4.5 Article

The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection

Related references

Note: Only part of the references are listed.
Article Infectious Diseases

Reduced risk of hospitalisation among reported COVID-19 cases infected with the SARS-CoV-2 Omicron BA.1 variant compared with the Delta variant, Norway, December 2021 to January 2022

Lamprini Veneti et al.

Summary: A study found that the Omicron variant of COVID-19 has a 73% reduced risk of hospitalization compared to the Delta variant. Omicron cases who had received two doses of the vaccine 7-179 days before diagnosis had a lower risk compared to Delta (66% vs 93%), while those who received three doses had a similar risk reduction (86% vs 88%).

EUROSURVEILLANCE (2022)

Article Medicine, General & Internal

Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study

Nicole Wolter et al.

Summary: According to data analysis from South Africa, individuals infected with the omicron variant have a lower likelihood of hospitalization compared to those infected with non-omicron variants. Furthermore, individuals infected with the omicron variant have a lower odds of severe disease compared to individuals infected with the earlier delta variant.

LANCET (2022)

Article Infectious Diseases

Decreased severity of disease during the first global omicron variant covid-19 outbreak in a large hospital in tshwane, south africa

F. Abdullah et al.

Summary: This study analyzed the clinical data of COVID-19 patients admitted to a hospital in Tshwane during the Omicron wave, and found that the severity of the disease was decreased compared to previous waves, with lower death rates and ICU admissions.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2022)

Article Microbiology

Analysis of SARS-CoV-2 in Nasopharyngeal Samples from Patients with COVID-19 Illustrates Population Variation and Diverse Phenotypes, Placing the Growth Properties of Variants of Concern in Context with Other Lineages

Tessa Prince et al.

Summary: New variants of SARS-CoV-2 are continuously emerging. Understanding virus evolution and selection pressures requires considering population dynamics and new variants.

MSPHERE (2022)

Article Biology

Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers

Xiaofeng Dong et al.

Summary: The transcription strategy of SARS-CoV-2 for viral subgenomic mRNAs (sgmRNAs) plays a crucial role in nucleic acid diagnostics. LeTRS, a bioinformatics tool, has been developed to identify leader-TRS junctions and quantify sgmRNAs, providing insights into virus biology. LeTRS has been tested on different species and shown to have implications for transmission models and nucleic acid-based diagnostics.

GIGASCIENCE (2022)

Article Biochemistry & Molecular Biology

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Erik Volz et al.

Summary: The study suggests a positive selection for the SARS-CoV-2 spike protein variant D614G in the UK, but no evidence of differences in COVID-19 mortality or clinical severity in patients infected with this variant. 614G is associated with higher viral load and younger age of patients compared to 614D.
Article Virology

Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution

Jeremy Ratcliff et al.

Summary: Members of the APOBEC family exhibit antiviral activities in mammalian cells through lethal editing of the genomes of various viruses, including RNA viruses like coronaviruses. APOBEC-like C-*U transitions are significantly overrepresented in the SARS-CoV-2 genome sequences during the COVID-19 pandemic, which may leave evolutionary imprints on coronavirus genomes. This process may lead to homoplasy and amino acid sequence changes in viral proteins, potentially explaining global depletion of C and excess of U bases in human seasonal coronavirus genomes.

VIROLOGY (2021)

Article Immunology

SARS-CoV-2 nsp12 attenuates type I interferon production by inhibiting IRF3 nuclear translocation

Wenjing Wang et al.

Summary: The study found that SARS-CoV-2 nsp12 suppresses host antiviral responses by attenuating specific IFN promoter activation and impacting the function of IRF3. These findings provide new insights into the viral pathogenesis.

CELLULAR & MOLECULAR IMMUNOLOGY (2021)

Article Multidisciplinary Sciences

Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A

Kris M. White et al.

Summary: The study revealed that plitidepsin possesses potent antiviral activity against SARS-CoV-2, more effective than the approved drug remdesivir. By inhibiting the eukaryotic translation elongation factor 1A, plitidepsin can significantly reduce viral replication of SARS-CoV-2 in the lungs of mice, making it a promising candidate for COVID-19 treatment.

SCIENCE (2021)

Article Multidisciplinary Sciences

SARS-CoV-2 within-host diversity and transmission

Katrina A. Lythgoe et al.

Summary: The study found that SARS-CoV-2 infections in clinical samples in the UK are characterized by low levels of within-host diversity and a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with shared diversity not persisting.

SCIENCE (2021)

Article Multidisciplinary Sciences

Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes

Chadi M. Saad-Roy et al.

Summary: Given vaccine dose shortages and logistical challenges, various deployment strategies are being proposed to increase population immunity levels to SARS-CoV-2. While focusing on one dose may decrease infections in the short term, the long-term outcomes depend on the relative immune robustness of this approach. Under conditions of partial population immunity, a one-dose policy may increase the potential for antigenic evolution.

SCIENCE (2021)

Article Multidisciplinary Sciences

Comparison of rhesus and cynomolgus macaques as an infection model for COVID-19

Francisco J. Salguero et al.

Summary: This study demonstrates that SARS-CoV-2 replicates in the upper and lower respiratory tract of both rhesus and cynomolgus macaques, causing pulmonary lesions. Immune responses against SARS-CoV-2 are similar in both species, suggesting that both macaque species authentically represent mild to moderate forms of COVID-19. The findings provide valuable insights for evaluating interventions against SARS-CoV-2.

NATURE COMMUNICATIONS (2021)

Article Medicine, General & Internal

Growth, reproduction numbers and factors affecting the spread of SARS-CoV-2 novel variants of concern in the UK from October 2020 to July 2021: a modelling analysis

Thomas Ward et al.

Summary: This study analyzed the transmission patterns of new variants of SARS-CoV-2 in England from October 2020 to July 2021, taking into account different age groups, geographic locations, and ethnicities. The B.1.617.2 variant showed a clear transmission advantage over the B.1.1.7 variant, with exponential growth observed in all age groups. Early interventions were effective in reducing the growth of the B.1.617.2 variant in specific ethnic groups.

BMJ OPEN (2021)

Article Immunology

Resistance of SARS-CoV-2 variants to neutralization by convalescent plasma from early COVID-19 outbreak in Singapore

Bei Wang et al.

Summary: The rapid spread of SARS-CoV-2 variants B.1.1.7 from the UK and B.1.351 from South Africa has led to a second wave of COVID-19 cases globally. Antibody-mediated neutralization activity was reduced for B.1.1.7 and significantly attenuated for B.1.351, cautioning against solely relying on RBD mutations to evaluate vaccine efficacy. The study highlights the need for new SARS-CoV-2 vaccines not solely based on the ancestral Spike gene sequence.

NPJ VACCINES (2021)

Review Biotechnology & Applied Microbiology

SARS-CoV-2 one year on: evidence for ongoing viral adaptation

Thomas P. Peacock et al.

Summary: SARS-CoV-2 virus is believed to have originated from animals and can cause a range of outcomes in humans, from asymptomatic cases to COVID-19. Over a year into the pandemic, the virus continues to mutate, driven by factors such as single nucleotide polymorphisms and insertions/deletions, which may impact its transmissibility and pathogenicity.

JOURNAL OF GENERAL VIROLOGY (2021)

Article Genetics & Heredity

Phylogenomics and population genomics of SARS- CoV-2 in Mexico during the pre- vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms

Francisco Barona-Gomez et al.

Summary: Understanding the genetic patterns of SARS-CoV-2 in Mexico, including concerning mutations and imported variants, provides a baseline for tracking these during the vaccination stage. Population genetic analysis revealed differences between symptomatic and asymptomatic carriers, highlighting the roles of spike and nucleocapsid proteins in the virus's adaptive evolution.

MICROBIAL GENOMICS (2021)

Article Multidisciplinary Sciences

SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts

Rafail Nikolaos Tasakis et al.

Summary: This study explores the evolution, key mutations, and features of the SARS-CoV-2 genome in the United States, and found many accumulating Single Nucleotide Variations (SNVs) in the virus genome throughout 2020 and early 2021. The results suggest that viral genomes are dynamically evolving over time, with periods of mutational bursts and unabated mutation accumulation. The high level of existing variation, especially in the Spike-encoding region, may become problematic during super-spreader events, driving rare mutations to prominence.

PLOS ONE (2021)

Article Multidisciplinary Sciences

Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

Moritz U. G. Kraemer et al.

Summary: Understanding the spatial invasion dynamics of the B.1.1.7 lineage, researchers found a multistage process with early growth rates linked to human mobility and asymmetric lineage export from dominant source locations. Additionally, they explored how the spread of B.1.1.7 was influenced by nonpharmaceutical interventions and spatial variation in previous attack rates. The study emphasizes the importance of considering behavioral and epidemiological contexts in accurately interpreting the growth rates of emerging variants of concern.

SCIENCE (2021)

Article Multidisciplinary Sciences

Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant

Sten Ilmjaerv et al.

Summary: The combination of G614 and L323 mutations in the Spike protein of SARS-CoV-2 creates a viral G/L variant that has replaced the initial D/P variant, with P323L mutation being crucial for the current variant's epidemiological success. While there is no significant correlation between COVID-19 mortality rates in different countries and the prevalence of Wuhan versus G/L variants, the G/L variant demonstrates major epidemiological supremacy over the original variant in terms of speed of emergence and ultimate predominance in individual countries.

SCIENTIFIC REPORTS (2021)

Article Virology

A Founder Effect Led Early SARS-CoV-2 Transmission in Spain

Francisco Diez-Fuertes et al.

Summary: Whole-genome analysis of SARS-CoV-2 identified five large clades worldwide that emerged in 2019 and 2020. Spain had 62 independent introductions of the virus, with 19B being the most prevalent in the early stages, later replaced by G614-bearing viruses. The G614 variant showed enhanced infectivity, suggesting a fitness advantage and potential driving force for the variant shift observed in Spain.

JOURNAL OF VIROLOGY (2021)

Article Multidisciplinary Sciences

Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform

Tran Thi Nhu Thao et al.

NATURE (2020)

Article Biochemistry & Molecular Biology

Syncytia formation by SARS-CoV-2-infected cells

Julian Buchrieser et al.

EMBO JOURNAL (2020)

Article Biochemistry & Molecular Biology

Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders

Alberto Gomez-Carballa et al.

GENOME RESEARCH (2020)

Article Biochemistry & Molecular Biology

Crowding and the shape of COVID-19 epidemics

Benjamin Rader et al.

NATURE MEDICINE (2020)

Article Multidisciplinary Sciences

Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations

Hsin-Chou Yang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo

Yixuan J. Hou et al.

SCIENCE (2020)

Article Genetics & Heredity

Genomic characterization of a novel SARS-CoV-2

Rozhgar A. Khailany et al.

GENE REPORTS (2020)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Multidisciplinary Sciences

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

Michiru Nishita et al.

SCIENTIFIC REPORTS (2017)

Article Computer Science, Interdisciplinary Applications

Fitting Linear Mixed-Effects Models Using lme4

Douglas Bates et al.

JOURNAL OF STATISTICAL SOFTWARE (2015)

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

Article Biotechnology & Applied Microbiology

Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity

Stuart D. Dowall et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)