An overview of viral mutagenesis and the impact on pathogenesis of SARS-CoV-2 variants

Khan, Muhammad Zafar; Nazli, Adila; Al-furas, Hawaa; Asad, Muhammad; Ajmal, Iqra; Khan, Dildar; Shah, Jaffer; Farooq, Muhammad Asad; Jiang, Shou-xiang Kinor

doi:10.3389/fimmu.2022.1034444

Cited by 14 publications

(10 citation statements)

References 182 publications

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“…However, a bigger sample size is warranted to fully comprehend the significance of sex with mutation frequencies for SARS-CoV-2. Notably, the rate of viral mutations also depends on community characteristics like sex, age [ 25 ], ethnicities [ 26 ], and host genetic variabilities [ 27 , 28 ]. Furthermore, the different types of selective pressures determine the types of mutations to occur.…”

Section: Discussionmentioning

confidence: 99%

Unravelling the link between SARS-CoV-2 mutation frequencies, patient comorbidities, and structural dynamics

Azzeri,

Mohamed,

Wan Rosli

et al. 2024

PLoS ONE

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Genomic surveillance is crucial for tracking emergence and spread of novel variants of pathogens, such as SARS-CoV-2, to inform public health interventions and to enforce control measures. However, in some settings especially in low- and middle- income counties, where sequencing platforms are limited, only certain patients get to be selected for sequencing surveillance. Here, we show that patients with multiple comorbidities potentially harbour SARS-CoV-2 with higher mutation rates and thus deserve more attention for genomic surveillance. The relationship between the patient comorbidities, and type of amino acid mutations was assessed. Correlation analysis showed that there was a significant tendency for mutations to occur within the ORF1a region for patients with higher number of comorbidities. Frequency analysis of the amino acid substitution within ORF1a showed that nsp3 P822L of the PLpro protease was one of the highest occurring mutations. Using molecular dynamics, we simulated that the P822L mutation in PLpro represents a system with lower Root Mean Square Deviation (RMSD) fluctuations, and consistent Radius of gyration (Rg), Solvent Accessible Surface Area (SASA) values—indicate a much stabler protein than the wildtype. The outcome of this study will help determine the relationship between the clinical status of a patient and the mutations of the infecting SARS-CoV-2 virus.

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Section: Discussionmentioning

confidence: 99%

Unravelling the link between SARS-CoV-2 mutation frequencies, patient comorbidities, and structural dynamics

Azzeri,

Mohamed,

Wan Rosli

et al. 2024

PLoS ONE

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“…SARS-CoV-2 variants arise from the well-recognized virus mutation process [8][9][10][11][12][82][83][84]. Millions of random mutations are thrust out into the world population and its various people groups.…”

Section: Structure-function and Other Aspects Of Variant Age Dependencementioning

confidence: 99%

Age Profiles for SARS-CoV-2 Variants in England and Wales and States of the USA (2020 to 2022): Impact on All-Cause Mor-Tality

Jones¹,

Ponomarenko²

2023

Preprint

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Since 2020 COVID-19 has caused serious mortality around the world. Given the ambiguity in es-tablishing COVID-19 as the direct cause of death we first investigate the effects of age and sex upon all-cause mortality during 2020 and 2021 in England and Wales. Since infectious agents have their own unique age profile for death, we explore several methods to adjust single year of age deaths in England and Wales during 2019 (the pre-COVID-19 base year) to a pathogen-neutral single year of age baseline. This adjusted base year is then used to confirm the widely reported higher deaths in males for most ages above 43 years in both 2020 and 2021. During 2020 (+ COVID-19 but no vac-cination) both male and female population-adjusted deaths were significantly increased above age 35. A significant reduction in all-cause mortality among both males and females aged 75+ could be demonstrated in 2021 during widespread COVID–19 vaccination, however, below age 75 deaths progressively increased. This finding arises from a mix of vaccination and year of age profiles of deaths for the different SARS-CoV-2 variants. In addition, specific effects for age around puberty were demonstrated where females had higher deaths rather than males. There is evidence that year-of-birth cohorts may also be involved, indicating that immune priming to specific pathogen outbreaks in the past may lead to lower deaths for some birth cohorts. To specifically identify the age profile for the COVID-19 variants in 2020 to 2023, we employ the proportion of total deaths at each age which are potentially due to or ‘with’ COVID-19. The original Wuhan strain, and the Alpha variant show somewhat limited divergence in the age profile with the Alpha variant shifted to a moderately higher proportion of deaths below age 84. The Delta variant specifically targeted persons below age 65. The Omicron variants showed significantly lower proportion of overall mortality, with markedly higher relative proportion of deaths above age 65 steeply increasing with age to a maximum around 100 years of age. A similar age profile for the variants can be seen in the age-banded deaths in US states – although slightly obscured by using age bands rather than single year of age. However, the US data shows that higher male deaths are greatly dependent on age and the COVID-variant. Deaths determined as ‘due to’ COVID-19 (as opposed to ‘involving’ COVID-19) in England and Wales were especially over-estimated in 2021 relative to the change in all-cause mortality. This arose as a by-product of an increase in COVID-19 testing capacity in late 2020. Potential structure-function mechanisms for the year of age specificity of SARS-CoV-2 var-iants are discussed. The question is posed as to whether vaccines based on different variants carry the specific age profile through into the vaccine.

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“…This receptor is predominantly found in the epithelial cell membranes of the lungs, mucosa, and small intestines. Person-to-person virus transmission relies on aerosol droplets released from an infected individual ( 53 ).…”

Section: Probiotic Research Against Infectious Disease Covid-19 In Mi...mentioning

confidence: 99%

Overview of anti-viral effects of probiotics via immune cells in pre-, mid- and post-SARS-CoV2 era

Kanauchi,

Low,

Jounai

et al. 2023

Front. Immunol.

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The COVID-19 outbreak has caused significant global changes and increased public awareness of SARS-CoV-2. Substantial progress in developing vaccines, enhancing sanitation practices, and implementing various measures to combat the virus, including the utilization of probiotics has been made. This comprehensive review examined the medical impact of clinically proven probiotics on infectious diseases, considering three crucial time periods: before (pre-), during (mid-), and after (post-) COVID-19 pandemic era. This review also showed a perspective on the use of probiotics to stimulate the innate immune system and prevent infectious diseases. In pre-COVID-19 era, several probiotic strains were found to be clinically effective in addressing gastrointestinal infectious diseases, the common cold and flu. However, the mechanism by which probiotics exerted their antiviral effects remained relatively unclear during that period. Nevertheless, probiotics, Lactococcus lactis strain Plasma (LC-Plasma), and others have gained attention for their unique ability to modulate the immune system and demonstrate antiviral properties. While some probiotics have shown promise in alleviating gastrointestinal symptoms linked to COVID-19, their direct effectiveness in treating or preventing COVID-19 progression has not yet been conclusively established. As we transition into the post-COVID-19 era, the relationship between COVID-19 and plasmacytoid dendritic cells (pDCs), a vital component of the innate immune system, has been gradually elucidated. These findings are now being applied in developing novel vaccines and treatments involving interferons and in immune activation research using probiotics as adjuvants, comparable to CpG-DNA through TLR9. The role of the local innate immune system, including pDCs, as the first line of defense against viral infections has gained increasing interest. Moving forward, insight of the immune system and the crosstalk between probiotics and the innate immune system is expected to highlight the role of probiotics in adjunctive immunoregulatory therapy. In combination with drug treatments, probiotics may play a more substantial role in enhancing immune responses. The immunoregulatory approach using probiotics such as LC-Plasma, which can induce anti-infectious factors such as interferons, holds promise as a viable therapeutic and prophylactic option against viral infectious diseases due to their good safety profile and protective efficacy.

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An overview of viral mutagenesis and the impact on pathogenesis of SARS-CoV-2 variants

Cited by 14 publications

References 182 publications

Unravelling the link between SARS-CoV-2 mutation frequencies, patient comorbidities, and structural dynamics

Unravelling the link between SARS-CoV-2 mutation frequencies, patient comorbidities, and structural dynamics

Age Profiles for SARS-CoV-2 Variants in England and Wales and States of the USA (2020 to 2022): Impact on All-Cause Mor-Tality

Overview of anti-viral effects of probiotics via immune cells in pre-, mid- and post-SARS-CoV2 era

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