A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain)

Andrés, Cristina; Piñana, María; Borras-Bermejo, Blanca; González-Sánchez, Alejandra; García-Cehic, Damir; Esperalba, Juliana; Rando, Ariadna; Zules-Oña, Ricardo; Campos, Carolina; Codina, María Gema; Blanco‐Grau, Albert; Colomer-Castell, Sergi; Martín, Maria Carmen; Castillo, Carla; García-Comuñas, Karen; Vásquez-Mercado, Rodrigo; Martins-Martins, Reginaldo; Campins-Martí, Magda; Pumarola, Tomás; Quer, Josep; Antón, Andrés

doi:10.1080/22221751.2021.2011617

Cited by 20 publications

(26 citation statements)

References 41 publications

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“…Amino acids consistently substituted from Wuhan-Hu-1 across all variants are ORF1AB P4715L/F and spike D618G. The D618G has been covered in previous works [5,[21][22][23][24][25][26][27][28]. ORF1AB P4715L/F has also been described [29,30].…”

Section: Discussionmentioning

confidence: 99%

Whole-genome comparison of representatives of all variants of SARS-CoV-2, including subvariant BA.2 and the GKA clade

Suardana

Mahardika

Pharmawati

et al. 2022

Preprint

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Since its discovery at the end of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly evolved into many variants, including subvariant BA.2 and the GKA clade. Genomic clarification is needed for better management of the current pandemic as well as the possible re-emergence of novel variants. The sequence of the original strain Wuhan-Hu-1 and approximately 20 representatives of each variant were downloaded from GenBank and GISAID. Two representatives with no track of un-definitive nucleotides were selected. The sequences were aligned using Muscle. The location of insertion/deletion (indel) in the genome was mapped following the open reading frame (ORF) of Wuhan-Hu-1. Amino acid substitutions in all ORFs were analysed separately. Evolutionary analysis was inferred using maximum likelihood. There are two indel sites in ORF1AB, eight in spike, and one each in ORF3A, Matrix (MA), Nucleoprotein (NP), and the 3’-untranslated regions (3’UTR). Some indel sites are not unique, and some are variant specific. There are 10 residues shared by the Omicron, BA2, and GKA lineages. Three deletions in NP are unique to Omicron and BA.2; two substitutions in ORF1AB, four in spike, three in NP, and two in ORF7A and ORF8 were exclusive to the Delta and GPA clades. Delta, Omicron, and BA.2 share the same single residue spike. Three insertions in spike are unique for Omicron and GKA. Phylogenetic analysis shows that the Omicron, BA.2, and GKA clades share a common cluster that emerged from Delta. In conclusion, whole-genome comparison reveals indels and polymorphic amino acids specific to variants or sub-variants. We propose that the GKA clade is an Omicron subvariant. Finally, the higher transmissibility of BA.2 might be attributed to a 48-nucleotide deletion in the 3’UTR.

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Section: Discussionmentioning

confidence: 99%

Whole-genome comparison of representatives of all variants of SARS-CoV-2, including subvariant BA.2 and the GKA clade

Suardana

Mahardika

Pharmawati

et al. 2022

Preprint

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“…Zika sequencing was able to confirm the origin and spread of the virus in the Americas with a Brazilian origin of the virus that spread through the Americas [ 27 ] and that the Caribbean was the main source of Zika in Miami, particularly from cruise ships [ 28 ]; and sequencing also revealed that the causal agent of severe respiratory illness and acute flaccid myelitis in some children in Spain in 2016 was enterovirus D68 [ 29 ]. In the case of SARS-CoV-2, it is clear that sequencing is required for continuous surveillance, for studying nosocomial or community outbreaks such as those in nursing homes or among health care workers, for confirming reinfection after a long period of negative PCR detection, identifying new variants with different transmission capabilities such as vaccine escape mutants, drug resistance genomes or viral dynamics in a chronically (long-COVID) infected patient [ 8 , 30 , 31 , 32 , 33 , 34 ]. For example, NGS application for viral surveillance was able to describe, at the beginning of the first wave of SARS-CoV-2 infection ( Figure 1 ), the predominance of the variant B.1.5 (51%) in our geographic area of Barcelona until May 2020, when variant B.1.1 (33%) significantly increased, coinciding with the start of de-escalation.…”

Section: Ngs For Confronting the Devastating Effects Of A Pandemicmentioning

confidence: 99%

“…However, the end of the lockdown (June–July 2020) and opening of summer activities coincided with the detection of variant B.1.177, which became the predominant lineage during the entire second wave until the end of 2020. At the beginning of 2021, B.1.1.7 (Alpha variant) gradually replaced B.1.177 and became dominant during the late third (55.44%) and early fourth (86.00%) waves, until original B.1.617.2 (Delta variant) and related sub-lineages (AY.xx numbered) entered our population, completely replacing the other variants to comprise almost 100% of all sequenced samples by July 2021 [ 8 ]. At this point, a new VOC named Omicron has promptly emerged and is putting world health systems in check again [ 35 ] due to its higher transmissibility and probably higher resistance to current COVID-19 vaccines.…”

Section: Ngs For Confronting the Devastating Effects Of A Pandemicmentioning

confidence: 99%

“…Other ways to describe NGS include deep-sequencing, massive parallel sequencing, high-throughput sequencing, all equally valid, to differentiate it from Sanger sequencing. During the current SARS-CoV-2 pandemic, NGS technologies have allowed for the development in record time (months) of highly effective vaccines based on mRNA/DNA [ 6 ], the development of qualitative and quantitative diagnostic solutions [ 7 ], and the identification of variants and relevant mutations in continuous surveillance [ 8 ], especially of variants with evidence of mutations impacting transmissibility, severity and/or immunity, known as variants of concern (VOC), and of their dominance and spread throughout the world [ 9 ]. Early detection of VOC is important because any delayed or null identification of circulating viral agents calls into question the efficacy of a health system in preventing and responding efficiently to viral infections [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

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Next-Generation Sequencing for Confronting Virus Pandemics

Quer

Colomer-Castell

Campos

et al. 2022

Viruses

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Virus pandemics have happened, are happening and will happen again. In recent decades, the rate of zoonotic viral spillover into humans has accelerated, mirroring the expansion of our global footprint and travel network, including the expansion of viral vectors and the destruction of natural spaces, bringing humans closer to wild animals. Once viral cross-species transmission to humans occurs, transmission cannot be stopped by cement walls but by developing barriers based on knowledge that can prevent or reduce the effects of any pandemic. Controlling a local transmission affecting few individuals is more efficient that confronting a community outbreak in which infections cannot be traced. Genetic detection, identification, and characterization of infectious agents using next-generation sequencing (NGS) has been proven to be a powerful tool allowing for the development of fast PCR-based molecular assays, the rapid development of vaccines based on mRNA and DNA, the identification of outbreaks, transmission dynamics and spill-over events, the detection of new variants and treatment of vaccine resistance mutations, the development of direct-acting antiviral drugs, the discovery of relevant minority variants to improve knowledge of the viral life cycle, strengths and weaknesses, the potential for becoming dominant to take appropriate preventive measures, and the discovery of new routes of viral transmission.

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“…Two years after the onset of the coronavirus disease (COVID-19) pandemic, the clinical, laboratory, and imaging features of patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have been widely described[1–5]. The wide clinical spectrum of COVID-19 became obvious during the first wave, and although the effect of inoculum size should be considered [6, 7], variation has been mainly attributed to host factors, as variants of concern only appeared later [8][9]. The analysis of the first wave has obvious advantages for the identification of host factors and their biomarkers.…”

Section: Introductionmentioning

confidence: 99%

Exposing Limitations of Clinical Laboratory Tests in COVID-19 and the Promise of Immunological Biomarkers

Sánchez-Montalvà

Álvarez‐Sierra

Martínez-Gallo

et al. 2022

Preprint

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BackgroundAlmost two years since the onset of the COVID-19 pandemic no predictive algorithm has been generally adopted, nor new tests identified to improve the prediction and management of SARS-CoV-2 infection.MethodsRetrospective observational analysis of the predictive performance of clinical parameters and laboratory tests in hospitalised patients with COVID-19. Outcomes were 28-day survival and maximal severity in a cohort of 1,579 patients and two validation cohorts of 598 and 434 patients. A pilot study conducted in a patient subgroup measured 17 cytokines and 27 lymphocyte phenotypes to explore additional predictive laboratory tests.Findings1) Despite a strong association of 22 clinical and laboratory variables with the outcomes, their joint prediction power was limited due to redundancy. 2) Eight variables: age, comorbidity index, oxygen saturation to fraction of inspired oxygen ratio, neutrophil-lymphocyte ratio, C- reactive protein, aspartate aminotransferase/alanine aminotransferase ratio, fibrinogen, and glomerular filtration rate captured most of the statistical predictive power. 3) The interpretation of clinical and laboratory variables was improved by grouping them in categories. 4) Age and organ damage-related tests were the best predictors of survival, and inflammatory-related tests were the best predictors of severity. 5) The pilot study identified several immunological tests (including chemokine ligand 10, chemokine ligand 2, and interleukin 1 receptor antagonist), that performed better than currently used tests.ConclusionsCurrently used tests for clinical management of COVID-19 patients are of limited value due to redundancy, as all measure aspects of two major processes: inflammation, and organ damage. There are no independent predictors based on the quality of the nascent adaptive immune response. Understanding the limitations of current tests would improve their interpretation and simplify clinical management protocols. A systematic search for better biomarkers is urgent and feasible.

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A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain)

Cited by 20 publications

References 41 publications

Whole-genome comparison of representatives of all variants of SARS-CoV-2, including subvariant BA.2 and the GKA clade

Whole-genome comparison of representatives of all variants of SARS-CoV-2, including subvariant BA.2 and the GKA clade

Next-Generation Sequencing for Confronting Virus Pandemics

Exposing Limitations of Clinical Laboratory Tests in COVID-19 and the Promise of Immunological Biomarkers

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