The DOI matches its Crossref record; 52 of the 54 references it cites were found in a registry or an index, and 2 are not checked yet; none of the 12 sources its claims cite is checked for support yet.
Spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Open accessAbstract
Following its emergence in late 2019, the spread of SARS-CoV-2 1,2 has been tracked by phylogenetic analysis of viral genome sequences in unprecedented detail 3-5. Although the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, travel within Europe resumed in the summer of 2020. Here we report on a SARS-CoV-2 variant, 20E (EU1), that was identified in Spain in early summer 2020 and subsequently spread across Europe. We find no evidence that this variant has increased transmissibility, but instead demonstrate how rising incidence in Spain, resumption of travel, and lack of effective screening and containment may explain the variant's success. Despite travel restrictions, we estimate that 20E (EU1) was introduced hundreds of times to European countries by summertime travellers, which is likely to have undermined local efforts to minimize infection with SARS-CoV-2. Our results illustrate how a variant can rapidly become dominant even in the absence of a substantial transmission advantage in favourable epidemiological settings. Genomic surveillance is critical for understanding how travel can affect transmission of SARS-CoV-2, and thus for informing future containment strategies as travel resumes.
Checked 2026-10-06 · 2 references not checked yet
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Claims the paper makes
41 Own result · 24 Own interpretation · 11 Own method · 8 Not checked yet · 7 No basis given
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Norway and Iceland, for example, seem to have only a small number of introductions over the summer that led to substantial further spread.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Expansion and spread across Europe
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In contrast, countries like Switzerland, the Netherlands, or the United Kingdom have sampled sequences that correspond to a large number of independent introductions that include most major genotypes observed in Spain.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Expansion and spread across Europe
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Most basal genotypes have been observed both in Spain and a large number of other countries, suggesting repeated exports.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Expansion and spread across Europe
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Sequences from Hong Kong, Australia, New Zealand, and Singapore, presumably exports from Europe, were first detected between mid-August and mid-October (see Supplementary Table I).”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Early observations of 20E (EU1)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The dose-response curves were indistinguishable for the SARS-CoV-2 2PS and the SARS-CoV-2 2P A222V D614G S ectodomain trimers (observed by ELISA, Fig. ED3a-d)”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Characterization of S:A222V
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In many European countries, we observe a gradual rise starting in mid-July before settling at a level between 15 and 80% in September or October.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Early observations of 20E (EU1)
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Several other smaller clusters defined by the spike mutations D80Y, S98F, N439K are also seen in multiple countries (see Table ED I and Fig. ED1).”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Abstract
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In addition to S:A222V, 20E (EU1) has the amino acid mutations ORF10:V30L, N:A220V and ORF14:L67F.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Characterization of S:A222V
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Epidemiological data from Spain indicates the earliest sequences in the cluster are associated with two known outbreaks in the north-east of the country.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Expansion and spread across Europe
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“By the end of August, 20E (EU1) also included sequences from Belgium, Switzerland, France, Denmark, the UK, Germany, Latvia, Sweden, Norway and Italy.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Early observations of 20E (EU1)
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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- It may state two separate claims as one. 38
- Probably not a substantial claim. 8
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The tree indicates that 20E (EU1) harbors substantial diversity and most major genotypes have been observed in many European countries.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Expansion and spread across Europe
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In Fig. ED4a, the majority of sequences from these countries fall into one sector, the remainder are singletons or very small clusters that have not spread.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Expansion and spread across Europe
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Throughout July and August 2020, Spain had a higher per capita incidence than most other European countries (see Fig ED5) and 20E (EU1) was much more prevalent in Spain then elsewhere, suggesting Spain as likely origin of most 20E (EU1) introductions to other countries.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Expansion and spread across Europe
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Lentiviral particles with the A222V mutant spike had slightly higher titers than those without (mean 1.3-fold higher), although the difference was not statistically significant after normalization by p24 concentration (Fig. ED3e-h).”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Characterization of S:A222V
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“20E (EU1) first rose in frequency in Spain, jumping to around 50% prevalence within a month of the first sequence being detected before rising to 80%.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Early observations of 20E (EU1)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“S:N439K is present in two larger clusters found across Europe 19 and arose several times independently.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Abstract
What the sources say
- Not checked yetcites [19] Thomson, E. C. et al. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell 184, 1171–1187 (2021). source
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Similarly, for Germany and Switzerland we would expect around 320 and 90 introductions of 20E (EU1), respectively.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
- The authors state this as an assumption: Returning tourists have a similar SARS-CoV-2 incidence to the reported provincial incidence in Spain.
- The authors state this as an assumption: Reported provincial incidence in Spain is accurate and representative for the import model.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“While there is little data to inform estimates of R e for 20E (EU1) in July and it differs little from the prior, there is some evidence that 20E (EU1) was growing faster than other variants in August.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A novel variant (orange; 20E (EU1)) with mutation S:A222V on a S:D614G background emerged in early summer and is common in most countries with recent sequences.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“There were also a small number of larger transmission chains including more than 53 transmissions (20 across all data sets) which are not shown in the histograms.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“After p24 normalization, the titer difference shrinks fom 1.28 to 1.14 fold, increasing the p-value to 0.16.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Pseudotyped Lentivirus Production and Titering
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The number of confirmed SARS-CoV-2 cases in Spain rose from around 10 cases per 100k inhabitants per week in early July to 100 in late August, while case numbers remained low in most of Europe during this time.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Notably, the peak in August in the Swiss analysis is larger under the 'min' definition (f) than under the 'max' definition (e), consistent with a more conservative definition of a cluster which would then require more onward transmission.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“From 1 June 2020 to 30 September 2020, the Swiss Federal Office of Public Health (FOPH) reported 23,199 confirmed SARS-CoV-2 cases.14,583 (62.9%) cases provided information about their likely place of exposure and country of infection in a clinical registration form.Of these, 3,304 (22.7%) reported an exposure abroad and 136 (0.9%) named Spain as the country of infection.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Estimation of contributions from imports
plainn = 23,199- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“After sub-sampling, the 20E (EU1) cluster within the Nextstrain build contains 5,145 sequences, 3,369 of which are unique (accounting for Ns).”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Phylogenetic analysis
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Switzerland reported 131 infections in travel returnees, while the model predicts 130.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Travel resumed quickly and peaked during July and August, see Fig. 3.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The substitution A222V in spike has no substantial effect on antigenic properties (a-d) and replication of pseudotyped lentiviruses (e-h).”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In Europe, we see 206 20E (EU1) singletons (46% of all 20E (EU1) introductions).”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“While initial introductions of the variant likely originated from Spain, 20E (EU1) cases outside of Spain surpassed those in Spain in late September and later cross-border transmissions likely originated in other countries (see Fig ED5 B).”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Expansion and spread across Europe
hedgedconditional- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Different mutations between positions 180 and 220 in N are observed in almost every major lineage and we are not aware of any evidence suggesting that these mutations have important phenotypic consequence.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Characterization of S:A222V
hedged- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Residue S477 is close to the receptor binding site (Fig ED2) and part of the epitope recognized by the S2E12 and C102 neutralizing antibodies 17,18 .”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Abstract
What the sources say
- Not checked yetcites [17] Barnes, C. O. et al. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature 588, 682–687 (2020). source
- Not checked yetcites [18] Tortorici, M. A. et al. Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms. Science 370, 950–957 (2020). source
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Despite limitations in sampling, Fig. ED4a clearly shows that most major genotypes in this cluster were distributed to multiple countries, suggesting that identical genotypes were introduced into many countries .”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Expansion and spread across Europe
boosteddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
- The authors state this as an assumption: The majority of mutations observed in the tree arose once and were carried between countries.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The variant seems to have initially spread among agricultural workers in Aragon and Catalonia, then moved into the local population, where it was able to travel to the Valencia Region and on to the rest of the country.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Expansion and spread across Europe
hedgeddirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, countries where 20E (EU1) was rare (Belgium, France, Czech Republic, Fig. ED1) have seen similarly rapid increases, suggesting that this rise was not driven by any particular lineage and that 20E (EU1) has no substantial difference in transmissibility.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
hedged- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The fact that the rapid increase of the frequency of 20E (EU1) slowed or stopped in most countries after the summer travel period and didn't fully replace other variants is consistent with import driven dynamics with little or no competitive advantage.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
hedged- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Though the jitter means branch lengths should be interpreted with caution, the smallest branches shown in the tree equal to 1 mutation.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Pseudotyped Lentivirus Production and Titering
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“It is important to remember that, particularly for countries other than the UK, the full circulating diversity of the variant is probably not being captured, thus intermediate transmissions cannot be ruled out.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Phylogeny and Geographic Distribution
hedged- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Countries like Norway and Iceland have relatively few clusters, with one or two large clusters dominating, suggesting a small number of introductions dominated 20E (EU1) circulation.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
hedgeddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“They are not in the database of commonly misidentified cell lines.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Enzyme-linked immunosorbent assay (ELISA)
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Countries with small (1-4 fold) and large (8-12 fold) discrepancies tend to visit distinct destinations in Spain, see Figs.ED6 and ED7(c-e), further suggesting that underestimation of incidence in travel returnees is determined by destination and behavior.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This selection will exclude any sequences with no coverage or reversions at these positions, but the similarity-based sampling during the Nextstrain run will identify these, as well as any other nearby sequences, and incorporate them into the dataset.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Defining the 20E (EU1) Cluster
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Further, we excluded several problematic sequences due to high intra-sample variation, wrong dates, and over-divergence (divergence values are implausible given the provided dates).”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Defining the 20E (EU1) Cluster
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Travel precautions such as quarantine should in principle have prevented spread of SARS-CoV-2 infections acquired abroad, but in practice failed to have the desired effect.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Countries like the UK and Denmark, on the other hand, show many clusters of varying size, indicating multiple introductions that led to onward spread.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“While we cannot rule out that 20E (EU1) has a slight transmission advantage compared to other variants circulating at the time, most of its spread is explained by epidemiological factors.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
plainconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In case of 20E (EU1) none of these seem to have changed substantially, making it an important example of how travel combined with large regional differences in prevalence can lead to substantial rapid shifts in the variant distribution without a dramatic transmission advantage.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Discussion
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In such a high incidence setting, travel alone cannot explain a rapid rise in frequency and the dynamics points to a bona fide transmission advantage.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Discussion
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The experiment shown is representative of two independent experiments.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This tree allows us to infer lower bounds for the number of introductions to each country, and to identify plausible origins of those introductions.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Phylogeny and Geographic Distribution
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Such association with particular demographics will decay rapidly and with it any associated increased transmission inferred by phylodynamics.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > A C C E L E R A T E D A R T I C L E P R E V I E W
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Gibco (Fisher) Expi293F Cells were used for protein production and have not been authenticated or tested for mycoplasma contamination.”
§ Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 > Enzyme-linked immunosorbent assay (ELISA)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The authors state this as an assumption.
Returning tourists have a similar SARS-CoV-2 incidence to the reported provincial incidence in Spain.
“assuming that returning tourists have a similar incidence”
The authors state this as an assumption.
20E (EU1) spread at the same rate as other variants in the resident countries.
“This model assumes that 20E (EU1) spread at the same rate as other variants in the resident countries”
The authors state this as an assumption.
The majority of mutations observed in the tree arose once and were carried between countries.
“it is reasonable to assume that the majority of mutations observed in the tree arose once and were carried (possibly multiple times) between countries.”
The authors state this as an assumption.
Reported provincial incidence in Spain is accurate and representative for the import model.
“Taking reported incidence in the provinces at face value”
The authors state this as an assumption.
20E (EU1) and non-20E (EU1) variants share a sampling probability.
“20E (EU1) and non-20E (EU1) variants share a sampling probability”
The paper relies on this without support.
Observed frequencies are subject to variable reporting delays.
“Observed frequencies are subject to variable reporting delays.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“the decline in the number of cases by June, 2020 led governments in Europe to rescind control measures and to encourage a return to life as usual, especially in the context of Europe's upcoming summer holidays; this relaxing of control measures led to another wave of infections in countries across Europe in September, 2020.”
From The Lancet Commission on lessons for the future from the COVID-19 pandemic (2022) · cites this paper as [180]
Citations
Cites
A novel coronavirus from patients with pneumonia in China, 2019
Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2001017 · Cited by 28,244
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027
IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era
(2019) · doi:10.1101/849372 · Cited by 16,873
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873
Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein
Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020) · doi:10.1101/2020.02.19.956581 · Cited by 8,586
Self-citationBEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kühnert, D., De Maio, N., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006650 · Cited by 4,556
Self-citationKorber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E. E., Bhattacharya, T., Foley, B., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.043 · Cited by 4,281
Nextstrain: real-time tracking of pathogen evolutionPreprint
Hadfield, J., Megill, C., Bell, S. M., et al. (2017) · bioRxiv · doi:10.1101/224048 · Cited by 3,172
Nextstrain: real-time tracking of pathogen evolution
Hadfield, J., Megill, C., Bell, S. M., Huddleston, J., Potter, B., Callender, C., Sagulenko, P., Bedford, T., & Neher, R. A. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty407 · Cited by 3,154
Self-citationGISAID: Global initiative on sharing all influenza data – from vision to reality
Shu, Y., & McCauley, J. (2017) · Eurosurveillance · doi:10.2807/1560-7917.es.2017.22.13.30494 · Cited by 3,039
Research works printed but not linked: 1
- Pearson, C. A. B. et al. Estimates of severity and transmissibility of novel SARS-CoV-2 variant 501Y.V2 in South Africa. Preprint at https://cmmid.github.io/topics/covid19/sa-novel-variant.html (2021).
Cited by
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Items 501–600 of 605
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WITHDRAWNPreprint
Datta, S. (2021) · ChemRxiv · doi:10.26434/chemrxiv.13102877.v32
Nakata, Y., Ode, H., Kubota, M., Matsuoka, K., MATSUDA, M., NAKASUJI, M., Mori, M., Imahashi, M., Yokomaku, Y., & Iwatani, Y. (2021) · Kansenshogaku zasshi · doi:10.11150/kansenshogakuzasshi.95.293
Desingu, P. A., & Nagarajan, K. (2021) · Research Square · doi:10.21203/rs.3.rs-721043/v1
Sendi, P., Baldan, R., Thierstein, M., Widmer, N., Gowland, P., Gahl, B., Büchi, A. E., Güntensperger, D., Wider, M., Blum, M. R., et al. (2021) · medRxiv · doi:10.1101/2021.08.09.21261789
Advanced Nanomaterial Based Solutions to Mitigate the Challenges of COVID-19 Pandemic
Yadav, A., Mathur, A. K., Hongyu, Z., Gupta, R. K., Kirabira, J. B., & Ssekatawa, K. (2021) · Biotechnology Kiosk · doi:10.37756/bk.21.3.2.1
The SARS-CoV-2 Alpha variant is associated with increased clinical severity of disease
Pascall, D. J., Mollett, G., Blacow, R., Bulteel, N., Campbell, R., Campbell, A., Clifford, S., Davis, C., Filipe, A. D. S., Fjodorova, L., et al. (2021)
Houwaart, T., Belhaj, S., Tawalbeh, E., Nagels, D., Finzer, P., Fröhlich, Y., Benmoumene, A., Asskali, D., Haidar, H., von Dahlen, J., et al. (2021) · medRxiv · doi:10.1101/2021.10.18.21264530
Datta, S. (2021) · doi:10.33774/chemrxiv-2021-l393t-v35
WITHDRAWNPreprint
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Nieto–Chaupis, H. (2021) · ACIS International Conference on Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing (SNPD) · doi:10.1109/snpd51163.2021.9704981
Li, K., Wang, A. K. Y., Liu, S., Fang, S., Lu, A. Z., Shen, J., Yang, L., Hu, C., Yang, K., & Wan, J. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.813964
WITHDRAWNPreprint
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WITHDRAWNPreprint
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WITHDRAWNPreprint
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WITHDRAWNPreprint
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WITHDRAWNPreprint
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WITHDRAWNPreprint
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WITHDRAWNPreprint
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WITHDRAWNPreprint
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WITHDRAWNPreprint
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WITHDRAWNPreprint
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Yan, Y., & Hu, Q. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2111-0_2
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Cadenas, F. G. (2021) · Ambiociencias · doi:10.18002/ambioc.i19.7331
A Pedagogy of COVID-19: Facts from 30 Pandemic Months
Roccetti, M. (2022) · AHFE international · doi:10.54941/ahfe1002788
Turabián, J. L. (2022) · Journal of Diseases Disorders & Treatments · doi:10.47363/jddt/2022(2)117
(2022) · Letters in Applied NanoBioScience · doi:10.33263/lianbs123.087
Padilla‐Blanco, M., Gucciardi, F., Rubio, V., Lastra, A., Lorenzo-Bermejo, T., Ballester, B., González-Pastor, A., Veses, V., Macaluso, G., Sheth, C. C., et al. (2023) · Frontiers in Public Health · doi:10.3389/fpubh.2023.1098965
Reichmuth, M. L., Hodcroft, E. B., & Althaus, C. L. (2023) · medRxiv · doi:10.1101/2023.03.13.23287198
Self-citationNovel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK
Pacchiarini, N., Cronin, M., Sawyer, C., Williams, C., Beazer, A., Cottrell, S. L., Morgan, M., Saunders, V., Moore, C., Connor, T. R., et al. (2023) · Microbial Genomics · doi:10.1099/mgen.0.000984
Author response: Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020
Coppée, R., Blanquart, F., Jary, A., Leducq, V., Ferré, V. M., Yusti, A.-M. F., Daniel, L., Charpentier, C., Lebourgeois, S., Zafilaza, K., et al. (2023) · eLife · doi:10.7554/elife.82538.sa2
Kiprijanovska, S., Bozhinovski, G., Noveski, P., Kostovska, I. M., Stefanovska, E. S., Vujovikј, M., Dichevska, H., Jakovchevska, S., Jovanovska, N., Gjorgoski, I., et al. (2023) · PRILOZI · doi:10.2478/prilozi-2023-0018
Turabián, J. L. (2023) · Archives of Community Medicine and Public Health · doi:10.17352/2455-5479.000201
Virological Diagnosis of SARS-CoV-2 in a Tunisian Orthopedic Institute
(2023) · Translational Medicine Open Access · doi:10.33140/tmoa.01.01.01
Soroush, S., Rad, I., Meghdadi, J., Khodayari, K., & Rahjerdi, A. K. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.19.563051
Sharma, R., Kumar, K., Tyagi, P., Suri, V., Dhiman, D., Saini, L. K., Yadav, J., Sharma, D., & Ghai, B. (2023) · Indian Journal of Social Psychiatry · doi:10.4103/ijsp.ijsp_251_22
Improving infectious disease control in care facilities
van Hensbergen, M. (2024) · doi:10.26481/dis.20240131mh
Singh, P., Kumar, P., Jigar, T. K., Thapa, S., Tuli, H. S., Bansal, P., Shahwan, M. J., Garg, V. K., & Bhatia, G. K. (2024) · Lecture notes in networks and systems · doi:10.1007/978-981-99-8476-3_33
Nonaka, C. K. V., Ribeiro, A. M. D. J., Rocha, G. V., da Hora, H. S., Júnior, A. A. F., Lima, F. D. M., Bastos, I. N., Teles, S. A. S., Weber, T. G. L., Costa, V. F., et al. (2024) · Viruses · doi:10.3390/v16030467
Linosefa, L., Hasmiwati, H., Jamsari, J., & Putra, A. E. (2024) · Pakistan Journal of Biological Sciences · doi:10.3923/pjbs.2024.182.189
Natalia, Y. A., Molenberghs, G., Faes, C., & Neyens, T. (2024) · Spatial and Spatio-temporal Epidemiology · doi:10.1016/j.sste.2024.100660
Data-Driven Methods for Viral Variants’ Identification
Bernasconi, A. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95502-7.00087-7
Neher, R. A. (2024) · eLife · doi:10.7554/elife.98102.1.sa2
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Hensel, Z. (2024) · eLife · doi:10.7554/elife.98102.1
Sironi, M., & Gónzález‐Candelas, F. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-28818-0.00012-4
Shen, Y., Steele, R. J., & Buckeridge, D. L. (2024) · Studies in health technology and informatics · doi:10.3233/shti240818
Phylogeogenomic analysis of the earliest reported sequences of SARS‐CoV‐2 from 161 countries
Laskar, R., Hoque, M., & Ali, S. (2024) · Apmis · doi:10.1111/apm.13499
Secondary structure of the SARS-CoV-2 genome is predictive of nucleotide substitution frequencyPreprint
Hensel, Z. (2025) · eLife · doi:10.7554/elife.98102.2
Neher, R. A. (2025) · eLife · doi:10.7554/elife.98102.3.sa0
Self-citationNègre, P., Tayac, D., Jamme, T., Combis, M.-S., & Maupas‐Schwalm, F. (2025) · Infectious Diseases Now · doi:10.1016/j.idnow.2025.105086
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Seth-Smith, H. M. B., Rooney, A. M., & Egli, A. (2025) · Wiley eBooks · doi:10.1002/9781683674597.ch4
Suita, F., Padilla‐Blanco, M., Aguiló-Gisbert, J., Lorenzo-Bermejo, T., Ballester, B., Cardells, J., Rubio, V., Maiques, E., Lizana, V., & Rubio‐Guerri, C. (2025) · Animals · doi:10.3390/ani15111636
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Infantas, I. (2020) · The Conversation · doi:10.64628/aao.kwwcr9r6u
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K, Y. K. Y. (2025) · Research Square · doi:10.21203/rs.3.rs-7664696/v1
Tracking down the origin and subsequent spread of SARS-CoV-2 lineage B.1.619
Bollen, N., Hong, S. L., Potter, B. I., Lienhard, R., Tritten, M.-L., Sierro, N., Guedj, E., Dulize, R., Bornand, D., Auberson, M., et al. (2025) · Virus Evolution · doi:10.1093/ve/veaf017
Meletis, G., Pappa, S., Gioula, G., Exindari, M., Christoforidi, M., & Papa, A. (2025) · Epidemiologia · doi:10.3390/epidemiologia6040078
Additional file 1 of Detection of SARS-CoV-2 in a dog with hemorrhagic diarrhea
Padilla‐Blanco, M., Vega, S., Enjuanes, L., Morey, A., Lorenzo, T., Marín, C., Ivorra, C., Maiques, E., Rubio, V., & Rubio‐Guerri, C. (2022) · Figshare · doi:10.6084/m9.figshare.21321430
Santos, J. D., Sobral, D., Pinheiro, M. M., Isidro, J., Bogaardt, C., Pinto, M., Eusébio, R., Santos, A., Mamede, R., Horton, D. L., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26711534
Phylogenetics for Genomic Epidemiology
van Dorp, L., & Balloux, F. (2025) · Springer eBooks · doi:10.1007/978-3-031-76448-6_3
Kreitman, A., Mushegian, A. A., Nelson, M. I., Banakis, S., Mederos, C., Chung, M. C., Roder, A. E., Peguero, A., Mueses, S., Cuevas, P., et al. (2026) · Microbiology Spectrum · doi:10.1128/spectrum.01105-25
Zhang, Y., Rob, P., Chen, K., Overton, C. E., Jung, J., & Jo, Y. (2026) · medRxiv · doi:10.64898/2026.02.04.26345559
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Hishiki, T., Yoshimura, Y., Suzuki, R., Murakami, A., Saito, Y., Tanga, N., Shimizu, J., Watashi, K., Takasaki, T., & Miyazaki, K. (2026) · Microbiology and Immunology · doi:10.1111/1348-0421.70053
Epidémiologie génomique des pathogènes au Sénégal : mycobacterium tuberculosis et SARS-CoV-2
Padane, A. (2023) · theses.fr (ABES) · doi:10.70675/e6b26f76z05baz4f66z9706zbde0e41a2626
Caractérisation de la diversité génétique de SARS-CoV-2 dans des échantillons cliniques
Bader, W. (2022) · theses.fr (ABES) · doi:10.70675/09aee16fz8ab8z4823za3d0z6866bfbc0a6c
Fuzzy-Based Maxout–LSTM Based Variant Impact Predictions Using SARS-CoV2 Database
Divya, Aggarwal, A., & Maram, B. (2026) · Iranian Journal of Science and Technology Transactions of Electrical Engineering · doi:10.1007/s40998-026-01086-3
Simpler is not always better: Phylodynamic misspecification and deep-learning correctionsPreprint
Xie, R., Gascuel, O., & Zhukova, A. (2026) · medRxiv · doi:10.64898/2026.05.07.26352661
A method that TRACS multi-species transmission at scale
(2026) · Nature Microbiology · doi:10.1038/s41564-026-02360-0
Global health preparedness for biosecurity threats: a review of emerging technologies and solutions
Ijarotimi, O. A., Amuda, A. A., Omokanye, C. O., & Amuda, M. (2026) · Frontiers in Public Health · doi:10.3389/fpubh.2026.1786846
AI in Healthcare: Promise, Pitfalls, and Future Directions
Nguyen, N. P., Le, T. D. V., Nguyen, N. G. U. Y. E. N., Truong, T. N., Chau, N. C., Nguyen, J., Nguyen, N. G. U. Y. E. N., Nguyen, T. U. O. N. G., Vu, L. T., & Nguyen, T. N. (2026) · TTU Journal of Science · doi:10.53901/tjs.2026.v01.issue02.art02
Metadata
- Authors
- Hodcroft, E. B., Zuber, M., Nadeau, S., Vaughan, T. G., Crawford, K. H. D., Althaus, C. L., Reichmuth, M. L., Bowen, J. E., Walls, A. C., Corti, D., Bloom, J. D., Veesler, D., Mateo, D., Hernando, A., Comas, I., González-Candelas, F., SeqCOVID-SPAIN consortium, González-Candelas, F., Goig, G. A., Chiner-Oms, Á., Cancino-Muñoz, I., López, M. G., Torres-Puente, M., Gomez-Navarro, I., Jiménez-Serrano, S., Ruiz-Roldán, L., Bracho, M. A., García-González, N., Martínez-Priego, L., Galán-Vendrell, I., Ruiz-Hueso, P., De Marco, G., Ferrús, M. L., Carbó-Ramírez, S., D’Auria, G., Coscollá, M., Ruiz-Rodríguez, P., Roig-Sena, F. J., Sanmartín, I., Garcia-Souto, D., Pequeno-Valtierra, A., Tubio, J. M. C., Rodríguez-Castro, J., Rabella, N., Navarro, F., Miró, E., Rodríguez-Iglesias, M., Galán-Sanchez, F., Rodriguez-Pallares, S., de Toro, M., Escudero, M. B., Azcona-Gutiérrez, J. M., Alberdi, M. B., Mayor, A., García-Basteiro, A. L., Moncunill, G., Dobaño, C., Cisteró, P., García-de-Viedma, D., Pérez-Lago, L., Herranz, M., Sicilia, J., Catalán-Alonso, P., Muñoz, P., Muñoz-Cuevas, C., Rodríguez-Rodríguez, G., Alberola-Enguidanos, J., Nogueira, J. M., Camarena, J. J., Rezusta, A., Tristancho-Baró, A., Milagro, A., Martínez-Cameo, N. F., Gracia-Grataloup, Y., Martró, E., Bordoy, A. E., Not, A., Antuori-Torres, A., Benito, R., Algarate, S., Bueno, J., del Pozo, J. L., Boga, J. A., Castelló-Abietar, C., Rojo-Alba, S., Alvarez-Argüelles, M. E., Melon, S., Aranzamendi-Zaldumbide, M., Vergara-Gómez, A., Fernández-Pinero, J., Martínez, M. J., Vila, J., Rubio, E., Peiró-Mestres, A., Navero-Castillejos, J., Posada, D., Valverde, D., Estévez-Gómez, N., Fernandez-Silva, I., de Chiara, L., Gallego-García, P., Varela, N., Moreno, R., Tirado, M. D., Gomez-Pinedo, U., Gozalo-Margüello, M., Eliecer-Cano, M., Méndez-Legaza, J. M., Rodríguez-Lozano, J., Siller, M., Pablo-Marcos, D., Oliver, A., Reina, J., López-Causapé, C., Canut-Blasco, A., Hernáez-Crespo, S., Cordón, M. L. A., Lecároz-Agara, M.-C., Gómez-González, C., Aguirre-Quiñonero, A., López-Mirones, J. I., Fernández-Torres, M., Almela-Ferrer, M. R., Gonzalo-Jiménez, N., Ruiz-García, M. M., Galiana, A., Sanchez-Almendro, J., Cilla, G., Montes, M., Piñeiro, L., Sorarrain, A., Marimón, J. M., Gomez-Ruiz, M. D., López-Hontangas, J. L., González Barberá, E. M., Navarro-Marí, J. M., Pedrosa-Corral, I., Sanbonmatsu-Gámez, S., Pérez-González, C., Chamizo-López, F., Bordes-Benítez, A., Navarro, D., Albert, E., Torres, I., Gascón, I., Torregrosa-Hetland, C. J., Pastor-Boix, E., Cascales-Ramos, P., Fuster-Escrivá, B., Gimeno-Cardona, C., Ocete, M. D., Medina-Gonzalez, R., González-Cantó, J., Martínez-Macias, O., Palop-Borrás, B., de Toro, I., Mediavilla-Gradolph, M. C., Pérez-Ruiz, M., González-Recio, Ó., Gutiérrez-Rivas, M., Simarro-Córdoba, E., Lozano-Serra, J., Robles-Fonseca, L., de Salazar, A., Viñuela-González, L., Chueca, N., García, F., Gómez-Camarasa, C., Carvajal, A., de la Puente, R., Martín-Sánchez, V., Fregeneda-Grandes, J.-M., Molina, A. J., Argüello, H., Fernández-Villa, T., Farga-Martí, M. A., Domínguez-Márquez, V., Costa-Alcalde, J. J., Trastoy, R., Barbeito-Castiñeiras, G., Coira, A., Pérez-del-Molino, M. L., Aguilera, A., Planas, A. M., Soriano, A., Fernandez-Cádenas, I., Pérez-Tur, J., Marcos, M. Á., Moreno-Docón, A., Viedma, E., Mingorance, J., Galán-Montemayor, J. C., Parra-Grande, M., Stadler, T., & Neher, R. A.
- Affiliations
- University of Bern (CH)
- University of Basel (CH)
- SIB Swiss Institute of Bioinformatics (CH)
- University of Washington (US)
- Vir Biotechnology (Switzerland) (CH)
- Howard Hughes Medical Institute (US)
- Consejo Superior de Investigaciones Científicas (ES)
- Universitat de València (ES)
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (ES)
- Universitat Autònoma de Barcelona (ES)
- Hospital de Sant Pau (ES)
- Hospital Clínic de Barcelona (ES)
- Hospital General Universitario Gregorio Marañón (ES)
- Hospital San Pedro de Alcántara (ES)
- Universidad de Zaragoza (ES)
- Hospital Universitario Miguel Servet (ES)
- Hospital Universitari Germans Trias i Pujol (ES)
- Hospital Clínico Universitario Lozano Blesa (ES)
- Servicio Gallego de Salud (ES)
- Universidade de Vigo (ES)
- Marqués de Valdecilla University Hospital (ES)
- Health Research Institute of the Balearic Islands (ES)
- Hospital Universitario Son Espases (ES)
- Osakidetza (ES)
- Hospital General Universitario de Elche (ES)
- Biogipuzkoa Health Research Institute (ES)
- Instituto de Investigación Biosanitaria de Granada (ES)
- Hospital Universitario de Gran Canaria Doctor Negrín (ES)
- INCLIVA Health Research Institute (ES)
- Hospital General de Elda (ES)
- Hospital General Universitario De Valencia (ES)
- Hospital Regional Universitario de Málaga (ES)
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (ES)
- Hospital General Universitario de Albacete (ES)
- Universidad de León (ES)
- Hospital Arnau de Vilanova (ES)
- Complejo Hospitalario Universitario de Santiago (ES)
- Hospital Universitario 12 De Octubre (ES)
- Hospital Universitario La Paz (ES)
- Hospital Universitario Ramón y Cajal (ES)
- Hospital Marina Baixa (ES)
- Corresponding author
- Hodcroft, Emma B.
- Neher, Richard A.
- ORCID
- 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
- López, Mariana Gabriela
- Jiménez-Serrano, Santiago
- Bracho, María Alma
- Ruiz-Hueso, Paula
- Carbó-Ramírez, Sandra
- D’Auria, Giuseppe
- Coscollá, Mireia
- Ruiz-Rodríguez, Paula
- Sanmartín, Isabel
- Navarro, Ferrán
- Miró, Elisenda
- Mayor, Alfredo
- Moncunill, Gemma
- Dobaño, Carlota
- Cisteró, Pau
- Sicilia, Jon
- Camarena, Juan José
- Rezusta, Antonio
- Tristancho-Baró, Alexander
- Milagro, Ana
- Martró, Elisa
- Bordoy, Antoni E.
- Not, Anna
- Benito, Rafael
- Algarate, Sonia
- Bueno, Jessica
- Martínez, Miguel J.
- Peiró-Mestres, Aida
- Posada, David
- Valverde, Diana
- Varela, Nair
- Gozalo-Margüello, Mónica
- Méndez-Legaza, José Manuel
- Siller, María
- Oliver, Antonio
- Reina, Jordi
- López-Causapé, Carla
- Aguirre-Quiñonero, Amaia
- Almela-Ferrer, Maria Rosario
- Gonzalo-Jiménez, Nieves
- Galiana, Antonio
- Cilla, Gustavo
- Montes, Milagrosa
- Piñeiro, Luis
- Sorarrain, Ane
- Marimón, José María
- Pedrosa-Corral, Irene
- Chamizo-López, Francisco
- Navarro, David
- Albert, Eliseo
- Torres, Ignacio
- Gimeno-Cardona, Concepción
- Medina-Gonzalez, Rafael
- Palop-Borrás, Begoña
- Pérez-Ruiz, Mercedes
- González-Recio, Óscar
- Chueca, Natalia
- Carvajal, Ana
- Molina, Antonio José
- Argüello, Héctor
- Costa-Alcalde, José Javier
- Trastoy, Rocío
- Coira, Amparo
- Aguilera, Antonio
- Planas, Anna M.
- Viedma, Esther
- Mingorance, Jesús
- Parra-Grande, Mónica
- Stadler, Tanja
- Neher, Richard A.
- Venue
- Nature
- Published
- 2021-06-07
- Volume
- 595
- Issue
- 7869
- Pages
- 707-712
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W3166766123
- Semantic Scholar
- 2469490cde7d14d5793b659c17202c99169479ec
- Cited by
- 425
- References
- 47
- Citations by year
- 2026: 12 · 2025: 34 · 2024: 53 · 2023: 80 · 2022: 128 · 2021: 115
- FWCI
- 29.76
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- edoc (University of Basel) (acceptedVersion)
- Buleria (Universidad de León) (submittedVersion, cc-by-nc-nd)
- RePEc: Research Papers in Economics (submittedVersion)
- Bern Open Repository and Information System (University of Bern) (submittedVersion, other-oa)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Repository of Digital Objects for Teaching Research and Culture (University of Valencia) (submittedVersion, other-oa)
- Zaguan (University of Zaragoza Repository) (submittedVersion, cc-by)
- Funders
- National Science Foundation
- Howard Hughes Medical Institute
- Burroughs Wellcome Fund
- Universität Basel
- Fast Grants
- European Commission (HORIZON2020, 101003688, COVID-19)
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (196046, 196267)
- Bundesamt für Gesundheit
- Eidgenössische Technische Hochschule Zürich
- Consejo Superior de Investigaciones Científicas
- Instituto de Salud Carlos III (COV20, COV20/00140)
- National Institute of General Medical Sciences (R01GM120553)
- National Institute of Allergy and Infectious Diseases (HHSN272201700059C, COVID-19, DP1AI158186, F30AI149928, R01AI141707)
- H2020 European Research Council (638553)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, COVID-19 pandemic, international travel, viral spread, genomic surveillance, travel restrictions, containment strategies, transmissibility, summer 2020, Europe, Spain
- MeSH terms
- COVID-19, SARS-CoV-2, Europe, Genotype, Humans, Phylogeny, Seasons, Time Factors, Travel
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-06, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-06 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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