ArticlePathogens (Basel, Switzerland)2022
Genomic Epidemiology Unveil the Omicron Transmission Dynamics in Rome, Italy.
Article in Pathogens (Basel, Switzerland), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers, 1 of them a synthesis that pooled it.
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Who cites it
3 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The relative prevalence of the Omicron variant within SARS-CoV-2 infected cohorts in different countries: A systematic review.Human vaccines & immunotherapeutics · 2023Pooled it
- Genomic Epidemiology of the Main SARS-CoV-2 Variants Circulating in Italy During the Omicron Era.Journal of medical virology · 2025Article
- Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementation.BMC infectious diseases · 2025Article
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Authors and funding
11 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Since 2020, the COVID-19 pandemic represented an important worldwide burden. Well-structured surveillance by reliable and timely genomic data collection is crucial. In this study, a genomic monitoring analysis of all SARS-CoV-2 positive samples retrieved at the Fondazione Policlinico Universitario Campus Bio-Medico, in Rome, Italy, between December 2021 and June 2022, was performed. Two hundred and seventy-four SARS-CoV-2-positive samples were submitted to viral genomic sequencing by Illumina MiSeqII. Consensus sequences were generated by de novo assembling using the iVar tool and deposited on the GISAID database. Lineage assignment was performed using the Pangolin lineage classification. Sequences were aligned using ViralMSA and maximum-likelihood phylogenetic analysis was performed by IQ-TREE2. TreeTime tool was used to obtain dated trees. Our genomic monitoring revealed that starting from December 2021, all Omicron sub-lineages (BA.1, BA.2, BA.3, BA.4, and BA.5) were circulating, although BA.1 was still the one with the highest prevalence thought time in this early period. Phylogeny revealed that Omicron isolates were scattered throughout the trees, suggesting multiple independent viral introductions following national and international human mobility. This data represents a sort of thermometer of what happened from July 2021 to June 2022 in Italy. Genomic monitoring of the circulating variants should be encouraged considering that SARS-CoV-2 variants or sub-variants emerged stochastically and unexpectedly.
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