Selection of Ideal Reference Genes for Gene Expression Analysis in COVID-19 and Mucormycosis

Kumar, Sunil; Ahmad, Ayaan; Kushwaha, Namrata; Shokeen, Niti; Negi, Sheetal; Gautam, Kamini; Singh, Anup; Tiwari, Punit; Garg, Rakesh; Agarwal, Richa; Trikha, Anjan; Thakar, Alok; Saini, Vikram

doi:10.1128/spectrum.01656-22

Cited by 9 publications

(7 citation statements)

References 59 publications

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“…Second, both host factors (previous infection history) and viral factors (different SARS-CoV-2 variants) may have had a significant impact on the dynamics of viral load, which in turn may have influenced the effectiveness of nasal irrigation [5]. In addition, considering the significant variations in Ct values that are commonly observed across COVID-19 patient groups, it would be important to adjust our results by the corresponding content of the house keeping gene [36]. Another important consideration with respect to the measurement of SARS-CoV-2 viral RNA is the discrimination between infectious and inactivated viral particles so as to decrease false-positive result rates.…”

Section: Discussionmentioning

confidence: 99%

A Hypertonic Seawater Nasal Irrigation Solution Containing Algal and Herbal Natural Ingredients Reduces Viral Load and SARS-CoV-2 Detection Time in the Nasal Cavity

Pantazopoulos

Chalkias

Miziou

et al. 2023

JPM

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Nasal irrigation is thought to decrease the viral load present in the nasal cavity. Our aim was to assess the effect of a hypertonic seawater solution [with algal and herbal natural ingredients (Sinomarin®)] on the viral load of nasopharynx in patients hospitalized with severe COVID-19 pneumonia. We conducted a prospective, randomized, controlled trial from June 2022 to December 2022. We allocated 56 patients with COVID-19 pneumonia into two groups (28 in each group)—the hypertonic seawater group [nasal irrigations with a hypertonic seawater solution (Sinomarin®) every 4 h for 16 h per day, for two consecutive days] and the control group (no nasal irrigations). A second nasopharyngeal swab was collected 48 h after the baseline nasopharyngeal swab (8 h after the last wash in the hypertonic seawater group) to estimate the SARS-CoV-2 viral load as determined by cycle threshold (Ct) values. In the hypertonic seawater group, the mean Ct values significantly increased two days after the initial measurement [ΔCt 48−0 h = 3.86 ± 3.03 cycles, p < 0.001 (95%CI: 2.69 to 5.04)]. No significant differences in the Ct values were observed in the control group [ΔCt 48−0 h = −0.14 ± 4.29, p = 0.866 (95%CI: −1.80 to −1.52)]. At follow-up, 17 patients from the hypertonic seawater group had negative test results compared to only 9 patients from the control group (p = 0.03). Nasal irrigations with a hypertonic seawater solution containing algal and herbal natural ingredients significantly decreased nasopharyngeal viral load and the detection time of SARS-CoV-2 in the nasal cavity.

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Section: Discussionmentioning

confidence: 99%

A Hypertonic Seawater Nasal Irrigation Solution Containing Algal and Herbal Natural Ingredients Reduces Viral Load and SARS-CoV-2 Detection Time in the Nasal Cavity

Pantazopoulos

Chalkias

Miziou

et al. 2023

JPM

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“…CYP belongs to the immunophilin family and has peptidyl-prolyl cis - trans isomerase (PPIase) activity, which catalyzes the cis - trans isomerization process of proline residues. CypA demonstrated the most consistent expression irrespective of disease severity and emerged as the most suitable reference gene in COVID−19 and CAM [ 56 ].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Candidate Reference Genes for Gene Expression Analysis in Wild Lamiophlomis rotata

Wang

Qian

Geng

et al. 2023

Genes

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Lamiophlomis rotata (Benth.) Kudo is a perennial and unique medicinal plant of the Qinghai–Tibet Plateau. It has the effects of diminishing inflammation, activating blood circulation, removing blood stasis, reducing swelling, and relieving pain. However, thus far, reliable reference gene identifications have not been reported in wild L. rotata. In this study, we identified suitable reference genes for the analysis of gene expression related to the medicinal compound synthesis in wild L. rotata subjected to five different-altitude habitats. Based on the RNA-Seq data of wild L. rotata from five different regions, the stability of 15 candidate internal reference genes was analyzed using geNorm, NormFinder, BestKeeper, and RefFinder. TFIIS, EF-1α, and CYP22 were the most suitable internal reference genes in the leaves of L. rotata from different regions, while OBP, TFIIS, and CYP22 were the optimal reference genes in the roots of L. rotata. The reference genes identified here would be very useful for gene expression studies with different tissues in L. rotata from different habitats.

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“…One notable example is the identification of DPP9, which is correlated with an elevated risk of developing severe illness due to COVID-19. [15] In addition, a recent study recognized interleukin 10 receptor subunit beta (IL10RB) as the primary candidate gene target for COVID-19 susceptibility. This study revealed an essential link between IL10RB, infection, and outcomes, highlighting it as the most promising candidate gene for further in-depth investigation.…”

Section: Genetic Factors Influencing Susceptibility To Covid-19mentioning

confidence: 99%

“…One notable example is the identification of DPP9 , which is correlated with an elevated risk of developing severe illness due to COVID-19. [15]…”

Section: Genetic Factors Influencing Susceptibility To Covid-19mentioning

confidence: 99%

Genetic Basis for Mucormycosis Progression in COVID-19 Patients: From Susceptibility to Severity

Muruganantham,

Veerabathiran

2024

Infect Dis Immun

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The dynamics of COVID-19 and mucormycosis reveal a complex interplay of genetic factors that influence the susceptibility, severity, and immune responses. COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), exhibits an increased incidence of mucormycosis, particularly in individuals with comorbidities or corticosteroid therapy. Mucormycosis is a fungal infection that affects the sinuses, orbits, and lungs and demands timely intervention with antifungal medications and surgery because of its life-threatening nature. Research on the genetic underpinnings of this intersection has unveiled key insights into the pathogenicity of Mucorales. Breakthroughs in genetic tools have exposed virulence factors, such as the CotH protein family and high-affinity iron-uptake mechanisms. Genetic susceptibility is a pivotal element in identifying individuals at risk of developing COVID-19, facilitating early detection, and allowing for personalized treatment strategies. DPP9, MIF, and TYK2 are among the genes implicated in COVID-19 severity, emphasizing the intricate relationship between genetic makeup and viral response. The genetic landscape extends to viral entry mechanisms, thereby affecting infection efficiency. Specific polymorphisms in genes such as IFNAR2, OAS3, and TYK2 are associated with COVID-19 severity, indicating shared genetic bases between severe and hospitalized cases. Mucormycosis is genetically predisposed, particularly in immunocompromised individuals. The challenge lies in understanding the genetic factors influencing susceptibility and offering insights into pathogenesis and potential therapeutic avenues. Organ transplantation adds another layer, increasing susceptibility to infections such as COVID-19 and mucormycosis. The impact of immunosuppression on COVID-19 severity remains elusive, necessitating ongoing research on the immunological mechanisms. Despite the challenges posed by emerging SARS-CoV-2 variants, the intricate connection between genetic factors and the interplay of COVID-19 and mucormycosis presents an opportunity for personalized treatment, targeted interventions, and refined public health strategies.

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Selection of Ideal Reference Genes for Gene Expression Analysis in COVID-19 and Mucormycosis

Abstract: Gene expression studies are critical to develop new diagnostics, therapeutics, and prognostic modalities. However, accurate determination of expression requires data normalization with a reference gene, whose expression does not vary across different disease stages.

Cited by 9 publications

References 59 publications

A Hypertonic Seawater Nasal Irrigation Solution Containing Algal and Herbal Natural Ingredients Reduces Viral Load and SARS-CoV-2 Detection Time in the Nasal Cavity

A Hypertonic Seawater Nasal Irrigation Solution Containing Algal and Herbal Natural Ingredients Reduces Viral Load and SARS-CoV-2 Detection Time in the Nasal Cavity

Evaluation of Candidate Reference Genes for Gene Expression Analysis in Wild Lamiophlomis rotata

Genetic Basis for Mucormycosis Progression in COVID-19 Patients: From Susceptibility to Severity

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