Microbiological and Clinical Findings of SARS-CoV-2 Infection after 2 Years of Pandemic: From Lung to Gut Microbiota

Abstract

Early recognition and prompt management are crucial for improving survival in COVID-19 patients, and after 2 years of the pandemic, many efforts have been made to obtain an early diagnosis. A key factor is the use of fast microbiological techniques, considering also that COVID-19 patients may show no peculiar signs and symptoms that may differentiate COVID-19 from other infective or non-infective diseases. These techniques were developed to promptly identify SARS-CoV-2 infection and to prevent viral spread and transmission. However, recent data about clinical, radiological and laboratory features of COVID-19 at time of hospitalization could help physicians in early suspicion of SARS-CoV-2 infection and distinguishing it from other etiologies. The knowledge of clinical features and microbiological techniques will be crucial in the next years when the endemic circulation of SARS-CoV-2 will be probably associated with clusters of infection. In this review we provide a state of the art about new advances in microbiological and clinical findings of SARS-CoV-2 infection in hospitalized patients with a focus on pulmonary and extrapulmonary characteristics, including the role of gut microbiota.

The Spread of SARS-CoV-2 Omicron Variant in CALABRIA: A Spatio-Temporal Report of Viral Genome Evolution

“…These data are in agreement with previous reports showing a higher frequency of mutations in N protein compared to M in the Omicron variant compared to variants such as Alpha, Gamma, and Delta [ 51 , 52 , 53 ]. It is of note that N genomic region along with the S gene is widely used in clinical practice to diagnose SARS-CoV-2 positivity [ 54 ].…”

Molecular Characterization and Cluster Analysis of SARS-CoV-2 Viral Isolates in Kahramanmaraş City, Turkey: The Delta VOC Wave within One Month

“…In our cohort, diagnosis was performed using the gold standard method, RT-PCR, despite several methods that were developed to detect SARS-CoV-2 RNA in respiratory and saliva specimens [ 7 ]. To diagnose COVID-19 infections, the U.S. Food and Drug Administration (FDA) authorized many commercial tests, each of which has its own accuracy (specificity and sensitivity), usually stated by manufacturers [ 7 , 33 ]. We used the Bio-Speedy kit with a 98% sensitivity, as its performance agrees with other molecular assays, such as the Panther Fusion SARS-CoV-2 with a 98.3% accuracy [ 33 ].…”

“…The median Ct value for Delta infections was 23, significantly lower than wild-type N genes (Ct 36) [ 13 ]. On the other hand, the performance of antigenic assays is lower compared to the gold standard [ 7 ]. The Ellume antigenic test, performed on nasal swab, and the Innova rapid lateral flow COVID-19 test, carried out on nasal or throat samples, correctly identified 96% of individuals with COVID-19 symptoms and 95% of participants with high viral loads, respectively [ 33 ].…”

“…In June 2021, the capacity to diagnose SARS-CoV-2 infection by real-time reverse transcription–polymerase chain reaction (RT-PCR) was expanded to all 81 provinces, increasing the number of laboratories able to perform molecular tests to 482 [ 5 ]. Real-time RT-PCR carried out by nasopharyngeal/oropharyngeal swab is considered the gold standard to detect SARS-CoV-2 RNA and to provide quantitative information using the cycle threshold (Ct) values of the viral load [ 7 ].…”

The three facets of the SARS-CoV-2 pandemic during the first two waves in the northern, central, and southern Italy

“…Inclusion criteria were as follows: 1) age ≥ 18 years; 2) positive SARS-CoV-2 real-time polymerase chain reaction (RT-PCR) assay on nasal and pharyngeal swabs; 3) need for hospitalization for COVID-19; and 4) admission during first or second pandemic waves in the temporal range between February 1, 2020 and January 31, 2021. [21] , [22] Death and/or ICU transfer were defined as composite outcome.

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