Molecular detection of SARS-CoV-2 being challenged by virus variation and asymptomatic infection

Jiang, Congshan; Li, Xiaowei; Ge, Changrong; Ding, Yuanyuan; Zhang, Tao; Cao, Shuai; Meng, Liesu; Lu, Shemin

doi:10.1016/j.jpha.2021.03.006

Cited by 21 publications

(22 citation statements)

References 88 publications

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“…The SARS-CoV-2 genome size is significant and amounts to 29.99 kb [9]. Its organization is similar to that of other CoVs and consists mainly of open reading frames (ORF).…”

Section: General Characteristics Of Sars-cov-2 Infectionmentioning

confidence: 99%

“…Overall, the genome of the current epidemic SARS-CoV-2 virus has undergone significant changes compared to the reference genome obtained in January 2020. The most significant mutations that significantly alter virulence and pathogenicity occur in the Sprotein [9]. Harmful variations in nsp12, in the N-protein, were also described [55,56].…”

Section: General Characteristics Of Sars-cov-2 Infectionmentioning

confidence: 99%

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SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19

Gusev

Sarapultsev

Соломатина

et al. 2022

IJMS

181

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The review aims to consolidate research findings on the molecular mechanisms and virulence and pathogenicity characteristics of coronavirus disease (COVID-19) causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and their relevance to four typical stages in the development of acute viral infection. These four stages are invasion; primary blockade of antiviral innate immunity; engagement of the virus’s protection mechanisms against the factors of adaptive immunity; and acute, long-term complications of COVID-19. The invasion stage entails the recognition of the spike protein (S) of SARS-CoV-2 target cell receptors, namely, the main receptor (angiotensin-converting enzyme 2, ACE2), its coreceptors, and potential alternative receptors. The presence of a diverse repertoire of receptors allows SARS-CoV-2 to infect various types of cells, including those not expressing ACE2. During the second stage, the majority of the polyfunctional structural, non-structural, and extra proteins SARS-CoV-2 synthesizes in infected cells are involved in the primary blockage of antiviral innate immunity. A high degree of redundancy and systemic action characterizing these pathogenic factors allows SARS-CoV-2 to overcome antiviral mechanisms at the initial stages of invasion. The third stage includes passive and active protection of the virus from factors of adaptive immunity, overcoming of the barrier function at the focus of inflammation, and generalization of SARS-CoV-2 in the body. The fourth stage is associated with the deployment of variants of acute and long-term complications of COVID-19. SARS-CoV-2’s ability to induce autoimmune and autoinflammatory pathways of tissue invasion and development of both immunosuppressive and hyperergic mechanisms of systemic inflammation is critical at this stage of infection.

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“…The SARS-CoV-2 genome size is significant and amounts to 29.99 kb [9]. Its organization is similar to that of other CoVs and consists mainly of open reading frames (ORF).…”

Section: General Characteristics Of Sars-cov-2 Infectionmentioning

confidence: 99%

Section: General Characteristics Of Sars-cov-2 Infectionmentioning

confidence: 99%

SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19

Gusev

Sarapultsev

Соломатина

et al. 2022

IJMS

181

View full text Add to dashboard Cite

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“…Asymptomatic patients are the carriers of the live, replicating virus and contribute to the unknown viral transmission and spread. In some cases, the methods used for SARS-CoV-2 detection in these subjects can be less sensitive than in the symptomatic ones [109,122,123]. It is worth noting that only a limited number of studies reviewed here have considered the asymptomatic population [70,76].…”

Section: Asymptomatic Infection and The Spread Of New Sars-cov-2 Variantsmentioning

confidence: 99%

“…In addition to asymptomatic infection, SARS-CoV-2 variants are another challenge for virus detection [123,124]. In fact, new variants caused by mutations in the genome of the SARS-CoV-2 are now emerging as the virus spreads throughout the world, and this is of great relevance considering that such mutations may alter various aspects of virus biology such as pathogenicity, infectivity, transmissibility, and/or antigenicity [125].…”

Section: Asymptomatic Infection and The Spread Of New Sars-cov-2 Variantsmentioning

confidence: 99%

MALDI MS-Based Investigations for SARS-CoV-2 Detection

Preianò

Correnti

Pelaia

et al. 2021

BioChem

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The urgent need to fight the COVID-19 pandemic has impressively stimulated the efforts of the international scientific community, providing an extraordinary wealth of studies. After the sequence of the virus became available in early January 2020, safe and effective vaccines were developed in a time frame much shorter than everybody expected. However, additional studies are required since viral mutations have the potential of facilitating viral transmission, thus reducing the efficacy of developed vaccines. Therefore, improving the current laboratory testing methods and developing new rapid and reliable diagnostic approaches might be useful in managing contact tracing in the fight against both the original SARS-CoV-2 strain and the new, potentially fast-spreading CoV-2 variants. Mass Spectrometry (MS)-based testing methods are being explored, with the challenging promise to overcome the many limitations arising from currently used laboratory testing assays. More specifically, MALDI-MS, since its advent in the mid 1980s, has demonstrated without any doubt the great potential to overcome many unresolved analytical challenges, becoming an effective proteomic tool in several applications, including pathogen identification. With the aim of highlighting the challenges and opportunities that derive from MALDI-based approaches for the detection of SARS-CoV-2 and its variants, we extensively examined the most promising proofs of concept for MALDI studies related to the COVID-19 outbreak.

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“…Efficient and accurate diagnosis of COVID-19 is crucial for controlling the pandemic in early time. Reverse transcription polymerase chain reaction (RT-PCR) technology is the most widely used among the common diagnostic methods ( 6 ). Mutations at the probe or primer sites could have effects on the accuracy of diagnosis, such as loss of primer efficacy.…”

Section: Introductionmentioning

confidence: 99%

VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes

Sun

Shu

Shi

et al. 2021

Nucleic Acids Research

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The genomic variations of SARS-CoV-2 continue to emerge and spread worldwide. Some mutant strains show increased transmissibility and virulence, which may cause reduced protection provided by vaccines. Thus, it is necessary to continuously monitor and analyze the genomic variations of SARS-COV-2 genomes. We established an evaluation and prewarning system, SARS-CoV-2 variations evaluation and prewarning system (VarEPS), including known and virtual mutations of SARS-CoV-2 genomes to achieve rapid evaluation of the risks posed by mutant strains. From the perspective of genomics and structural biology, the database comprehensively analyzes the effects of known variations and virtual variations on physicochemical properties, translation efficiency, secondary structure, and binding capacity of ACE2 and neutralizing antibodies. An AI-based algorithm was used to verify the effectiveness of these genomics and structural biology characteristic quantities for risk prediction. This classifier could be further used to group viral strains by their transmissibility and affinity to neutralizing antibodies. This unique resource makes it possible to quickly evaluate the variation risks of key sites, and guide the research and development of vaccines and drugs. The database is freely accessible at www.nmdc.cn/ncovn.

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Molecular detection of SARS-CoV-2 being challenged by virus variation and asymptomatic infection

Cited by 21 publications

References 88 publications

SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19

SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19

MALDI MS-Based Investigations for SARS-CoV-2 Detection

VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes

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