key: cord-0931631-hp5a8qmy
authors: Funk, Tjede; Pharris, Anastasia; Spiteri, Gianfranco; Bundle, Nick; Melidou, Angeliki; Carr, Michael; Gonzalez, Gabriel; Garcia-Leon, Alejandro; Crispie, Fiona; O’Connor, Lois; Murphy, Niamh; Mossong, Joël; Vergison, Anne; Wienecke-Baldacchino, Anke K.; Abdelrahman, Tamir; Riccardo, Flavia; Stefanelli, Paola; Di Martino, Angela; Bella, Antonino; Lo Presti, Alessandra; Casaca, Pedro; Moreno, Joana; Borges, Vítor; Isidro, Joana; Ferreira, Rita; Gomes, João Paulo; Dotsenko, Liidia; Suija, Heleene; Epstein, Jevgenia; Sadikova, Olga; Sepp, Hanna; Ikonen, Niina; Savolainen-Kopra, Carita; Blomqvist, Soile; Möttönen, Teemu; Helve, Otto; Gomes-Dias, Joana; Adlhoch, Cornelia
title: Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021
date: 2021-04-22
journal: Euro Surveill
DOI: 10.2807/1560-7917.es.2021.26.16.2100348
sha: 51ae4827f0cce508988131eeef60b2a84d47f7fe
doc_id: 931631
cord_uid: hp5a8qmy

We compared 19,207 cases of SARS-CoV-2 variant B.1.1.7/S gene target failure (SGTF), 436 B.1.351 and 352 P.1 to non-variant cases reported by seven European countries. COVID-19 cases with these variants had significantly higher adjusted odds ratios for hospitalisation (B.1.1.7/SGTF: 1.7, 95% confidence interval (CI): 1.0–2.9; B.1.351: 3.6, 95% CI: 2.1–6.2; P.1: 2.6, 95% CI: 1.4–4.8) and B.1.1.7/SGTF and P.1 cases also for intensive care admission (B.1.1.7/SGTF: 2.3, 95% CI: 1.4–3.5; P.1: 2.2, 95% CI: 1.7–2.8).

Y453F = Y453F associated with farmed minks; defined by mutation: Y453F VARIANT_OTHER = Novel variant of potential concern. Provide details in VirusVariantOther WILD_TYPE = None of the variants described for this variable UNK = Sequence information unknown or not available COVID-19 case with a variant virus of SARS-CoV-2 according to mutation pattern of specific concern identified by sequence analysis of the case, or in some cases by a specific RT-PCR pattern. If several apply, choose the most specific variant (highest number of matching mutations).

Finland:

In Finland we test everyone with any suitable symptoms for Covid-19 and also screen asymptomatic exposed people in the context of contact tracing and border surveillance upon entry.

From January 2020 to December 2020 we sequenced a sample of all positive cases mainly for research purposes (no variant findings). We started extensive variant screening and sequencing in week 51, December 2020 upon variant findings in Europe. The first findings were from entry screening and their contacts. We also screened contacts of known variant cases in transmission chains. From February 2021 onwards, we have sequenced a random sample of all positive cases throughout the country and also positive cases from entry screening and contacts of known variant cases (not all).

We report the sequencing data to Tessy according to the ECDC algorithm. We aim to submit all sequences to GISAID including those of non-variant cases, this is pending.

Real-time PCR testing is performed on all symptomatic cases and a subset of samples with Ct values ≤25 are selected for sequencing, being representative of age range and geographical distribution of the COVID-19 positive cases in the country. A small percentage of samples are sequenced based on SGD and N501Y or E484K mutation-specific PCRs. All variants of concern and variants of interest are reported to public health for enhanced action and to TESSy.

Italy has implemented a thorough testing strategy amid rapidly increased its testing capacity. The current national weekly average of testing is over 3600 swab tests per 100,000 inhabitants per week with 6.6% of positive tests.

Sequencing is recommended in all cases of confirmed SARS-CoV-2 infection: from countries with high VOC SARS-CoV-2 variant circulation, epidemiologically linked to cases with VOC SARS-CoV-2 infections, with S-gene target failure and in cases of reinfection or of vaccination failure.

Regional reference laboratories coordinate sequencing activities in their catchment area under the overall coordination of the National Reference Laboratory in ISS, Rome. Reporting is performed in the National Integrated surveillance platform for COVID-19 that combines epidemiological and basic microbiological metadata, this data is regularly sent to TESSy.

The national reference laboratory for acute respiratory infections at LNS implements the following weekly sequencing activities for SARS-CoV2:

Sequencing specimens from all hospitalized positive cases 2) Sequencing specimens from all positive cases from Airport testing program

Sequencing specimens from all outbreaks and identified clusters 4) Systematic sequencing of specimens from reinfections and post-vaccination-infections 5) Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

All positive SARS-CoV-2 samples are referred from diagnostic laboratories nationwide to LNS where primary samples are extracted and processed for RT-PCR to select the eligible samples for sequencing (criterion: CT value < or = 35 are sequenced). Results of successfully sequenced samples are reported to the health inspection and referring hospitals. Variant surveillance is done by amplicon based whole genome sequencing on an Illumina platform (to be extended by variant specific RT-PCR). The sequence coverage of all positive cases is on average 30%. Sequencing results are integrated in the contact tracing database hosted by the health inspection to follow up particular clusters (e.g. nursing homes, schools). Pseudonymised data is sent via Tessy to ECDC on a weekly basis.

Portugal performs monthly sequencing nationwide surveys. In parallel, the Portuguese NIH continuously sequences suspected samples of: 1) VOCs (signalled by SNP assays and/or travelhistory); 2) potential vaccine failures; 3) potential re-infection, etc. So far, this targeted sequencing usually accounts for less than 3% of all monthly sequenced samples. All sequences are deposited in GISAID and reported to TESSy. Figure S1 . Total number of sequences by data source per week This figure bases on data submitted to TESSy up to week 2021-12 and extracted from GISAID EpiCoV database (https://www.gisaid.org/) by 30 March 2021. As the data extraction was done later than the rest of the analysis, slight differences to what was used for the analysis may exist due to retrospective data updates by countries. Figure S2 . Weekly variant distribution by country and data source (Data shown from the source with highest number of sequences in the period. Estimates only shown for weeks with a valid denominator) Note: Estimates only shown for weeks and data source in which the weekly sequencing volume was at least 500 sequences or 10% of all cases (this excludes Cyprus and Estonia). As not all generated sequences are reported there may be under-estimation of the sequencing activities in some countries. This figure bases on data submitted to TESSy up to week 2021-12 and extracted from GISAID EpiCoV database (https://www.gisaid.org/) by 30 March 2021. As the data extraction was done later than the rest of the analysis, slight differences to what was used for the analysis may exist due to retrospective data updates by countries. 20% 40% 60% 80% Figure S5 . 

Portugal Number of cases