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Article
Genetics & Heredity
Alvin X. Han et al.
Summary: The first step in SARS-CoV-2 genomic surveillance is testing, but testing rates are declining globally and remain low in low- and middle-income countries. Simulations showed that low testing rates and spatiotemporal biases delay detection of new variants and lead to unreliable estimates of variant prevalence. Increase in wider access to diagnostics can enable timely detection and reliable estimation of variant prevalence, improving the performance of global SARS-CoV-2 genomic surveillance programs.
Article
Immunology
K. L. Brown et al.
Summary: Mutations in the SARS-CoV-2 genome can have various effects on diagnostic tests, including negative impacts, no effects, or opportunities for screening variants. By combining sequence surveillance and computed PCR efficiencies, we identified a primer-template mismatch specific to the Omicron variant, allowing for its rapid identification. This experience highlights the importance of monitoring sequences, predicting the impact of mismatches, utilizing mismatches as surrogate markers, and adapting diagnostic tests for evolving pathogens.
EMERGING MICROBES & INFECTIONS
(2023)
Article
Virology
Pia Laine et al.
Summary: While most spontaneous mutations in the viral genome have no consequences, some can affect diagnostic tests. A variant strain found in Southern Finland in February 2021 showed mutations in the N gene that led to negative results in PCR tests. This variant belongs to the B.1.1.318 Pango lineage and differs from the Beta variant in certain aspects.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Multidisciplinary Sciences
Kenrie P. Y. Hui et al.
Summary: SARS-CoV-2 variants pose a threat to global public health. The Omicron variant replicates faster in bronchi but less efficiently in the lung parenchyma compared to other variants. All variants of concern have similar cellular tropism.
Article
Multidisciplinary Sciences
Huseyin Tombuloglu et al.
Summary: This study describes a fast and accurate multiplex SARS-CoV-2 RT-PCR detection method that can simultaneously detect viral genes and a human gene, with high sensitivity and specificity. It can be used as a diagnostic tool for SARS-CoV-2 in medical institutions and for research purposes.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Karrie K. K. Ko et al.
Summary: This study reveals a previously unreported mutation in the N gene of SARS-CoV-2, which may render certain commercial tests unable to accurately detect the virus, highlighting the importance of real-time surveillance of viral variants.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Mohammad Alkhatib et al.
Summary: This study reports a case of an Italian male infected with Delta sublineage AY.4 carrying an atypical deletion that causes N gene target failure. The importance of performing SARS-CoV-2 sequencing and characterizing new mutations/deletions that could affect the interpretation of molecular diagnostic tests is underscored.
Article
Multidisciplinary Sciences
Marciela M. DeGrace et al.
Summary: The SAVE program is a real-time risk assessment initiative established by the National Institute of Allergy and Infectious Diseases to address the public health threat posed by the emergence of SARS-CoV-2 variants. Its goal is to evaluate the potential impact of these variants on transmission, virulence, and immunity induced through infection or vaccination.
Review
Genetics & Heredity
Mari E. K. Niemi et al.
Summary: In this article, the authors discuss how large-scale genomics studies are helping us to better understand the impact of host genetics on COVID-19 susceptibility and severity. These studies have identified genomic regions associated with the disease and provided insights into its pathology and potential therapeutic opportunities. The findings have implications for genetic risk prediction, drug repurposing, and understanding the long-term consequences of SARS-CoV-2 infection.
NATURE REVIEWS GENETICS
(2022)
Review
Virology
Veronica Roxana Flores-Vega et al.
Summary: This review discusses the mutations of SARS-CoV-2 that contribute to the emergence of new viral variants, their impact on viral spread, disease severity, and immune evasion. It also highlights the virus classification systems used by various organizations and provides an overview of the timeline of variant emergence and spike protein mutations related to immune evasion.
Article
Multidisciplinary Sciences
Sandra Isabel et al.
Summary: The emergence of a mutation in the N gene of SARS-CoV-2 has led to dropouts in molecular detection assays. This mutation has been found in multiple Canadian provinces and is present in different variants of interest and concern. However, the lack of publicly available primer/probe sequences hampers the detection and tracking of diagnostic escape mutations.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Chiara Ippoliti et al.
Summary: PCR assay is an effective method for rapid detection of the Omicron variant in respiratory tract samples. By targeting specific mutations in the nucleocapsid (N) gene region, the assay can accurately identify the Omicron variant.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Walid Hossain et al.
Summary: The study aimed to reduce the run time of multiplex RT-PCR for detecting SARS CoV-2 N1 and N2 sequences and human RNase P (RP) sequence. By optimizing the Fast PCR protocol and comparing it with conventional PCR, the researchers found that Fast PCR significantly shortened the run time while yielding comparable results to conventional PCR.
Review
Engineering, Biomedical
Nestor Jonguitud-Borrego et al.
Summary: The COVID-19 pandemic is a global challenge, and automation testing is crucial for high-throughput screening and efficient diagnosis. Case studies in China, Spain, and the UK have proven the effectiveness of automation in mass testing.
FRONTIERS IN MEDICAL TECHNOLOGY
(2022)
Article
Medicine, General & Internal
Manuela Colosimo et al.
Summary: The clinical presentation of COVID-19 is non-specific, therefore an accurate diagnostic method is needed to limit the spread of the SARS-CoV-2 virus. This study tested 500 nasopharyngeal swab specimens using two different methods, Allplex(TM) 2019-nCoV assay and TaqPath(TM) COVID-19 kit, and found that both methods accurately confirmed the diagnosis of SARS-CoV-2 infection. Despite its semi-automated workflow, TaqPath(TM) COVID-19 did not introduce bias and supported the identification of variants of concern.
Letter
Microbiology
Mohammad Rubayet Hasan et al.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Review
Multidisciplinary Sciences
Juan Li et al.
Summary: Since the emergence of COVID-19 in Wuhan in 2019, the world has faced a devastating pandemic with millions of cases and fatalities. This article provides insights into the spread and genetic variations of the SARS-CoV-2 virus, emphasizes the importance of genomic surveillance, and highlights the international transmission of major variants identified late in 2020.
Article
Virology
Jessika Cristina Chagas Lesbon et al.
Summary: The article highlights the evolution of the COVID-19 virus and the potential impact on RT-PCR testing accuracy, identifying gene mutations that affect N gene detection and emphasizing the importance of continuous monitoring of genetic mutations to ensure diagnostic effectiveness.
Article
Virology
Sanghoo Lee et al.
Summary: Commercially available reverse transcription-polymerase chain reaction (RT-PCR) kits are widely used for diagnosing SARS-CoV-2 infection, but lack extensive clinical evaluation due to the urgency of the COVID-19 pandemic. A novel insertion/deletion mutation in the nucleocapsid (N) gene of SARS-CoV-2 samples was found to cause negative results in a commonly used assay, highlighting genetic variability and rapid evolution of the virus.
Article
Biochemistry & Molecular Biology
Olga A. Postnikova et al.
Summary: The SARS-CoV-2 Spike glycoprotein has acquired a unique insert sequence that could affect virus spread and infection mechanisms, prompting further investigation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Julianne R. Brown et al.
Summary: This study evaluated the impact of four different RTqPCR master mixes on the performance of SARS-CoV-2 diagnostic PCRs, with assay C consistently detecting the lowest quantity of partial N gene RNA transcript. The Takara One Step PrimeScriptTM III RT-PCR Kit mastermix enabled all primer pairs to detect the entire dynamic range, indicating potential options for SARS-CoV-2 diagnosis.
JOURNAL OF VIROLOGICAL METHODS
(2021)
Article
Multidisciplinary Sciences
Minkyung Baek et al.
Summary: Through the three-track network, we achieved accuracies approaching those of DeepMind in CASP14, enabling rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and providing insights into the functions of proteins with currently unknown structure.
Article
Virology
Aine O'Toole et al.
Summary: The global virus genomics community has responded unprecedentedly to the SARS-CoV-2 pandemic, leading to significant advances in 'real-time' generation and sharing of genomic data. The development of new analytical methods, such as pangolin, has been necessary to handle the rapid growth in virus genome data production. Pangolin has processed nearly two million virus genomes, aiding in SARS-CoV-2 genomic epidemiology and providing researchers with valuable information about the pandemic's transmission lineages.
Letter
Biochemistry & Molecular Biology
Kristian G. Andersen et al.
Review
Immunology
Andrew G. Harrison et al.
TRENDS IN IMMUNOLOGY
(2020)
