key: cord-0968255-gy0kojwr
authors: Micheli, Valeria; Bracchitta, Fiorenza; Rizzo, Alberto; Mancon, Alessandro; Mileto, Davide; Lombardi, Alessandra; Stefanelli, Paola; Gismondo, Maria Rita
title: First identification of the new SARS-CoV-2 Omicron variant (B.1.1.529) in Italy
date: 2022-01-21
journal: Clin Infect Dis
DOI: 10.1093/cid/ciab1044
sha: 3f3837745c54466b68b19af4608a64f318b01101
doc_id: 968255
cord_uid: gy0kojwr

We identified the first case in Italy of SARS-CoV-2 B.1.1.529 variant by whole genome sequencing in an Italian subject travelling from Mozambique. Specific mutation profiles deserve further investigations to clarify potential effects on vaccination efficacy. This case highlights the crucial role of rapid and continuous surveillance of SARS-CoV-2 variant circulation.

M a n u s c r i p t

Since the worldwide emergence of the COVID-19 outbreak, SARS-CoV-2 pandemic has been characterized by subsequent waves of viral propagation sustained by different viral strains with peculiar transmissibility, disease severity, risk of death, and potential escape from the immune response. The strong sequencing effort put in place by the international scientific community allowed to characterize numerous lineages differing in abundance and type of amino-acidic mutations. Particular in immunity and natural infection course has still to be generated [3] .

The arising concerns about Omicron variant are based on its unprecedentedly large mutation pattern and its rapid diffusion that have strongly stimulated containment measures and travel policy strategies worldwide to prevent global spread.

According to the Italian SARS-CoV-2 surveillance program indication for travellers of 2 nd March 2021 (updated on 22 nd October 2021) the countries are classified into 5 classes of risk and only inbound travellers from specific places are tested for SARS-CoV-2. In particular, the subjects coming from Africa are requested to fill in the Passenger Locator Form, to have a negative molecular or antigenic test for SARS-CoV-2 within 72 hours and to observe a 10-day isolation period or staying in Italy less than 120 hours [4] .

Here we report the first case of SARS-CoV-2 B. A c c e p t e d M a n u s c r i p t subjects as well as vaccinated ones [6] . Since mutations in S gene were associated with higher infectivity, escape to monoclonal antibodies and immune response, as well as to syncytium formation, it is crucial to identify aminoacidic alterations and test their effect on human antibodies activity [7] [8] [9] . Moreover, the comparison with the other VOCs can contribute to better estimate the level of concern of Omicron variant [10] .The in vitro results could contribute to strengthen the third COVID-19 vaccine dose recommendation considering also the dangers of potential waning immunity [11] .

The multistep approach based on specific variant RT-PCR assay and the subsequent WGS of samples with atypical pattern of mutations could be a powerful algorithm for a first step screening before the sequencing of the entire genome of SARS-CoV-2 in order to report the new SARS-CoV-2 variants to public health authorities.

A prompt and accurate surveillance of SARS-CoV-2 variant at national level could play a crucial role not only to quickly identify new variants but also for public health purposes.

Thanks to this rapid report, on 26 th November 2021 health authorities have immediately released an urgent update to manage arrivals from Sub-Saharan Africa. In addition to previous rules, it's necessary to perform a molecular or antigenic test at the airport or harbor upon arrival and to undergo a 10-day isolation period with another molecular test thereafter.

In conclusion, the excellent integrated surveillance system implemented in Italy allowed us to rapidly reveal the new variant and to limit its circulation, even if in an interconnected world travel bans might slow but unfortunately will not eliminate global spread.

A c c e p t e d M a n u s c r i p t Notes

European Centre for Disease Prevention and Control (ECDC)

Heavily mutated Omicron variant puts scientists on alert

Online ahead of print

Italian Ministry of Health)

Evaluation of Humoral Immune Response after SARS-CoV-2 Vaccination Using Two Binding Antibody Assays and a Neutralizing Antibody Assay. Microbiol Spectr

Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Rep

SARS-CoV-2 variants, spike mutations and immune escape

Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K and N501Y variants by BNT162b2 vaccine-elicited sera

SARS-CoV-2 mRNA vaccine BNT162b2 triggers a consistent crossvariant humoral and cellular response

A c c e p t e d M a n u s c r i p t