Virus Variant First Found in Britain Now Spreading Rapidly
Feb 7, 2021 16:51:05 GMT
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Post by Deleted on Feb 7, 2021 16:51:05 GMT
Virus Variant First Found in Britain Now Spreading Rapidly in U.S.
REF:link
A more contagious variant of the coronavirus first found in Britain is spreading rapidly in the United States, doubling roughly every 10 days, according to a new study.
Analyzing half a million coronavirus tests and hundreds of genomes, a team of researchers predicted that in a month this variant could become predominant in the United States, potentially bringing a surge of new cases and increased risk of death.
The new research offers the first nationwide look at the history of the variant, known as B.1.1.7, since it arrived in the United States in late 2020. Last month, the Centers for Disease Control and Prevention warned that B.1.1.7 could become predominant by March if it behaved the way it did in Britain. The new study confirms that projected path.
“Nothing in this paper is surprising, but people need to see it,” said Kristian Andersen, a co-author of the study and a virologist at the Scripps Research Institute in La Jolla, Calif. “We should probably prepare for this being the predominant lineage in most places in the United States by March.”
Dr. Andersen’s team estimated that the transmission rate of B.1.1.7 in the United States is 30 percent to 40 percent higher than that of more common variants, although those figures may rise as more data comes in, he said. The variant has already been implicated in surges in other countries, including Ireland, Portugal and Jordan.
Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States
REF:link
Discussion
The B.1.1.7 variant established itself as the dominant SARS-CoV-2 lineage in the U.K. within acouple of months after its detection (Bal et al., 2020; Chand et al., 2020). Since then, the varianthas been increasingly observed across many European countries, including Portugal and Ireland,which, like the U.K., observed devastating waves of COVID-19 after B.1.1.7 became dominant(ECDC, 2021). In this study, we show that B.1.1.7 is currently at a relatively low frequency in the U.S., but our estimates show that its growth rate is at least 35-45% increased and doubling everyweek and a half. These findings are consistent with those from other countries (Volz et al., 2021),and given the current trajectory of B.1.1.7 in the U.S., it is almost certainly destined to becomethe dominant SARS-CoV-2 lineage by March, 2021 across many U.S. states, which is consistentwith modeling analyses from the U.S. Centers for Disease Control and Prevention (Galloway etal., 2021). However, obtaining accurate estimates of the prevalence of B.1.1.7 across the countryis complicated by uneven and biased sampling, combined with a lack of a national SARS-CoV-2genomics surveillance program, like those implemented in the U.K., Denmark, Australia, NewZealand, among other places. In the current study, we obtain relatively robust estimates fromCalifornia and Florida, but our analyses outside these places are limited.
Our phylogenetic analyses indicate that there have been multiple introductions of B.1.1.7 into theU.S., with the earliest dating back to the end of November, 2020. These analyses revealed largeclades of closely related SARS-CoV-2 lineages clustering within individual states, as well asnational spread indicated by several smaller clades defined by mixtures of samples from patientswho reside in different U.S. states. These findings are consistent with community transmissionfollowing several of these introductions, including spread across U.S. states However, unresolvedpolytomies of sequences belonging to different regions nationally and internationally at severalbasal nodes in our phylogenies, mean that we are unable to fully resolve directionality and likelyorigins for the U.S. sequences (Grubaugh et al., 2019a). However, our TMRCA estimates coincidewith increased periods of travel, where the U.S. Transportation Security Administration reportedover one million travelers crossing checkpoints for several days during the peak Thanksgivingseason (November 20-29, 2020) and for twelve of eighteen days surrounding the Christmas andNew Year’s holidays (December 18, 2020 to January 4, 2021) (TSA, 2021), providing a likelyexplanation for how B.1.1.7 may have been introduced via international travel and spread acrossthe U.S. via domestic travel.
In addition to well-supported local clades in California, Florida, and Georgia from our phylogeneticanalyses, many of the initial B.1.1.7 cases in the U.S. did not report recent international travelprior to infection (Davis, 2020; Romo, 2020). These findings suggest that significant communitytransmission of the B.1.1.7 variant is already ongoing across the U.S., which is likely fueled by itsincreased growth rate and transmissibility of B.1.1.7. We found the growth rates in California (~6%/ day) to be slightly lower than those in Florida (~8% / day). This difference may be due todifferences in statewide or regional social distancing protocols or mobility patterns, populationdensity, biases in sampling and/or demographics, or competition from other SARS-CoV-2variants, like the B.1.429 variant recently described in California (CDPH, 2021). The nationwidegrowth rate of ~7% / day is a little lower than those observed in Portugal (10% / day (Borges,2021)), Denmark (10.3% / day (Statens Serums Institute)) and the United Kingdom (10.4% / day(Davies et al., 2020)). The reason for the slightly lower growth rate of B.1.1.7 in the U.S. comparedto European countries require further investigation, but may be down to the relative sparsity ofthe current dataset, the lack of strong mitigation efforts in this country, or competition from othermore transmissible SARS-CoV-2 variants.
Our study shows that although SGTF is not yet a universal proxy for the B.1.1.7 variant in theU.S., the increased growth rate of B.1.1.7 compared to other SGTF variants (Volz et al., 2021)will likely lead to B.1.1.7 overtaking other SGTF variants in a matter of weeks. This will allow thesimple SGTF testing anomaly to be used to monitor the spread of B.1.1.7 in the U.S. in theabsence of nationwide genomic surveillance.While B.1.1.7 is of current interest given the concerns regarding increased transmissiondynamics, the results here reinforce the need for ongoing SARS-CoV-2 genomic surveillance tomonitor the dynamics of B.1.1.7 and other emerging SARS-CoV-2 variants, including those yet tobe discovered. Because laboratories in the U.S. are only sequencing a small subset of SARSCoV-2 samples, the true sequence diversity of SARS-CoV-2 in this country is still unknown. Themore established surveillance programs in other countries have provided important warningsabout variants of concern that can impact the U.S., with B.1.1.7 representing only one variant thatdemonstrates the capacity for exponential growth. As viral surveillance efforts increase in theU.S., we will no doubt find additional SARS-CoV-2 variants, some at high prevalence and otherswith increased fitness. Only with consistent, unbiased sequencing at scale that includes allgeographic and demographic populations including those often underrepresented, together withcontinued international scientific collaborations and open data sharing, will we be able toaccurately assess and follow new variants that emerge during the COVID-19 pandemic. Giventhat the SARS-CoV-2 VOCs B.1.1.7, B.1.351, and P.1 are still at relatively low frequency in theU.S., there is still time to implement the necessary surveillance programs and mitigation efforts inthe weeks to come. Unless decisive and immediate public health action is taken, the increasedtransmission rate of these lineages and resultant higher effective reproduction number of SARSCoV-2 will likely have devastating consequences to COVID-19 mortality and morbidity in the U.S.in a few months, if decisive action is not immediately taken.
REF:link
A more contagious variant of the coronavirus first found in Britain is spreading rapidly in the United States, doubling roughly every 10 days, according to a new study.
Analyzing half a million coronavirus tests and hundreds of genomes, a team of researchers predicted that in a month this variant could become predominant in the United States, potentially bringing a surge of new cases and increased risk of death.
The new research offers the first nationwide look at the history of the variant, known as B.1.1.7, since it arrived in the United States in late 2020. Last month, the Centers for Disease Control and Prevention warned that B.1.1.7 could become predominant by March if it behaved the way it did in Britain. The new study confirms that projected path.
“Nothing in this paper is surprising, but people need to see it,” said Kristian Andersen, a co-author of the study and a virologist at the Scripps Research Institute in La Jolla, Calif. “We should probably prepare for this being the predominant lineage in most places in the United States by March.”
Dr. Andersen’s team estimated that the transmission rate of B.1.1.7 in the United States is 30 percent to 40 percent higher than that of more common variants, although those figures may rise as more data comes in, he said. The variant has already been implicated in surges in other countries, including Ireland, Portugal and Jordan.
Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States
REF:link
Discussion
The B.1.1.7 variant established itself as the dominant SARS-CoV-2 lineage in the U.K. within acouple of months after its detection (Bal et al., 2020; Chand et al., 2020). Since then, the varianthas been increasingly observed across many European countries, including Portugal and Ireland,which, like the U.K., observed devastating waves of COVID-19 after B.1.1.7 became dominant(ECDC, 2021). In this study, we show that B.1.1.7 is currently at a relatively low frequency in the U.S., but our estimates show that its growth rate is at least 35-45% increased and doubling everyweek and a half. These findings are consistent with those from other countries (Volz et al., 2021),and given the current trajectory of B.1.1.7 in the U.S., it is almost certainly destined to becomethe dominant SARS-CoV-2 lineage by March, 2021 across many U.S. states, which is consistentwith modeling analyses from the U.S. Centers for Disease Control and Prevention (Galloway etal., 2021). However, obtaining accurate estimates of the prevalence of B.1.1.7 across the countryis complicated by uneven and biased sampling, combined with a lack of a national SARS-CoV-2genomics surveillance program, like those implemented in the U.K., Denmark, Australia, NewZealand, among other places. In the current study, we obtain relatively robust estimates fromCalifornia and Florida, but our analyses outside these places are limited.
Our phylogenetic analyses indicate that there have been multiple introductions of B.1.1.7 into theU.S., with the earliest dating back to the end of November, 2020. These analyses revealed largeclades of closely related SARS-CoV-2 lineages clustering within individual states, as well asnational spread indicated by several smaller clades defined by mixtures of samples from patientswho reside in different U.S. states. These findings are consistent with community transmissionfollowing several of these introductions, including spread across U.S. states However, unresolvedpolytomies of sequences belonging to different regions nationally and internationally at severalbasal nodes in our phylogenies, mean that we are unable to fully resolve directionality and likelyorigins for the U.S. sequences (Grubaugh et al., 2019a). However, our TMRCA estimates coincidewith increased periods of travel, where the U.S. Transportation Security Administration reportedover one million travelers crossing checkpoints for several days during the peak Thanksgivingseason (November 20-29, 2020) and for twelve of eighteen days surrounding the Christmas andNew Year’s holidays (December 18, 2020 to January 4, 2021) (TSA, 2021), providing a likelyexplanation for how B.1.1.7 may have been introduced via international travel and spread acrossthe U.S. via domestic travel.
In addition to well-supported local clades in California, Florida, and Georgia from our phylogeneticanalyses, many of the initial B.1.1.7 cases in the U.S. did not report recent international travelprior to infection (Davis, 2020; Romo, 2020). These findings suggest that significant communitytransmission of the B.1.1.7 variant is already ongoing across the U.S., which is likely fueled by itsincreased growth rate and transmissibility of B.1.1.7. We found the growth rates in California (~6%/ day) to be slightly lower than those in Florida (~8% / day). This difference may be due todifferences in statewide or regional social distancing protocols or mobility patterns, populationdensity, biases in sampling and/or demographics, or competition from other SARS-CoV-2variants, like the B.1.429 variant recently described in California (CDPH, 2021). The nationwidegrowth rate of ~7% / day is a little lower than those observed in Portugal (10% / day (Borges,2021)), Denmark (10.3% / day (Statens Serums Institute)) and the United Kingdom (10.4% / day(Davies et al., 2020)). The reason for the slightly lower growth rate of B.1.1.7 in the U.S. comparedto European countries require further investigation, but may be down to the relative sparsity ofthe current dataset, the lack of strong mitigation efforts in this country, or competition from othermore transmissible SARS-CoV-2 variants.
Our study shows that although SGTF is not yet a universal proxy for the B.1.1.7 variant in theU.S., the increased growth rate of B.1.1.7 compared to other SGTF variants (Volz et al., 2021)will likely lead to B.1.1.7 overtaking other SGTF variants in a matter of weeks. This will allow thesimple SGTF testing anomaly to be used to monitor the spread of B.1.1.7 in the U.S. in theabsence of nationwide genomic surveillance.While B.1.1.7 is of current interest given the concerns regarding increased transmissiondynamics, the results here reinforce the need for ongoing SARS-CoV-2 genomic surveillance tomonitor the dynamics of B.1.1.7 and other emerging SARS-CoV-2 variants, including those yet tobe discovered. Because laboratories in the U.S. are only sequencing a small subset of SARSCoV-2 samples, the true sequence diversity of SARS-CoV-2 in this country is still unknown. Themore established surveillance programs in other countries have provided important warningsabout variants of concern that can impact the U.S., with B.1.1.7 representing only one variant thatdemonstrates the capacity for exponential growth. As viral surveillance efforts increase in theU.S., we will no doubt find additional SARS-CoV-2 variants, some at high prevalence and otherswith increased fitness. Only with consistent, unbiased sequencing at scale that includes allgeographic and demographic populations including those often underrepresented, together withcontinued international scientific collaborations and open data sharing, will we be able toaccurately assess and follow new variants that emerge during the COVID-19 pandemic. Giventhat the SARS-CoV-2 VOCs B.1.1.7, B.1.351, and P.1 are still at relatively low frequency in theU.S., there is still time to implement the necessary surveillance programs and mitigation efforts inthe weeks to come. Unless decisive and immediate public health action is taken, the increasedtransmission rate of these lineages and resultant higher effective reproduction number of SARSCoV-2 will likely have devastating consequences to COVID-19 mortality and morbidity in the U.S.in a few months, if decisive action is not immediately taken.