Post by Admin on Oct 31, 2020 5:53:33 GMT
Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020
A variant of SARS-CoV-2 emerged in early summer 2020, presumably in Spain, and
has since spread to multiple European countries. The variant was first observed in
Spain in June and has been at frequencies above 40% since July. Outside of Spain,
the frequency of this variant has increased from very low values prior to 15th July
to 40-70% in Switzerland, Ireland, and the United Kingdom in September. It is also
prevalent in Norway, Latvia, the Netherlands, and France. Little can be said about
other European countries because few recent sequences are available. Sequences in this
cluster (20A.EU1) differ from ancestral sequences at 6 or more positions, including the
mutation A222V in the spike protein and A220V in the nucleoprotein. We show that this
variant was exported from Spain to other European countries multiple times and that
much of the diversity of this cluster in Spain is observed across Europe. It is currently
unclear whether this variant is spreading because of a transmission advantage of the
virus or whether high incidence in Spain followed by dissemination through tourists is
sufficient to explain the rapid rise in multiple countries.
INTRODUCTION
Following its emergence in Wuhan in late 2019 (WHO
Emergency Committee, 2020; Zhu et al., 2020), SARSCoV-2 has
caused a global pandemic resulting in unprecedented efforts to
reduce transmission and develop therapies and vaccines. The
spread of the virus across the world has been tracked with phylogenetic
analysis of viral genome sequences (Worobey et al., 2020; Hadfield et al.,
2018; Pybus et al., 2020) which were and still are generated at
a rate far greater than for any other pathogen.
More than 157,000 full genomes are available in GISAID
as of October 2020 (Shu and McCauley, 2017).
In addition to tracking the viral spread, these genome
sequences have been used to monitor mutations which
might change the transmission, pathogenesis, or antigenic
properties of the virus. One mutation in particular, D614G in
the spike protein, has received much attention. This variant
(Nextstrain clade 20A) seeded large outbreaks in Europe in early
2020 and subsequently dominated the outbreaks in the Americas,
thereby largely replacing previously circulating lineages.
This rapid rise has led to the suggestion that this variant is
more transmissible (Korber et al., 2020; Volz et al., 2020).
While the virus spread globally in early 2020 before borders were
closed and viral variants circulating were distributed across the
world, intercontinental travel remained suppressed through the
summer of 2020.
The paucity of intercontinental travel allowed continent
specific variants to emerge. Within Europe, however,
travel resumed in the summer of 2020. Here we report
on a novel SARS-CoV-2 variant 20A.EU1 (S:A222V) that
emerged in early summer 2020, presumably in Spain,
and subsequently spread to multiple locations in Europe.
Over the summer, it rose in frequency in parallel in multiple
countries. As we report here, this variant, 20A.EU1,
and a second variant 20A.EU2 with mutation S:S477N
in the spike protein account for the majority of recent
sequences in Europe. It is unclear at present whether
the rapid spread of either variant is due to association
with particular demographics, properties of the virus, or
chance but the dynamics of both should be carefully monitored.
A variant of SARS-CoV-2 emerged in early summer 2020, presumably in Spain, and
has since spread to multiple European countries. The variant was first observed in
Spain in June and has been at frequencies above 40% since July. Outside of Spain,
the frequency of this variant has increased from very low values prior to 15th July
to 40-70% in Switzerland, Ireland, and the United Kingdom in September. It is also
prevalent in Norway, Latvia, the Netherlands, and France. Little can be said about
other European countries because few recent sequences are available. Sequences in this
cluster (20A.EU1) differ from ancestral sequences at 6 or more positions, including the
mutation A222V in the spike protein and A220V in the nucleoprotein. We show that this
variant was exported from Spain to other European countries multiple times and that
much of the diversity of this cluster in Spain is observed across Europe. It is currently
unclear whether this variant is spreading because of a transmission advantage of the
virus or whether high incidence in Spain followed by dissemination through tourists is
sufficient to explain the rapid rise in multiple countries.
INTRODUCTION
Following its emergence in Wuhan in late 2019 (WHO
Emergency Committee, 2020; Zhu et al., 2020), SARSCoV-2 has
caused a global pandemic resulting in unprecedented efforts to
reduce transmission and develop therapies and vaccines. The
spread of the virus across the world has been tracked with phylogenetic
analysis of viral genome sequences (Worobey et al., 2020; Hadfield et al.,
2018; Pybus et al., 2020) which were and still are generated at
a rate far greater than for any other pathogen.
More than 157,000 full genomes are available in GISAID
as of October 2020 (Shu and McCauley, 2017).
In addition to tracking the viral spread, these genome
sequences have been used to monitor mutations which
might change the transmission, pathogenesis, or antigenic
properties of the virus. One mutation in particular, D614G in
the spike protein, has received much attention. This variant
(Nextstrain clade 20A) seeded large outbreaks in Europe in early
2020 and subsequently dominated the outbreaks in the Americas,
thereby largely replacing previously circulating lineages.
This rapid rise has led to the suggestion that this variant is
more transmissible (Korber et al., 2020; Volz et al., 2020).
While the virus spread globally in early 2020 before borders were
closed and viral variants circulating were distributed across the
world, intercontinental travel remained suppressed through the
summer of 2020.
The paucity of intercontinental travel allowed continent
specific variants to emerge. Within Europe, however,
travel resumed in the summer of 2020. Here we report
on a novel SARS-CoV-2 variant 20A.EU1 (S:A222V) that
emerged in early summer 2020, presumably in Spain,
and subsequently spread to multiple locations in Europe.
Over the summer, it rose in frequency in parallel in multiple
countries. As we report here, this variant, 20A.EU1,
and a second variant 20A.EU2 with mutation S:S477N
in the spike protein account for the majority of recent
sequences in Europe. It is unclear at present whether
the rapid spread of either variant is due to association
with particular demographics, properties of the virus, or
chance but the dynamics of both should be carefully monitored.