Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy

Equestre, Michele; Marcantonio, Cinzia; Marascio, Nadia; Centofanti, Federica; Martina, Antonio; Simeoni, Matteo; Suffredini, Elisabetta; La Rosa, Giuseppina; Bonanno Ferraro, Giusy; Mancini, Pamela; Veneri, Carolina; Matera, Giovanni; Quirino, Angela; Costantino, Angela; Taffon, Stefania; Tritarelli, Elena; Campanella, Carmelo; Pisani, Giulio; Nisini, Roberto; Spada, Enea; Verde, Paola; Ciccaglione, Anna Rita; Bruni, Roberto

doi:10.3390/microorganisms11112711

Cited by 3 publications

(1 citation statement)

References 81 publications

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“…Regional analysis of SARS-CoV-2 variants and their impact on the number of cases has been carried out before [33]; concerning the Italian case, there was a thorough analysis of the incidence during the first 2 years of the pandemic [34] and also some analysis regarding the relative incidence of Delta and Omicron subvariants [35,36]. However, we went on making a direct comparison with European data in order to understand how local data mirror the wide-scale dynamics of the epidemic.…”

Section: Discussionmentioning

confidence: 99%

Surfing the Waves of SARS-CoV-2: Analysis of Viral Genome Variants Using an NGS Survey in Verona, Italy

Tonon,

Cecchetto,

Diani

et al. 2024

Microorganisms

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The availability of new technologies for deep sequencing, including next-generation sequencing (NGS), allows for the detection of viral genome variations. The epidemiological determination of SARS-CoV-2 viral genome changes during the pandemic waves displayed the genome evolution and subsequent onset of variants over time. These variants were often associated with a different impact on viral transmission and disease severity. We investigated, in a retrospective study, the trend of SARS-CoV-2-positive samples collected from the start of the Italian pandemic (January 2020) to June 2023. In addition, viral RNAs extracted from 938 nasopharyngeal swab samples were analyzed using NGS between February 2022 and June 2023. Sequences were analyzed with bioinformatic tools to identify lineages and mutations and for phylogenetic studies. Six pandemic waves were detected. In our samples, we predominantly detected BA.2, BQ.1, BA.5.1, BA.5.2, and, more recently, XBB.1 and its subvariants. The data describe the SARS-CoV-2 genome evolution involved in viral interactions with the host and the dynamics of specific genome mutations and deletions.

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Section: Discussionmentioning

confidence: 99%

Surfing the Waves of SARS-CoV-2: Analysis of Viral Genome Variants Using an NGS Survey in Verona, Italy

Tonon,

Cecchetto,

Diani

et al. 2024

Microorganisms

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Wastewater sequencing from a rural community enables identification of widespread adaptive mutations in a SARS-CoV-2 Alpha variant

Conway,

Novay,

Pusch

et al. 2024

Preprint

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Background: Central Michigan University (CMU) participated in a state-wide wastewater monitoring program starting in 2021. One rural site consistently produced higher concentrations of SARS-CoV-2 genome copies. Samples from this site were sequenced retrospectively and exclusively contained a derivative of Alpha variant lineage B.1.1.7 that shed from the same site for 20-28 months. Results: Complete reconstruction of each SARS-CoV-2 open reading frame (ORF) and alignment to an early B.1.1.7 clinical isolate identified novel mutations that were selected in non-structural (nsp1, nsp2, nsp3, nsp4, nsp5/3CLpro, nsp6, RdRp, nsp15, nsp16, ORF3a, ORF6, ORF7a, and ORF7b) and structural genes (Spike, M, and N). These were rare mutations that have not accumulated in clinical samples worldwide. Mutational analysis revealed divergence from the reference Alpha variant lineage sequence over time. We present each of the mutations on available structural models and discuss the potential role of these mutations during a chronic infection. Conclusions: This study further supports that small wastewater treatment plants can enhance resolution of rare events and facilitate reconstruction of viral genomes due to the relative lack of contaminating sequences and identifies mutations that may be associated with chronic infections.

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Prevalence of Enteric Pathogens and Antibiotic Resistance: Results of a Six-Year Active Surveillance Study on Patients Admitted to a Teaching Hospital

Marascio,

Pavia,

Brescia

et al. 2024

Antibiotics

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Background: Acute Infectious Diarrhea (AID) and the short- and long-term complications associated with it are major causes of hospitalization worldwide. In Italy, due to a lack of robust surveillance programs, only limited data has been collected on their prevalence and circulation. This study aims to evaluate the resistance pattern of enteric pathogens and their epidemiological trends over a six-year period. Methods: This cross-sectional retrospective study was conducted from January 2018 to December 2023. Stool samples were analyzed during routine diagnosis with culture methods, syndromic molecular tests, and enzyme immunoassay. Results: Bacteria were the most isolated enteric pathogens (62.2%), followed by fungi (29.0%), viruses (8.2%), and parasites (0.6%). Most bacteria were isolated from outpatients (29.5%) and from patients in the Oncology ward (26.2%). The most prevalent target was EPEC (11.1%), followed by C. difficile toxin A/B-producing strains (8.3%), C. jejuni (2.5%), and S. enterica, (1%.). Norovirus and Candida spp. were the most prevalent in pediatric patients (6.5% and 39.6%, respectively). In the last years, enteric pathogens have been a frequent cause of infections characterized by a problematic resistance to common antimicrobials. In our study, S. enterica showed resistance to amikacin, gentamicin, ampicillin, levofloxacin, and ciprofloxacin. C. jejuni was susceptible to all tested drugs. Conclusion: Timely notification of gastroenteric infections is crucial in identifying potential outbreak sources and ensuring strict adherence to food safety and hygiene practices, so as to protect the most vulnerable populations. The present study offers insights into the epidemiological characteristics and the antibiotic susceptibility of the main enteric AID pathogens in order to implement infection control measures in health care settings.

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Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy

Cited by 3 publications

References 81 publications

Surfing the Waves of SARS-CoV-2: Analysis of Viral Genome Variants Using an NGS Survey in Verona, Italy

Surfing the Waves of SARS-CoV-2: Analysis of Viral Genome Variants Using an NGS Survey in Verona, Italy

Wastewater sequencing from a rural community enables identification of widespread adaptive mutations in a SARS-CoV-2 Alpha variant

Prevalence of Enteric Pathogens and Antibiotic Resistance: Results of a Six-Year Active Surveillance Study on Patients Admitted to a Teaching Hospital

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