.Petersburg recruited with the random digit dialing (RDD), accompanied by a telephone interview to collect information on both individuals who accepted and declined the invitation for testing and account for non-response. We have used enzyme-linked immunosorbent assay CoronaPass total antibodies test (Genetico, Moscow, Russia) to report seroprevalence. We corrected the estimates for non-response using the bivariate probit model and also accounted the test performance characteristics, obtained from independent assay evaluation. In addition, we have summarised the official registered cases statistics, the number of hospitalised patients, the number of COVID-19 deaths, excess deaths, tests performed, data from the ongoing SARS-CoV-2 variants of concern (VOC) surveillance, the vaccination uptake, and St. Petersburg search and mobility trends. The infection fatality ratios (IFR) have been calculated using the Bayesian evidence synthesis model. Findings: After calling 113,017 random mobile phones we have reached 14,118 individuals who responded to computer-assisted telephone interviewing (CATI) and 2,413 provided blood samples at least once through the seroprevalence study. The adjusted seroprevalence in May-June, 2020 was 9.7% (95%: 7.7-11.7), 13.3% (95% 9.9-16.6) in July-August, 2020, 22.9% (95%: 20.3-25.5) in October-December, 2021 and 43.9% (95%: 39.7-48.0) in February-April, 2021. History of any symptoms, history of COVID-19 tests, and non-smoking status were significant predictors for higher seroprevalence. Most individuals remained seropositive with a maximum 10 months follow-up. 92.7% (95% CI 87.9-95.7) of participants who have reported at least one vaccine dose were seropositive. Hospitalisation and COVID-19 death statistics and search terms trends reflected the pandemic course better than the official case count, especially during the spring 2020. SARS-CoV-2 circulation showed rather low genetic SARS-CoV-2 lineages diversity that increased in the spring 2021. Local VOC (AT.1) was spreading till April 2021, but B.1.617.2 substituted all other lineages by June 2021. The IFR based on the excess deaths was equal to 1.04 (95% CI 0.80-1.31) for the adult population and 0.86% (95% CI 0.66-1.08) for the entire population. Conclusion: Approximately one year after the COVID-19 pandemic about 45% of St. Petersburg, Russia residents contracted the SARS-CoV-2 infection in, or 2.2 mln people. Combined with vaccination uptake of about 10% it was enough to slow the pandemic until the Delta VOC started to spread. Combination of several surveillance tools provides a comprehensive pandemic picture. Funding: Polymetal International plc.

SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19 (preprint)

Evolution of SARS-CoV-2 in immunocompromised hosts may result in novel variants with changed properties, but the mode of selection underlying this process remains unclear. While escape from humoral immunity certainly plays a role in intra-host evolution, escape from cellular immunity is poorly understood. Here, we report a case of long-term COVID-19 in an immunocompromised patient with non-Hodgkin’s lymphoma who received treatment with rituximab and lacked neutralizing antibodies. Over the 318 days of the disease, the SARS-CoV-2 genome gained a total of 40 changes, 34 of which were present by the end of the study period. Among the acquired mutations, 12 reduced or prevented binding of known immunogenic SARS-CoV-2 HLA class I antigens, suggesting that virus immunoediting is largely driven by cytotoxic CD8 T cell clones. The two changes with the strongest effect, nsp3:T504A and nsp3:T504P, were experimentally assessed in a cytotoxic assay of the patient's CD8 T cells. Both these changes were associated with immune escape, with a stronger effect observed for nsp3:T504P, the change which ultimately got fixed. Together, these results suggest that CD8 T cell escape may be an underappreciated contributor to SARS-CoV-2 evolution in humans.

Spread of endemic SARS-CoV-2 lineages in Russia (preprint)

In 2021, the COVID-19 pandemic is characterized by global spread of several lineages with evidence for increased transmissibility. Russia is 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, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) or P.1 (501Y.V3), none have been sampled in Russia before January 2021. Instead, since summer 2020, the epidemic in Russia has been characterized by the spread of two lineages that are rare elsewhere: B.1.1.317 and a sublineage of B.1.1 including B.1.1.397 (hereafter, B.1.1.397+). In February-March 2021, these lineages reached frequencies of 26.9% (95% C.I.: 23.1%-31.1%) and 32.8% (95% C.I.28.6%-37.2%) respectively in Russia. Their frequency has increased in different parts of Russia. Together with the fact that these lineages carry several spike mutations of interest, this suggests that B.1.1.317 and B.1.1.397+ may be more transmissible than the previously predominant B.1.1, although there is no direct data on change in transmissibility. Comparison of frequency dynamics of lineages carrying subsets of characteristic mutations of B.1.1.317 and B.1.1.397+ suggests that, if indeed some of these mutations affect transmissibility, the transmission advantage of B.1.1.317 may be conferred by the (S:D138Y+S:S477N+S:A845S) combination; while the advantage of B.1.1.397+ may be conferred by the S:M153T change. On top of these lineages, in January 2021, B.1.1.7 emerged in Russia, reaching the frequency of 17.4% (95% C.I.: 12.0%-24.4%) in March 2021. Additionally, we identify three novel distinct lineages, AT.1, and two lineages prospectively named B.1.1.v1 and B.1.1.v2, 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:{Delta}140-142, S:{Delta}144 or S:{Delta}136-144), and nsp6:{Delta}106-108 (also known as ORF1a:{Delta}3675-3677). 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.v1 and B.1.1.v2, 15.2% (95% C.I.: 7.6%-28.2%). The combinations of mutations observed in B.1.1.317, B.1.1.397+, AT.1, B.1.1.v1 and B.1.1.v2 together with frequency increase of these lineages make them candidate variants of interest.

Fast prototyping of a local fuzzy search system for decision support and retraining of hospital staff during pandemic (preprint)

Purpose. COVID-19 pandemic has shown an urgent need for decision support systems to help doctors in a period of stress and uncertainty. However, significant differences in hospital conditions, as well as skepticism of doctors about machine learning algorithms, limit their introduction into clinical practice. Our goal was to test and apply a principle of "patient-like-mine" decision support in rapidly changing conditions of a pandemic.Methods. In the developed system we implemented a fuzzy search that allows a doctor to compare their medical case with similar cases recorded since the beginning of the pandemic in their medical center. Various distance metrics were tried for obtaining clinically relevant search results. With the use of R programming language, we designed the first version of the system in approximately a week. A set of features for the comparison of the cases was selected with the use of random forest algorithm implemented in Caret. Shiny package was chosen for the design of GUI. Results. The deployed tool allowed doctors to quickly estimate the current conditions of their patients by means of studying the most similar previous cases stored in the local health information system. Extensive testing of the system during the first wave of COVID-19 has shown that this approach helps not only to draw a conclusion about the optimal treatment tactics and to train medical staff in real-time but also to optimize patients’ individual testing plans.Conclusions. This project points to the possibility of rapid prototyping and effective usage of "patient-like-mine" search systems at the time of a pandemic caused by a poorly known pathogen.

Genomic epidemiology of the early stages of SARS-CoV-2 outbreak in Russia (preprint)

The ongoing pandemic of SARS-CoV-2 presents novel challenges and opportunities for the use of phylogenetics to understand and control its spread. Here, we analyze the emergence of SARS-CoV-2 in Russia in March and April 2020. Combining phylogeographic analysis with travel history data, we estimate that the sampled viral diversity has originated from 67 closely timed introductions into Russia, mostly in late February to early March. All but one of these introductions came from non-Chinese sources, suggesting that border closure with China has helped delay establishment of SARS-CoV-2 in Russia. These introductions resulted in at least 9 distinct Russian lineages corresponding to domestic transmission. A notable transmission cluster corresponded to a nosocomial outbreak at the Vreden hospital in Saint Petersburg; phylodynamic analysis of this cluster reveals multiple (2-4) introductions each giving rise to a large number of cases, with a high initial effective reproduction number of 3.7 (2.5-5.0).