Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April–December 2021 in Italy

Lai, Alessia; Bergna, Annalisa; Ventura, Carla Della; Menzo, Stefano; Bruzzone, Bianca; Sagradi, Fabio; Ceccherini‐Silberstein, Francesca; Weisz, Alessandro; Clementi, Nicola; Brindicci, Gaetano; Vicenti, Ilaria; Sasset, Lolita; Caucci, Sara; Corvaro, Benedetta; Ippoliti, S.; Acciarri, Carla; Pace, Vanessa De; Lanfranchi, Leonardo; Bellocchi, Maria Concetta; Giurato, Giorgio; Ferrarese, Roberto; Lagioia, Antonella; Francisci, Daniela; Colombo, Martina; Lazzarin, Samuel; Ogliastro, Matilde; Cappelletti, Maria Rosa; Iannetta, Marco; Rizzo, Francesca; Torti, Carlo; Fumi, Maurizio; d’Avenia, Morena; Brusa, Stefano; Greco, Francesca; Menchise, Angela; Letizia, Vittoria; Vaccaro, E; Santoro, Carmen Rita; Fraccalvieri, Chiara; Testa, Sophie; Carioti, Luca; Rocco, Teresa; Saracino, Annalisa; Cattelan, Anna María; Clementi, Massimo; Sarmati, Loredana; Riva, Agostino; Galli, Massimo; Antinori, Spinello; Zehender, Gianguglielmo

doi:10.3390/v14112508

Cited by 13 publications

(15 citation statements)

References 28 publications

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“…Next generation sequencing (NGS) has been pivotal for understanding the impact of SARS-CoV-2 variants on transmission, pathogenicity, disease severity, vaccine and therapy efficacy, and diagnostic detection (1). For instance, the Omicron variant has been shown to evade the immune response in patients previously infected with SARS-CoV-2 or vaccinated against SARS-CoV-2 (2)(3)(4)(5), render the majority of monoclonal antibody therapies ineffective (4), and cause more infections in younger patients compared to other variants (6). Conversely, the Omicron variant was associated with a lower 28-day mortality, ICU admission rate, and oxygen requirements compared to Delta (7).…”

Section: Introductionmentioning

confidence: 99%

NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges

Tartaninan

Mulroney

Poselenzny

et al. 2023

Front. Public Health

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Identification of SARS-CoV-2 lineages has shown to provide invaluable information regarding treatment efficacy, viral transmissibility, disease severity, and immune evasion. These benefits provide institutions with an expectation of high informational upside with little insight in regards to practicality with implementation and execution of such high complexity testing in the midst of a pandemic. This article details our institution’s experience implementing and using Next Generation Sequencing (NGS) to monitor SARS-CoV-2 lineages in the northern Chicagoland area throughout the pandemic. To date, we have sequenced nearly 7,000 previously known SARS-CoV-2 positive samples from various patient populations (e.g., outpatient, inpatient, and outreach sites) to reduce bias in sampling. As a result, our hospital was guided while making crucial decisions about staffing, masking, and other infection control measures during the pandemic. While beneficial, establishing this NGS procedure was challenging, with countless considerations at every stage of assay development and validation. Reduced staffing prompted transition from a manual to automated high throughput workflow, requiring further validation, lab space, and instrumentation. Data management and IT security were additional considerations that delayed implementation and dictated our bioinformatic capabilities. Taken together, our experience highlights the obstacles and triumphs of SARS-CoV-2 sequencing.

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Section: Introductionmentioning

confidence: 99%

NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges

Tartaninan

Mulroney

Poselenzny

et al. 2023

Front. Public Health

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“…For example, in Belgium, selection criteria for sequencing may include factors such as the severity of the infection. The results of the frequencies using the Belgian GISAID data of the variants in the population follow the same trend as has been observed in other studies that were based on either GISAID data or clinical samples at the same period (Beesley et al, 2023; Belgian Sequencing Consortium, 2022; Lai et al, 2022) (Figure 1).…”

Section: Resultsmentioning

confidence: 99%

Development of a reverse transcriptase digital droplet polymerase chain reaction‐based approach for SARS‐CoV‐2 variant surveillance in wastewater

Van Poelvoorde,

Gobbo,

Nauwelaerts

et al. 2024

Water Environment Research

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An urgent need for effective surveillance strategies arose due to the global emergence of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Although vaccines and antivirals are available, concerns persist about the evolution of new variants with potentially increased infectivity, transmissibility, and immune evasion. Therefore, variant monitoring is crucial for public health decision‐making. Wastewater‐based surveillance has proven to be an effective tool to monitor SARS‐CoV‐2 variants within populations. Specific SARS‐CoV‐2 variants are detected and quantified in wastewater in this study using a reverse transcriptase digital droplet polymerase chain reaction (RT‐ddPCR) approach. The 11 designed assays were first validated in silico using a substantial dataset of high‐quality SARS‐CoV‐2 genomes to ensure comprehensive variant coverage. The assessment of the sensitivity and specificity with reference material showed the capability of the developed assays to reliably identify target mutations while minimizing false positives and false negatives. The applicability of the assays was evaluated using wastewater samples from a wastewater treatment plant in Ghent, Belgium. The quantification of the specific mutations linked to the variants of concern present in these samples was calculated using these assays based on the detection of single mutations, which confirms their use for real‐world variant surveillance. In conclusion, this study provides an adaptable protocol to monitor SARS‐CoV‐2 variants in wastewater with high sensitivity and specificity. Its potential for broader application in other viral surveillance contexts highlights its added value for rapid response to emerging infectious diseases.Practitioner Points Robust RT‐ddPCR methodology for specific SARS‐CoV‐2 variants of concern detection in wastewater. Rigorous validation that demonstrates high sensitivity and specificity. Demonstration of real‐world applicability using wastewater samples. Valuable tool for rapid response to emerging infectious diseases.

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“…Besides, the epidemic periodical reports on SARS‐CoV‐2 variant dissemination in Italy and the data from the SCIRE collaborative study (which tracked SARS‐CoV‐2 variants in Italy) suggest that the Alfa variant (B.1.1.7 and B.1.1.7+E484K) was unequivocally preeminent from January to June 2021, while the Delta variant (B.1.617.2) became predominant from July to December 2021. Other minor circulating strains were the Beta variant (B.1.351) and the Gamma variant (P.1) 30–32 …”

Section: Discussionmentioning

confidence: 99%

Clinical efficacy of the first two doses of anti‐SARS‐CoV‐2 mRNA vaccines in solid cancer patients

et al. 2023

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Introduction Cancer patients are frail individuals, thus the prevention of SARS‐CoV‐2 infection is essential. To date, vaccination is the most effective tool to prevent COVID‐19. In a previous study, we evaluated the immunogenicity of two doses of mRNA‐based vaccines (BNT162b2 or mRNA‐1273) in solid cancer patients. We found that seroconversion rate in cancer patients without a previous exposure to SARS‐CoV‐2 was lower than in healthy controls (66.7% vs. 95%, p = 0.0020). The present study aimed to evaluate the clinical efficacy of the vaccination in the same population. Methods This is a single‐institution, prospective observational study. Data were collected through a predefined questionnaire through phone call in the period between the second and third vaccine dose. The primary objective was to describe the clinical efficacy of the vaccination, defined as the percentage of vaccinated subjects who did not develop symptomatic COVID‐19 within 6 months after the second dose. The secondary objective was to describe the clinical features of patients who developed COVID‐19. Results From January to June 2021, 195 cancer patients were enrolled. Considering that 7 (3.59%) patients tested positive for SARS‐CoV‐2 and 5 developed symptomatic disease, the clinical efficacy of the vaccination was 97.4%. COVID‐19 disease in most patients was mild and managed at home; only one hospitalization was recorded and no patient required hospitalization in the intensive care unit. Discussion Our study suggests that increasing vaccination coverage, including booster doses, could improve the prevention of infection, hospitalization, serious illness, and death in the frail population of cancer patients.

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Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April–December 2021 in Italy

Cited by 13 publications

References 28 publications

NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges

NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges

Development of a reverse transcriptase digital droplet polymerase chain reaction‐based approach for SARS‐CoV‐2 variant surveillance in wastewater

Clinical efficacy of the first two doses of anti‐SARS‐CoV‐2 mRNA vaccines in solid cancer patients

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