Dynamics of nasopharyngeal tract phageome and association with disease severity and age of patients during three waves of COVID‐19

Ferravante, Carlo; Arslan-Gatz, Berin S; Dell’Annunziata, Federica; Palumbo, Domenico; Lamberti, Jessica; Alexandrova, Elena; Rosa, Domenico Di; Strianese, Oriana; Giordano, Alessandro M.; Palo, Luigi; Giurato, Giorgio; Salzano, Francesco Antonio; Galdiero, Massimiliano; Weisz, Alessandro; Franci, Gianluigi; Rizzo, Francesca; Folliero, Veronica

doi:10.1002/jmv.27998

Cited by 3 publications

(2 citation statements)

References 31 publications

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“…Moreover, there was a large group of patients whose severity was unknown (N = 34); and (5) the study did not enroll any uninfected healthy controls, which would have made it possible to make interesting comparisons (Table S1) [ 67 ]. Another more recent work from the same authors used metagenomic sequencing to study the phageome of SARS-CoV-2 positive subjects with different disease severities, and observed a very high abundance of the bacteriophage families Siphoviridae and Myoviridae as well as some evidence suggesting that age and disease severity could be associated with the bacteriophage abundance in COVID-19 patients (Table S1) [ 70 ]. Unfortunately, this study did not include any uninfected healthy controls to compare with and, as the experimental design is mostly shared with the previously discussed work also from Ferravante and colleagues (Table S1) [ 67 ], both approaches share the same already commented limitations.…”

Section: Changes In the Nasopharyngeal Microbiota Of Sars-cov-2-infec...mentioning

confidence: 99%

“…Since it has already been described that the distinct SARS-CoV-2 variants of concern are able to elicit distinct responses in the host [ 79 , 80 ], it would not be surprising if these variants could differentially alter the nasopharyngeal microbiota. This is a particularly relevant issue to consider here, as some of these studies even state that their samples come from three different COVID-19 waves and from patients with different disease severities (Table S1) [ 66 , 67 , 70 ], which makes it very likely that they may be infected by distinct variants of the virus and, therefore, the results from the different patients enrolled in these studies would not be comparable.…”

Section: Changes In the Nasopharyngeal Microbiota Of Sars-cov-2-infec...mentioning

confidence: 99%

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The nasopharyngeal microbiome in COVID-19

Candel

Tyrkalska

Álvarez-Santacruz

et al. 2023

Emerging Microbes & Infections

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The development of novel culture-independent techniques of microbial identification has allowed a rapid progress in the knowledge of the nasopharyngeal microbiota and its role in health and disease. Thus, it has been demonstrated that the nasopharyngeal microbiota defends the host from invading pathogens that enter the body through the upper airways by participating in the modulation of innate and adaptive immune responses. The current COVID-19 pandemic has created an urgent need for fast-track research, especially to identify and characterize biomarkers to predict the disease severity and outcome. Since the nasopharyngeal microbiota diversity and composition could potentially be used as a prognosis biomarker for COVID-19 patients, which would pave the way for strategies aiming to reduce the disease severity by modifying such microbiota, dozens of research articles have already explored the possible associations between changes in the nasopharyngeal microbiota and the severity or outcome of COVID-19 patients. Unfortunately, results are controversial, as many studies with apparently similar experimental designs have reported contradictory data. Herein we put together, compare, and discuss all the relevant results on this issue reported to date. Even more interesting, we discuss in detail which are the limitations of these studies, that probably are the main sources of the high variability observed. Therefore, this work is useful not only for people interested in current knowledge about the relationship between the nasopharyngeal microbiota and COVID-19, but also for researchers who want to go further in this field while avoiding the limitations and variability of previous works.

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Section: Changes In the Nasopharyngeal Microbiota Of Sars-cov-2-infec...mentioning

confidence: 99%

Section: Changes In the Nasopharyngeal Microbiota Of Sars-cov-2-infec...mentioning

confidence: 99%

The nasopharyngeal microbiome in COVID-19

Candel

Tyrkalska

Álvarez-Santacruz

et al. 2023

Emerging Microbes & Infections

View full text Add to dashboard Cite

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Dynamics of nasopharyngeal tract phageome and association with disease severity and age of patients during three waves of COVID‐19

Ferravante

Arslan-Gatz

Dell’Annunziata

et al. 2022

Journal of Medical Virology

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In December 2019, several patients were hospitalized and diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection, which subsequently led to a global pandemic. To date, there are no studies evaluating the relationship between the respiratory phageome and the SARS‐CoV‐2 infection. The current study investigated the phageome profiles in the nasopharyngeal swabs collected from 55 patients during the three different waves of coronavirus disease 2019 (COVID‐19) in the Campania Region (Southern Italy). Data obtained from the taxonomic profiling show that phage families belonging to the order Caudovirales have a high abundance in the patient samples. Moreover, the severity of the COVID‐19 infection seems to be correlated with the phage abundance.

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Influence of Mycobiota in the Nasopharyngeal Tract of COVID-19 Patients

Folliero,

Ferravante,

Dell’Annunziata

et al. 2024

Microorganisms

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The nasopharyngeal tract contains a complex microbial community essential to maintaining host homeostasis. Recent studies have shown that SARS-CoV-2 infection changes the microbial composition of the nasopharynx. Still, little is known about how it affects the fungal microbiome, which could provide valuable insights into disease pathogenesis. Nasopharyngeal swabs were collected from 55 patients, during three distinct COVID-19 waves that occurred in the Campania Region (southern Italy). An RNA-seq-based analysis was performed to evaluate changes in mycobiota diversity, showing variations depending on the disease’s severity and the sample collection wave. The phyla Basidiomycota and Ascomycota were shown to have higher abundance in patients with severe symptoms. Furthermore, the diversity of the fungal population was greater in the second wave. Conclusion: According to our research, COVID-19 induces significant dysbiosis of the fungal microbiome, which may contribute to disease pathogenesis, and understanding its underlying mechanisms could contribute to developing effective treatments.

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Dynamics of nasopharyngeal tract phageome and association with disease severity and age of patients during three waves of COVID‐19

Cited by 3 publications

References 31 publications

The nasopharyngeal microbiome in COVID-19

The nasopharyngeal microbiome in COVID-19

Dynamics of nasopharyngeal tract phageome and association with disease severity and age of patients during three waves of COVID‐19

Influence of Mycobiota in the Nasopharyngeal Tract of COVID-19 Patients

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