Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity.

Postvaccination SARS-CoV-2 Alpha (B.1.1.7) lineage infection among healthcare workers on the background of IgG antibodies Like most vaccines, the effectiveness of COVID-19 vaccines developed so far is not 100% and a small percentage of fully vaccinated individuals still develop symptomatic or asymptomatic SARS-CoV-2 infections. 1 In addition, the emerging of novel mutations is likely to help the virus evade vaccines especially in regions with low vaccination coverage. 2 In this study, we analyzed SARS-CoV-2 infections in two healthcare workers (HCWs) fully vaccinated with the Pfizer-BioNTech COVID-19 vaccine (BNT162b2) and subsequently diagnosed with postvaccination SARS-CoV-2 on a background of IgG antibodies.Epidemiological and clinical data including, symptoms initial analysis and observations were obtained from the National electronic system for COVID-19 (Table 1).Blood samples of the HCWs were tested for anti-SARS-CoV-2 IgG antibodies. The analysis was performed using two different serological tests: The VIDAS ® SARS-COV-2 IgG Enzyme-Linked Fluorescent Assay (Biomerieux) and SARS -CoV-2 II Quant Abbott Architect (Abbott).Viral RNA was extracted from nasal swabs using an ExiPrep 48 Viral DNA/RNA Kit (Bioneer) following the manufacturer's instructions. Real-time PCR was performed using GeneFinder™ COVID-19 Plus RealAmp Kit (OSANG Healthcare Co., Ltd.).Whole-genome next-generation sequencing (NGS) of SARS-CoV-2 was performed by using a modified ARTIC v3 tailed amplicon method and Illumina MiSeq v2 reagent kit with 500 cycles (Illumina).

The study was supported by a grant from the Ministry of Education and Science, Bulgaria (contract: K?-06-H43/1-27.11.2020) "Molecular-virological analysis of the introduced and disseminated newly emerged pandemic virus SARS-CoV-2 in Bulgaria by using next-generation sequencing and combined epidemiological and phylogenetic analysis" and (contract: K?-06-H43/ 5-30.11.2020) "Molecular-genetic and clinical characteristics of human coronavirus. Study of the role of SARS-CoV-2 in co-inf

Background. Evolution of the emerging SARS-CoV-2 variants raises concerns about the possibility of accelerated transmission,  disease severity, diagnostic challenges, and reduced vaccine effectiveness in the ever-evolving COVID-19 pandemic worldwide. Objectives for this study were to build a comprehensive national system for monitoring and genomic surveillance of SARS-CoV-2  and to identify the introduced virus variants in the country. Methods. We analyzed SARS-CoV-2 infections in 7948 representative clinical samples collected in medical institutions in different  geographical regions of the country in 2022. Whole-genome next-generation sequencing of SARS-CoV-2 was performed on samples  from randomly selected SARS-CoV-2-positive individuals by using a modified ARTIC v3-tailed amplicon method. A bioinformatic and  phylogenetic analyses of the obtained sequences was carried out. Results. Significant dynamics was observed in the spread of viral variants in 2022, which is characterized by the introduction and  spread of multiple SARS-CoV-2 variants. The phylogenomic analysis identified a high genetic heterogeneiety composed of a total of 152 different viral clades divided into 3 main supergroups: 114 (75.0%) of which were Omicron sub-variants, 35 (23.0%) Delta sub-variants, and 3 (2.0%) recombinant forms. Conclusion. Viral variants and their sub-clades with different potentials to impact disease severity were identified and the  information was immediately published for use by decision-makers and the scientific community. The global pandemic of COVID-19  has shown the importance of molecular biological surveillance, which is an indispensable element of the modern approach in the  fight against infectious diseases.

Social distancing, mask-wearing, and travel restrictions during the COVID-19 pandemic have significantly impacted the spread of influenza viruses. The objectives of this study were to analyze the pattern of influenza virus circulation with respect to that of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Bulgaria during the 2021-2022 season and to perform a phylogenetic/molecular analysis of the hemagglutinin (HA) and neuraminidase (NA) sequences of representative influenza strains. Influenza infection was confirmed using real-time reverse transcription polymerase chain reaction in 93 (4.2%) of the 2193 patients with acute respiratory illness tested wherein all detected viruses were subtyped as A (H3N2). SARS-CoV-2 was identified in 377 (24.3%) of the 1552 patients tested.Significant differences in the incidence of influenza viruses and SARS-CoV-2 were found between individual age groups, outpatients/inpatients, and in the seasonal distribution of cases. Two cases of coinfections were identified. In hospitalized patients, the C t values of influenza viruses at admission were lower in adults aged ≥65 years (indicating higher viral load) than in children aged 0-14 years (p < 0.05). In SARS-CoV-2-positive inpatients, this association was not statistically significant. HA genes of all A(H3N2) viruses analyzed belonged to subclade 3C.2a1b.2a.The sequenced viruses carried 11 substitutions in HA and 5 in NA, in comparison to the vaccine virus A/Cambodia/e0826360/2020, including several substitutions in the HA antigenic sites B and C. This study revealed extensive changes in the typical epidemiology of influenza infection, including a dramatic reduction in the number of cases, diminished genetic diversity of circulating viruses, changes in age, and seasonal distribution of cases.