Circulating SARS-CoV-2 variants in Italy, October 2020–March 2021

Lai, Alessia; Bergna, Annalisa; Menzo, Stefano; Zehender, Gianguglielmo; Caucci, Sara; Ghisetti, Valeria; Rizzo, Francesca; Maggi, Fabrizio; Cerutti, F.; Giurato, Giorgio; Weisz, Alessandro; Turchi, Chiara; Bruzzone, Bianca; Silberstein, Francesca Ceccherini; Clementi, Nicola; Callegaro, Annapaola; Sagradi, Fabio; Francisci, Daniela; Rullo, Emmanuele Venanzi; Vicenti, Ilaria; Clementi, Massimo; Galli, Massimo; Balotta, Claudia; Gori, María; Bagnarelli, Patrizia; Baj, Andreina; Novazzi, Federica; Orsi, Andrea; Caligiuri, Patrizia; Boccotti, Simona; Bellocchi, Maria Concetta; Sarmati, Loredana; Andreoni, Massimo; Mancini, Nicasio; Criscuolo, Elena; Gallitelli, Rosa; Testa, Sophie; Dragoni, Filippo; Zazzi, Maurizio

doi:10.1186/s12985-021-01638-5

Cited by 40 publications

(56 citation statements)

References 12 publications

(8 reference statements)

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“…Data obtained in Italy (October 2020 -March 2021) show that the introduction of the UK Alpha variant, corresponded to the second relevant increase of infections registered in Italy during the second epidemic wave [39], when the Military field hospital of Aosta was built [40].…”

Section: Discussionmentioning

confidence: 99%

Prevention Procedures to Contain COVID-19 Contagion in the First Italian Army Field Hospital

Ciccotti¹,

Pagliaro²,

Peluso³

et al. 2021

IJSSE

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The COVID-19 outbreak in Italy saturated the public hospitals' intensive care units in March 2020. The Ministry of Health asked for the Military Health Unit's intervention to deal with the emergency. The first COVID-19 Army field hospital in the world was thus built in Piacenza, Italy, to address the emergency. We describe the architecture of the hospital and the preventive measures adopted to reduce COVID-19 contagion among the medical personnel. The hospital project with the "H" shape divides the "dirty path" of entry for operators and patients from the "clean path" of exit for operators. Hypochloritebased and alcohol-based solutions were used for personal protective equipment (PPE) decontamination before reuse. Although exposed to 50 confirmed COVID-19 patients, all primary care personnel tested negative to COVID-19, before the operation, 14 days after the first patient and 30 days after the closure of the military field hospital. Due to the reported discomfort and its potential toxicity, the hypochlorite-based disinfection method was substituted with alcohol-based disinfection solution, which displayed comparable effective results. The results of the present study pave the way for the creation of a protocol for future validation in larger studies aimed at providing guidelines in emergency conditions.

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Section: Discussionmentioning

confidence: 99%

Prevention Procedures to Contain COVID-19 Contagion in the First Italian Army Field Hospital

Ciccotti¹,

Pagliaro²,

Peluso³

et al. 2021

IJSSE

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“…Therefore, OSs individuals were likely to be carriers of G clade and its descendents GR and GV, considering their predominance in Italy during the second part of 2020. In particular, since we included samples from November 2020, it is likely that these samples mostly carried the GV clade, which rapidly spread throughout the country and reached a frequency of 96% in December 2020 [ 6 , 8 ]. OSs and αV groups were found to be almost similar in terms of age and gender composition.…”

Section: Discussionmentioning

confidence: 99%

“…To date, several viral strains have been reported. In Italy, the predominant clades from September 2020 to January 2021 were represented by GISAID clade G (lineage B.1, Nextstrain clade 20A) and related clades GR (lineage B.1.1.1, Nextstrain clade 20B and lineage C, Nextstrain clade 20D) and GV (lineage B.1.177, Nextstrain clade 20E, EU1) [ 6 , 7 , 8 ]. Moreover, different Variants Of Concerns (VOCs) occurred, with the alpha variant (αV) (lineage B.1.1.7, GISAID clade GRY, Nextstrain clade 20I/501.Y.V1) and the beta variant (lineage B.1.351, GISAID clade GH, Nextstrain clade 20H/501.Y.V2) being the most relevant for public safety [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

Age and Sex Modulate SARS-CoV-2 Viral Load Kinetics: A Longitudinal Analysis of 1735 Subjects

Caputo

Termine

Fabrizio

et al. 2021

JPM

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The COVID-19 pandemic caused by SARS-CoV-2 represents a public health emergency, which became even more challenging since the detection of highly transmissible variants and strategies against COVID-19 were indistinctly established. We characterized the temporal viral load kinetics in individuals infected by original and variant strains. Naso-oropharyngeal swabs from 33,000 individuals (admitted to the IRCCS Santa Lucia Foundation Drive-in, healthcare professionals and hospitalized patients who underwent routinary screening) from November 2020 to June 2021 were analyzed. Of them, 1735 subjects were selected and grouped according to the viral strain. Diagnostic analyses were performed by CE-IVD RT-PCR-based kits. The subgenomic-RNA component was assessed in 36 subjects using digital PCR. Infection duration, viral load decay speed, effects of age and sex were assessed and compared by extensive statistical analyses. Overall, infection duration and viral load differed between the groups (p < 0.05). Male sex was more present among both original and variant carriers affected with high viral load and showing fast decay speed, whereas original strain carriers with slow decay speed resulted in older (p < 0.05). Subgenomic-RNA was detected in the positive samples, including those with low viral load. This study provides a picture of the viral load kinetics, identifying individuals with similar patterns and showing differential effects of age and sex, thus providing potentially useful information for personalized management of infected subjects.

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“…In this study, we showed that the B.1.1.7 lineage rapidly spread becoming the prevalent lineage from January to March 2021. Indeed, a progressive increase in positive cases of SARS-CoV-2 infections and the concomitant emergence of the Alpha variant were reported in diverse regions of Italy [ 6 , 7 , 15 , 16 ]. Lai and colleagues reported that the B.1.1.7 lineage significantly increased from 3.5% in December 2020 to 86.7% in March 2021, replacing the previously circulating variant B.1.177 [ 7 ].…”

Section: Discussionmentioning

confidence: 99%

“…Indeed, a progressive increase in positive cases of SARS-CoV-2 infections and the concomitant emergence of the Alpha variant were reported in diverse regions of Italy [ 6 , 7 , 15 , 16 ]. Lai and colleagues reported that the B.1.1.7 lineage significantly increased from 3.5% in December 2020 to 86.7% in March 2021, replacing the previously circulating variant B.1.177 [ 7 ]. Moreover, they assessed that the most important increase in its prevalence was observed from the second week of January to the end of the same month, reaching 73.7% prevalence at the end of February.…”

Section: Discussionmentioning

confidence: 99%

Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia

et al. 2021

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In-depth study of the entire SARS-CoV-2 genome has uncovered many mutations, which have replaced the lineage that characterized the first wave of infections all around the world. In December 2020, the outbreak of variant of concern (VOC) 202012/01 (lineage B.1.1.7) in the United Kingdom defined a turning point during the pandemic, immediately posing a worldwide threat on the Covid-19 vaccination campaign. Here, we reported the evolution of B.1.1.7 lineage-related infections, analyzing samples collected from January 1st 2021, until April 15th 2021, in Friuli Venezia Giulia, a northeastern region of Italy. A cohort of 1508 nasopharyngeal swabs was analyzed by High Resolution Melting (HRM) and 479 randomly selected samples underwent Next Generation Sequencing analysis (NGS), uncovering a steady and continuous accumulation of B.1.1.7 lineage-related specimens, joined by sporadic cases of other known lineages (i.e. harboring the Spike glycoprotein p.E484K mutation). All the SARS-CoV-2 genome has been analyzed in order to highlight all the rare mutations that may eventually result in a new variant of interest. This work suggests that a thorough monitoring of the SARS-CoV-2 genome by NGS is essential to contain any new variant that could jeopardize all the efforts that have been made so far to resolve the emergence of the pandemic.

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Circulating SARS-CoV-2 variants in Italy, October 2020–March 2021

Cited by 40 publications

References 12 publications

Prevention Procedures to Contain COVID-19 Contagion in the First Italian Army Field Hospital

Prevention Procedures to Contain COVID-19 Contagion in the First Italian Army Field Hospital

Age and Sex Modulate SARS-CoV-2 Viral Load Kinetics: A Longitudinal Analysis of 1735 Subjects

Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia

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