Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020

Hodcroft, Emma B.; Zuber, Moira; Nadeau, Sarah; Vaughan, Timothy G.; Crawford, Katharine H.D.; Althaus, Christian L.; Reichmuth, Martina L.; Bowen, John E.; Walls, Alexandra C.; Corti, Davide; Bloom, Jesse D.; Veesler, David; Mateo, David; Hernando, Alberto; Comas, Iñaki; Gónzález-Candelas, Fernando; Stadler, Tanja; Neher, Richard A.

doi:10.1101/2020.10.25.20219063

Cited by 366 publications

(430 citation statements)

References 52 publications

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“…More patients were admitted during the second wave, they were younger and there were fewer deaths, in agreement with results reported by previous research in several countries [2,3,12]. The reasons for the clear differences between the two periods are not yet known although it has been suggested that a new variant of SARS-CoV-2 emerged in early summer 2020 in Spain [9], a variant that was linked to outbreaks among young agricultural workers in the north-east of the country. Transmission to the general population in that area was then replicated across the country.…”

Section: Discussionsupporting

confidence: 89%

First and second waves of coronavirus disease-19: A comparative study in hospitalized patients in Reus, Spain

Iftimie

López‐Azcona

Hernández-Flix

et al. 2020

Preprint

100

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Many countries have seen a two-wave pattern in reported cases of coronavirus disease-19 during the 2020 pandemic, with a first wave during spring followed by the current second wave in late summer and autumn. Empirical data show that the characteristics of the effects of the virus do vary between the two periods. Differences in age range and severity of the disease have been reported, although the comparative characteristics of the two waves still remain largely unknown. Those characteristics are compared in this study using data from two equal periods of 3 and a half months. The first period, between 15th March and 30th June, corresponding to the entire first wave, and the second, between 1st July and 15th October, corresponding to part of the second wave, still present at the time of writing this article. Two hundred and four patients were hospitalized during the first period, and 264 during the second period. Patients in the second wave were younger and the duration of hospitalization and case fatality rate were lower than those in the first wave. In the second wave, there were more children, and pregnant and post-partum women. The most frequent signs and symptoms in both waves were fever, dyspnea, pneumonia, and cough, and the most relevant comorbidities were cardiovascular diseases, type 2 diabetes mellitus, and chronic neurological diseases. Patients from the second wave more frequently presented renal and gastrointestinal symptoms, were more often treated with non-invasive mechanical ventilation and corticoids, and less often with invasive mechanical ventilation, conventional oxygen therapy and anticoagulants. Several differences in mortality risk factors were also observed. These results might help to understand the characteristics of the second wave and the behaviour and danger of SARS-CoV-2 in the Mediterranean area and in Western Europe. Further studies are needed to confirm our findings.

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Section: Discussionsupporting

confidence: 89%

First and second waves of coronavirus disease-19: A comparative study in hospitalized patients in Reus, Spain

Iftimie

López‐Azcona

Hernández-Flix

et al. 2020

Preprint

100

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“…From the Costa Rican sequenced cases, none harbors yet this mutation. Also, a European cluster (called 20A.EU1) has been reported with a significant spread in summer 2020, mainly in Spain (Hodcroft et al, 2020). Genome sequences in this group have at least six variants, including the mutation A222V in the Spike protein and A220V in the nucleoprotein.…”

Section: Other Variantsmentioning

confidence: 99%

“…Genetic diversity of SARS-CoV-2 genomes has demonstrated a large number of independent introductions of the virus into many countries of the world but China (van Dorp et al, 2020). Although strong relationships between specific variants or clades in SARS-CoV-2 and the clinical outcome have not been identified (Grubaugh, Hanage, & Rasmussen, 2020;Hodcroft et al, 2020;van Dorp et al, 2020), different relevant parameters could be impacted by mutations in the virus genome. These include transmissibility, severity, clinical management, mortality, vaccines as well as the performance of molecular tests for diagnosis (Hodcroft et al, 2020;Koyama, Platt, & Parida, 2020;Teng, Sobitan, Rhoades, Liu, & Tang, 2020).…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Genomic Surveillance in Costa Rica: Evidence of a Divergent Population and an Increased Detection of a Spike T1117I Mutation

Molina-Mora

Cordero-Laurent

Godínez

et al. 2020

Preprint

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Genome sequencing is a key strategy in the surveillance of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Latin America is the hardest hit region of the world, accumulating almost 20% of COVID-19 cases worldwide. Costa Rica was first exemplary for the region in its pandemic control, declaring a swift state of emergency on March 16th that led to a low quantity of cases, until measures were lifted in early May. From the first detected case in March 6th to December 31st almost 170 000 cases have been reported in Costa Rica, 99.5% of them from May onwards. We analyzed the genomic variability during the SARS-CoV-2 pandemic in Costa Rica using 185 sequences, 52 from the first months of the pandemic, and 133 from the current wave.Three GISAID clades (G, GH, and GR) and three PANGOLIN lineages (B.1, B.1.1, and B.1.291) are predominant, with phylogenetic relationships that are in line with the results of other Latin American countries, suggesting introduction and multiple re-introductions from other regions of the world. The whole-genome variant calling analysis identified a total of 283 distinct nucleotide variants. These correspond mostly to non-synonymous mutations (51.6%, 146) but 45.6% (129) corresponded to synonymous mutations. The 283 variants showed an expected power-law distribution: 190 single nucleotide mutations were identified in single sequences, only 16 single nucleotide mutations were found in >5% sequences, and only two mutations in >50% genomes. These mutations were distributed through the whole genome. However, 63.6% were present in ORF1ab, 11.7% in Spike gene and 10.6% in the Nucleocapsid gene. Additionally, the prevalence of worldwide-found variant D614G in the Spike (98.9% in Costa Rica), ORF8 L84S (1.1%) is similar to what is found elsewhere. Interestingly, the frequency of mutation T1117I in the Spike has increased during the current pandemic wave beginning in May 2020 in Costa Rica, reaching 29.2% detection in the full genome analyses in November 2020. This variant has been observed in less than 1% of the GISAID reported sequences worldwide in all the 2020. Structural modeling of the Spike protein with the T1117I mutation suggest a potential effect on the viral oligomerization needed for cell infection, but no differences with other genomes on transmissibility, severity nor vaccine effectiveness are predicted. Nevertheless, in-vitro experiments are required to support these in-silico findings. In conclusion, genome analyses of the SARS-CoV-2 sequences over the course of COVID-19 pandemic in Costa Rica suggest introduction of lineages from other countries as travel bans and measures were lifted, similar to results found in other studies, as well as an increase in the Spike-T1117I variant that needs to be monitored and studied in further analyses as part of the surveillance program during the pandemic.

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“…This mutation confers increased infectivity on the virus (37) and was readily generated in sufficient numbers to ensure its expansion. As of this writing, a second selective sweep appears to be underway in Europe, with the 2A.EU1 variant (38).…”

Section: Discussionmentioning

confidence: 92%

Risk of evolutionary escape from neutralizing antibodies targeting SARS-CoV-2 spike protein

Egeren

Novokhodko

Stoddard³

et al. 2020

Preprint

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As many prophylactics targeting SARS-CoV-2 are aimed at the spike protein receptor-binding domain (RBD), we examined the risk of immune evasion from previously published RBD-targeting neutralizing antibodies (nAbs). Epitopes for RBD-targeting nAbs overlap one another substantially and can give rise to escape mutants with ACE2 affinities comparable to wild type that still infect cells in vitro. Based on this demonstrated mutational tolerance of the RBD, we used evolutionary modeling to predict the frequency of immune escape before and after the widespread presence of nAbs raised by vaccines, administered as prophylactics, or produced through natural immunity. Our modeling suggests that SARS-CoV-2 mutants with one or two mildly deleterious mutations are expected to exist in high numbers due to neutral genetic variation, and likewise resistance to single or double antibody combinations will develop quickly under positive selection.One Sentence SummarySARS-CoV-2 will evolve quickly to evade widely deployed spike RBD-targeting monoclonal antibodies, requiring combinations with at least three antibodies to suppress viral immune evasion.

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Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020

Cited by 366 publications

References 52 publications

First and second waves of coronavirus disease-19: A comparative study in hospitalized patients in Reus, Spain

First and second waves of coronavirus disease-19: A comparative study in hospitalized patients in Reus, Spain

SARS-CoV-2 Genomic Surveillance in Costa Rica: Evidence of a Divergent Population and an Increased Detection of a Spike T1117I Mutation

Risk of evolutionary escape from neutralizing antibodies targeting SARS-CoV-2 spike protein

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