Correction: Gladkikh et al. Epidemiological Features of COVID-19 in Northwest Russia in 2021. Viruses 2022, 14, 931.

There was an error in the original publication [...].

Comparative Analysis of Library Preparation Approaches for SARS-CoV-2 Genome Sequencing on the Illumina MiSeq Platform.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for over two years of the COVID-19 pandemic and a global health emergency. Genomic surveillance plays a key role in overcoming the ongoing COVID-19 pandemic despite its relative successive waves and the continuous emergence of new variants. Many technological approaches are currently applied for the whole genome sequencing (WGS) of SARS-CoV-2. They differ in key stages of the process, and they feature some differences in genomic coverage, sequencing depth, and in the accuracy of variant-calling options. In this study, three different protocols for SARS-CoV-2 WGS library construction are compared: an amplicon-based protocol with a commercial primer panel; an amplicon-based protocol with a custom panel; and a hybridization capture protocol. Specific differences in sequencing depth and genomic coverage as well as differences in SNP number were found. The custom panel showed suitable results and a predictable output applicable for the epidemiological surveillance of SARS-CoV-2 variants.

Uninvited Guest: Arrival and Dissemination of Omicron Lineage SARS-CoV-2 in St. Petersburg, Russia.

Following its emergence at the end of 2021, the Omicron SARS-CoV-2 variant rapidly spread around the world and became a dominant variant of concern (VOC). The appearance of the new strain provoked a new pandemic wave with record incidence rates. Here, we analyze the dissemination dynamics of Omicron strains in Saint Petersburg, Russia's second largest city. The first case of Omicron lineage BA.1 was registered in St. Petersburg on 10 December 2021. Rapid expansion of the variant and increased incidence followed. The peak incidence was reached in February 2022, followed by an observed decline coinciding with the beginning of spread of the BA.2 variant. SARS-CoV-2 lineage change dynamics were shown in three categories: airport arrivals; clinical outpatients; and clinical inpatients. It is shown that the distribution of lineage BA.1 occurred as a result of multiple imports. Variability within the BA.1 and BA.2 lineages in St. Petersburg was also revealed. On the basis of phylogenetic analysis, an attempt was made to trace the origin of the first imported strain, and an assessment was made of the quarantine measures used to prevent the spread of this kind of infection.

Epidemiological Features of COVID-19 in Northwest Russia in 2021.

Appearing in Wuhan (China) and quickly spreading across the globe, the novel coronavirus infection quickly became a significant threat to global health. The year 2021 was characterized by both increases and decreases in COVID-19 incidence, and Russia was no exception. In this work, we describe regional features in the Northwestern federal district (FD) of Russia of the pandemic in 2021 based on Rospotrebnadzor statistics and data from SARS-CoV-2 genetic monitoring provided by the Saint Petersburg Pasteur Institute as a part of epidemiological surveillance. The epidemiological situation in the studied region was complicated by the presence of the megacity Saint Petersburg, featuring a high population density and its status as an international transport hub. COVID-19 incidence in the Northwestern FD fluctuated throughout the year, with two characteristic maxima in January and November. An analysis of fluctuations in the age structure, severity of morbidity, mortality rates, and the level of population vaccination in the region during the year is given. Assessment of epidemiological indicators was carried out in relation to changes in locally circulating genetic variants. It was seen that, during 2021, so-called variants of concern (VOC) circulated in the region (Alpha, Beta, Delta, Omicron), with Delta variant strains dominating from June to December. They successively replaced the variants of lines 20A and 20B circulating at the beginning of the year. An epidemiological feature of the northwestern region is the AT.1 variant, which was identified for the first time and later spread throughout the region and beyond its borders. Its share of the regional viral population reached 28.2% in May, and sporadic cases were observed until September. It has been shown that genetic variants of AT.1 lineages distributed in Russia and Northern Europe represent a single phylogenetic group at the base of the 20B branch on the global phylogenetic tree of SARS-CoV-2 strains. The progression of the COVID-19 pandemic occurred against the background of a vaccination campaign. The findings highlight the impact of vaccination on lowering severe COVID-19 case numbers and the mortality rate, despite ongoing changes in circulating SARS-CoV-2 genetic variants.

Characterization of a Novel SARS-CoV-2 Genetic Variant with Distinct Spike Protein Mutations.

The COVID-19 pandemic, which began in Wuhan (Hubei, China), has been ongoing for about a year and a half. An unprecedented number of people around the world have been infected with SARS-CoV-2, the etiological agent of COVID-19. Despite the fact that the mortality rate for COVID-19 is relatively low, the total number of deaths has currently already reached more than three million and continues to increase due to high incidence. Since the beginning of the pandemic, a large number of sequences have been obtained and many genetic variants have been identified. Some of them bear significant mutations that affect biological properties of the virus. These genetic variants, currently Variants of Concern (VoC), include the so-called United Kingdom variant (20I/501Y), the Brazilian variant (20J/501Y.V3), and the South African variant (20H/501Y.V2). We describe here a novel SARS-CoV-2 variant with distinct spike protein mutations, first obtained at the end of January 2021 in northwest Russia. Therefore, it is necessary to pay attention to the dynamics of its spread among patients with COVID-19, as well as to study in detail its biological properties.