Imported SARS-CoV-2 Variant P.1 in Traveler Returning from Brazil to Italy

Maggi, Fabrizio; Novazzi, Federica; Genoni, Angelo; Baj, Andreina; Spezia, Pietro Giorgio; Focosi, Daniele; Zago, Cristian; Colombo, Alberto; Cassani, Gianluca; Pasciuta, Renée; Tamborini, Antonio; Rossi, Agostino; Prestia, Martina; Capuano, Riccardo; Azzi, Lorenzo; Donadini, Annalisa; Catanoso, Giuseppe; Grossi, Paolo; Maffioli, Lorenzo; Bonelli, Gianni

doi:10.3201/eid2704.210183

Cited by 44 publications

(36 citation statements)

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“…An earlier study reported the presence of P.1 in three returning travelers from Brazil to Abruzzo sampled on 18 January 2021 [ 23 ], although we show here that this small cluster did not lead to (detectable) subsequent transmission events. A second study reported the presence of P.1 in a returning traveler from Brazil [ 28 ]. This individual was sampled on 22 January in Milan, North Italy.…”

Section: Discussionmentioning

confidence: 99%

Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy

Giallonardo

Puglia

Curini

et al. 2021

Viruses

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Italy’s second wave of SARS-CoV-2 has hit hard, with more than three million cases and over 100,000 deaths, representing an almost ten-fold increase in the numbers reported by August 2020. Herein, we present an analysis of 6515 SARS-CoV-2 sequences sampled in Italy between 29 January 2020 and 1 March 2021 and show how different lineages emerged multiple times independently despite lockdown restrictions. Virus lineage B.1.177 became the dominant variant in November 2020, when cases peaked at 40,000 a day, but since January 2021 this is being replaced by the B.1.1.7 ‘variant of concern’. In addition, we report a sudden increase in another documented variant of concern—lineage P.1—from December 2020 onwards, most likely caused by a single introduction into Italy. We again highlight how international importations drive the emergence of new lineages and that genome sequencing should remain a top priority for ongoing surveillance in Italy.

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Section: Discussionmentioning

confidence: 99%

Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy

Giallonardo

Puglia

Curini

et al. 2021

Viruses

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“…Interestingly, variants of interest and variants of concern currently emerging in different parts of the world show non-synonymous mutations within the here described GLD. The B1.525 variant harbors a Q677H mutation [ 60 ], the variant B1.1.7 reported in the United Kingdom carries A570D and P681H mutations [ 61 ], the P1 variant from Brazil shows the H655Y mutation [ 62 ], and the recently reported B.1.617 strain in India shows a P681R change [ 63 ]. Whether these mutations located within the same domain as T307I may induce a similar impact on the molecular dynamics warrants further investigation.…”

Section: Discussionmentioning

confidence: 99%

Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics

González-Puelma

Aldridge

et al. 2021

Viruses

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The emergence of SARS-CoV-2 variants, as observed with the D614G spike protein mutant and, more recently, with B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1) lineages, represent a continuous threat and might lead to strains of higher infectivity and/or virulence. We report on the occurrence of a SARS-CoV-2 haplotype with nine mutations including D614G/T307I double-mutation of the spike. This variant expanded and completely replaced previous lineages within a short period in the subantarctic Magallanes Region, southern Chile. The rapid lineage shift was accompanied by a significant increase of cases, resulting in one of the highest incidence rates worldwide. Comparative coarse-grained molecular dynamic simulations indicated that T307I and D614G belong to a previously unrecognized dynamic domain, interfering with the mobility of the receptor binding domain of the spike. The T307I mutation showed a synergistic effect with the D614G. Continuous surveillance of new mutations and molecular analyses of such variations are important tools to understand the molecular mechanisms defining infectivity and virulence of current and future SARS-CoV-2 strains.

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“…On 13 January 2021, researchers from Fiocruz Amazônia announced the identification of this variant in the capital of Amazonas, Manaus, where an upsurge in COVID-19 cases was registered in January of 2021 (Farias et al, 2021). To date, the P.1 variant has been identified either in Brazil, or in travellers from Brazil (mostly from the State of Amazonas), including one returning to Italy from Brazil (Maggi et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Rapid Screening for SARS-CoV-2 Variants of Concern in Clinical and Environmental Samples Using Nested RT-PCR Assays Targeting Key Mutations of the Spike Protein

Rosa

Mancini

Veneri

et al. 2021

Preprint

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New SARS-CoV-2 mutations are constantly emerging, raising concerns of increased transmissibility, virulence or escape from host immune response. We describe a nested RT-PCR assay (~1500 bps) to detect multiple key spike protein mutations distinctive of the major known circulating SARS-CoV-2 variants, including the three Variants of Concern (VOCs) 20I/501Y.V1 (United Kingdom), 20H/501Y.V2 (South Africa), and 20J/501Y.V3 (Brazil), as well as the 20E.EU1 variant (Spain), the CAL.20C recently identified in California, and the mink-associated variant (GR, lineage B.1.1.298). Prior to application to field samples, the discriminatory potential of this PCR assay was explored using GISAID and Nextclade. To extend variant detection to challenging matrices such as sewage, where the amplification of long fragments is problematic, two short nested RT-PCR assays (~300 bps) were also designed, targeting portions of the region spanned by the long nested assay. The three newly-designed assays were then tested on field samples, including 7 fully-sequenced viral isolates from swab samples and 34 urban wastewater samples, some of which collected in areas where circulation of VOCs had been reported. The long assay successfully amplified all the previously characterized viral isolates, allowing the correct identification of variants 20I/501Y.V1 and 20E.EU1 present in the panel. The sequences obtained using the short assays were consistent with those obtained with the long assay. Mutations characteristic of VOCs (UK and Brazilian variant) and of other variant (Spanish) were detected in sewage samples. To our knowledge, this is the first evidence of the presence of sequences harboring key mutations of 20I/501Y.V1 and 20J/501Y.V3 in urban wastewaters, highlighting the potential contribution of wastewater surveillance to explore SARS-CoV-2 diversity. The developed nested RT-PCR assays can be used as an initial rapid screening test to select clinical samples containing mutations of interest. This can speed up diagnosis and optimize resources since it allows full genome sequencing to be done only on clinically relevant specimens. The assays can be also employed for a rapid and cost-effective detection of VOCs or other variants in sewage for the purposes of wastewater-based epidemiology. The approach proposed here can be used to better understand SARS-CoV-2 variant diversity, geographic distribution and impact worldwide.

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Imported SARS-CoV-2 Variant P.1 in Traveler Returning from Brazil to Italy

Cited by 44 publications

References 1 publication

Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy

Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy

Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics

Rapid Screening for SARS-CoV-2 Variants of Concern in Clinical and Environmental Samples Using Nested RT-PCR Assays Targeting Key Mutations of the Spike Protein

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