Emergence of first strains of SARS-CoV-2 lineage B.1.1.7 in Romania (original) (raw)
Related papers
Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis (Preprint)
2021
BACKGROUND The United Kingdom reported the emergence of a new and highly transmissible SARS-CoV-2 variant (B.1.1.7) that rapidly spread to other countries. The impact of this new mutation—which occurs in the S protein—on infectivity, virulence, and current vaccine effectiveness is still under evaluation. OBJECTIVE The aim of this study is to sequence SARS-CoV-2 samples of cases in Romania to detect the B.1.1.7 variant and compare these samples with sequences submitted to GISAID. METHODS SARS-CoV-2 samples were sequenced and amino acid substitution analysis was performed using the CoV-GLUE platform. RESULTS We have identified the first cases of the B.1.1.7 variant in samples collected from Romanian patients, of which one was traced to the region of the United Kingdom where the new variant was originally sequenced. Mutations in nonstructural protein 3 (Nsp3; N844S and D455N) and ORF3a (L15F) were also detected, indicating common ancestry with UK strains as well as remote connections w...
Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis
2021
Background The United Kingdom reported the emergence of a new and highly transmissible SARS-CoV-2 variant (B.1.1.7) that rapidly spread to other countries. The impact of this new mutation—which occurs in the S protein—on infectivity, virulence, and current vaccine effectiveness is still under evaluation. Objective The aim of this study is to sequence SARS-CoV-2 samples of cases in Romania to detect the B.1.1.7 variant and compare these samples with sequences submitted to GISAID. Methods SARS-CoV-2 samples were sequenced and amino acid substitution analysis was performed using the CoV-GLUE platform. Results We have identified the first cases of the B.1.1.7 variant in samples collected from Romanian patients, of which one was traced to the region of the United Kingdom where the new variant was originally sequenced. Mutations in nonstructural protein 3 (Nsp3; N844S and D455N) and ORF3a (L15F) were also detected, indicating common ancestry with UK strains as well as remote connections w...
Short Communication:Evidence of Novel SARS-CoV-2 Variants Circulation in Romania
AIDS Research and Human Retroviruses
New SARS-CoV-2 variants are constantly emerging and putting a strain on public health systems by spreading faster and potentially evading immune protection through vaccination. One of these strains is the B.1.1.7 variant that has initially been described in the United Kingdom and has subsequently spread to several countries. Monitoring the amplification of the S gene-a major hotspot for molecular evolution-by reverse transcription polymerase chain reaction (RT-PCR) allows rapidly screening for such variants. This report describes the detection of sequence variants in Romania by using this strategy followed by next-generation sequencing of the entire genome for confirmation and further characterization. One B.1.1.7 and three B.1.258 sequences were confirmed. Each of these strains presented additional mutations with possible impact on the replicative capacity. Public health strategies should be devised to ensure molecular monitoring of SARS-CoV-2 evolution during the pandemic and allow adequate and rapid reaction.
Life
BACKGROUND: The spread of SARS-CoV-2 generated an unprecedented global public health crisis. Soon after Asia, Europe was seriously affected. Many countries, including Romania, adopted lockdown measures to limit the outbreak. AIM: We performed a molecular epidemiology analysis of SARS-CoV-2 viral strains circulating in Romania during the first two months of the epidemic in order to detect mutation profiles and phylogenetic relatedness. METHODS: Respiratory samples were directly used for shotgun sequencing. RESULTS: All Romanian sequences belonged to lineage B, with a different subtype distribution between northern and southern regions (subtype B.1.5 and B.1.1). Phylogenetic analysis suggested that the Romanian epidemic started with multiple introduction events from other European countries followed by local transmission. Phylogenetic links between northern Romania and Spain, Austria, Scotland and Russia were observed, as well as between southern Romania and Switzerland, Italy, France...
2020
Romania officially declared its first SARS-CoV-2 case on February 26, 2020. The first and largest COVID-19 outbreak in Romania was recorded in Suceava, N/E region of the country, and originated at the Suceava regional county hospital. Following sheltering-in-place measures, infection rates decreased, only to rise again after relaxation of measures. This study describes the incursion of SARS-CoV-2 in Suceava and other parts of Romania and analyzes the mutations and their association with clinical manifestation of the disease during the period of COVID-19 outbreak. Phylogenetic analysis indicated multiple sites of origin for SARS-CoV-2 strains in Suceava, specifically from Spain, Italy and Russia, but also other strains related to those from Czech Republic, Belgium and France. Most Suceava samples contained mutations common to European lineages, such as A20268G, however aproximately 10% of samples were missing such mutations, indicating a possible different origin. While overall genom...
Predominant Mutations of SARS-CoV-2: Their Geographical Distribution and Potential Consequences
Mediterranean Journal of Infection Microbes and Antimicrobials, 2021
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) emerged in late December 2019 in Wuhan, China. More than 83 million people have been infected, and more than 1.8 million people have died, as reported to the World Health Organization on the 3 rd of January, 2021. Analysis of genetic variations is critical for understanding the spreading pattern of SARS-CoV-2 across several countries. This review aimed to gather information about the prominent mutations of SARS-CoV-2 by analyzing the origin, viral pathogenesis, and mutation rate. Moreover, we concluded their potential impacts on SARS-CoV-2 therapeutics. Mutations in the spike protein (D614G, N501Y, E484K, A222V, S477N, and G485R), ORF1ab (P323L, N628N, Y455Y, A97V, and F106F), nucleocapsid protein (R203K and G204R), ORF8 (L84S), and ORF3a (Q57H and G251V) were examined in this review by analyzing relevant articles from the beginning of the current pandemic to the most recent date. A detailed analysis of articles demonstrates that D614G is the major variation distributed globally, and its frequency increased rapidly from early in March, followed by several other variations in either spike or different proteins. In addition, it was seen that the currently circulating N501Y and E484K variants revealed a public concern regarding vaccines' efficacy. Investigation of variations of SARS-CoV-2 would lead to understanding their potential mechanism of action against SARS-CoV-2, thereby suggesting suitable therapeutics. Several mechanisms were suggested to have a role in SARS-CoV-2 mutation rate and evolution. Possible therapeutics and vaccines against SARS-CoV-2 were proposed.
Identification of the First SARS-CoV-2 Lineage B.1.1.529 Virus Detected in Europe
Microbiology resource announcements, 2022
We report the complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (lineage B.1.1.529) from a Belgian patient with a history of recent travel to Egypt. At the time of writing, this genome constituted the first confirmed case of an infection with the Omicron variant in Europe. I n December 2019, a novel betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (genus Betacoronavirus, subfamily Orthocoronavirinae, family Coronaviridae), was identified in Wuhan, China (1, 2). Following its spread to the rest of the world, many unique mutations in the virus genome have been reported. The biological advantages conferred by some of these mutations have resulted in the establishment of specific genetic lineages that have largely outcompeted the original strain (3). Lineages that are characterized by increased transmissibility or virulence or that decrease the effectiveness of available countermeasures are classified by the WHO as variants of concern (VOCs) (4). On 26 November 2021, 2 days after it was reported for the first time in South Africa, a new lineage (B.1.1.529) was classified as variant Omicron, the fifth recognized VOC (5). Here, we report the genome sequence of the first reported Omicron variant in Europe. The sample was collected as part of routine COVID-19 diagnostics and selected for whole-genome sequencing following an S gene dropout in quantitative PCR (qPCR) testing (TaqPath COVID-19 CE-IVD reverse transcription [RT]-PCR kit; Thermo Fisher Scientific). This work was reviewed and approved by the KU/UZ Leuven Clinical Trial and Ethical review board (approval number S66037), which allows us to use patient samples for research and lookup and use specific metadata from the patient. The patient returned from Egypt to Belgium on 11 November 2021 and tested negative 3 days before travelling, as well as repeatedly testing negative during quarantine after arrival in Belgium. The patient developed mild symptoms 10 days after arrival and tested positive for SARS-CoV-2 on 24 November 2021. RNA was extracted from a nasopharyngeal swab sample using the QIAamp viral RNA minikit (Qiagen, Hilden, Germany), after which a barcoded Nanopore sequencing library was prepared using the COVID Midnight midikit (C19MIDI; Oxford Nanopore Technologies), which uses a tiled amplicon approach (;1,200-bp amplicons) to amplify the SARS-CoV-2 genome. The library was sequenced for 72 h on an R9.4.1 flow cell. Base calling and demultiplexing were done using the GridION built-in MinKNOW software (v21.05.25), and the resulting reads were processed using the ARTIC bioinformatics pipeline v1.1.3 (6). The genome sequence obtained has a total length of 29,684 nucleotides and a GC content of 38%, with an average coverage depth of 1,501Â. Because the genome termini are not covered by the amplicons used, the 54 first (59) and 151 last (39) nucleotides, compared to the SARS-CoV-2 reference genome (GenBank accession number NC_045512.2),
Investigating the mutations in the SARS-CoV-2 proteins among European countries
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new member of the Coronaviridae family, triggering more than 190 million cases and more than two million deaths in European societies. Emerging the new variants due to mutations in genomic regions are foremost responsible for influencing the infectivity and mortality potential of such a virus. In the current study, we considered mutations among spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins of SARS-CoV-2 in the Europe continent by exploring the frequencies of mutations and the timeline of emerging them. For this purpose, Amino-acid sequences (AASs) were gathered from the GISAID database, and Mutation tracking was performed by detecting any difference between samples and a reference sequence; Wuhan-2019. In the next step, we compared the achieved results with worldwide sequences. 8.6%, 63.6%, 24.7%, and 1.7% of S, E, M, and N samples did not demonstrate any mutation among European countries. Also,...
Implications of the Emerging SARS-CoV-2 Variant: Caution is the Key
Oman Medical Journal, 2021
Over the last few weeks, the United Kingdom (UK) has faced a rapid increase in COVID-19 cases in South East England, leading to enhanced epidemiological and virological investigations. Analysis of viral genome sequence data identified a large proportion of cases belonged to a new single phylogenetic cluster. The new variant is defined by multiple spike protein mutations (deletion 69-70, deletion 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H) present as well as mutations in other genomic regions. While it is known and expected that viruses constantly change through mutation leading to the emergence of new variants, preliminary analysis in the UK suggests that this variant is significantly more transmissible than previously circulating variants, with an estimated potential to increase the reproductive number (R) by 0.4 or greater with an estimated increased transmissibility of up to 70%. This new variant has emerged at a time of the year when there has traditionally been increased family and social mixing. There is no indication at this point of increased infection severity associated with the new variant. A few cases with the new variant have to date been reported by Denmark and the Netherlands and, according to media reports, in Belgium.