Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy

Giallonardo, Francesca Di; Duchêne, Sebastián; Puglia, Ilaria; Curini, Valentina; Profeta, Francesca; Cammà, Cesare; Marcacci, Maurilia; Calistri, Paolo; Holmes, Edward C.; Lorusso, Alessio

doi:10.3390/v12121438

Cited by 41 publications

(40 citation statements)

References 31 publications

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“…With the exception of this isolated event, there is no evidence of association between any other evolutionary lineage and a single locality. This could be attributed to elevated rates of spread due to freedom of host movement despite social distancing measures established (Di Giallonardo et al, 2020) . Accordingly, lineage representation in Rio Grande do Sul is similar to that found in Brazil.…”

Section: Resultsmentioning

confidence: 99%

Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

Francisco

Benites

Lamarca

et al. 2021

Preprint

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Emergence of novel SARS-CoV-2 lineages are under the spotlight of the media, scientific community and governments. Recent reports of novel variants in the United Kingdom, South Africa and Brazil (B.1.1.28-E484K) have raised intense interest because of a possible higher transmission rate or resistance to the novel vaccines. Nevertheless, the spread of B.1.1.28 (E484K) and other variants in Brazil is still unknown. In this work, we investigated the population structure and genomic complexity of SARS-CoV-2 in Rio Grande do Sul, the southernmost state in Brazil. Most samples sequenced belonged to the B.1.1.28 (E484K) lineage, demonstrating its widespread dispersion. We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484K) with either B.1.1.248 or B.1.91 lineages. Also, clustering analysis revealed the occurrence of a novel cluster of samples circulating in the state (named VUI-NP13L) characterized by 12 lineage-defining mutations. In light of the evidence for E484K dispersion, co-infection and emergence of VUI-NP13L in Rio Grande do Sul, we reaffirm the importance of establishing strict and effective social distancing measures to counter the spread of potentially more hazardous SARS-CoV-2 strains.HighlightsThe novel variant B.1.1.28 (E484K) previously described in Rio de Janeiro is currently spread across the southernmost state of Brazil;The novel variant VUI-NP13L was also identified by causing a local outbreak in Rio Grande do Sul;B.1.1.28 (E484K) is able to establish successful coinfection events co-occurring simultaneously with different lineages of SARS-CoV-2.

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Section: Resultsmentioning

confidence: 99%

Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

Francisco

Benites

Lamarca

et al. 2021

Preprint

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“…Sequences without a complete date of collection were removed. As per our previous study, cases were grouped according to geographical non-administrative macro areas in North (n=1,195), Central (n= 1,403), and South Italy (n= 3,917) 16 . SARS-CoV-2 lineages were assigned to each sequence using the Pangolin COVID-19 Lineage Assigner tool v2.0.7 (github.com/cov-lineages/pangolin).…”

Section: Methodsmentioning

confidence: 99%

Emergence and spread of SARS-CoV-2 lineages B.1.1.7 and P.1 in Italy

Giallonardo¹,

Puglia²,

Curini³

et al. 2021

Preprint

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Italy's second wave of SARS-CoV-2 has hit hard, with more than 3 million cases and over 100,000 deaths, representing an almost ten-fold increase on the numbers reported by August 2020. Herein, we present the analysis of 6,515 SARS-CoV-2 sequences sampled in Italy between 29th January 2020 and 1st 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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“…We previously showed that virus importation associated with travel, followed by local transmission, were key drivers of viral spread during the first wave of SARS-CoV-2 in Italy [ 16 ]. After a year into the pandemic, lockdown restrictions have proven effective in reducing virus transmission and limiting geographic spread [ 17 ], although international travel is still a major source for the introduction of new lineages into Italy [ 18 ].…”

Section: Introductionmentioning

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

Self Cite

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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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Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy

Cited by 41 publications

References 31 publications

Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

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

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