Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

Washington, Nicole; Gangavarapu, Karthik; Zeller, Mark; Bolze, Alexandre; Cirulli, Elizabeth T.; Barrett, Kelly; Larsen, Brendan B.; Anderson, Catelyn; White, Simon; Cassens, Tyler; Jacobs, Sharoni; Levan, Geraint; Nguyen, Jason; Ramirez, Jimmy M.; Rivera-Garcia, Charlotte; Sandoval, Efren; Wang, Xueqing; Wong, David; Spencer, Emily; Robles‐Sikisaka, Refugio; Kurzban, Ezra; Hughes, Laura D.; Deng, Xianding; Wang, Candace; Servellita, Venice; Valentine, Holly; Hoff, Peter De; Seaver, Phoebe; Sathe, Shashank; Gietzen, Kimberly; Sickler, Brad; Antico, Jay; Hoon, Kelly; Liu, Jianwen; Harding, Aaron; Bakhtar, Omid; Basler, Tracy; Austin, Brett; Isaksson, Magnus; Febbo, Phil; Becker, David G.; Laurent, Marc; McDonald, Eric; Yeo, G; Knight, Rob; Laurent, Louise C.; Feo, Eileen de; Worobey, Michael; Chiu, Charles Y.; Suchard, Marc A.; Lu, James T.; Lee, William; Andersen, Kristian G.

doi:10.1101/2021.02.06.21251159

Cited by 91 publications

(94 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…It has been found that the new variant VOC-202012/01 of lineage B.1.1.7. is more transmissible [2,[165][166][167]. Furthermore, some researchers have predicted that this new variant will likely become the dominant variant in many U.S. states by March 2021, leading to further surges of COVID-19 in the country, unless urgent mitigation efforts are immediately implemented [166].…”

Section: Discussionmentioning

confidence: 99%

Impact of a New SARS-CoV-2 Variant on the Population: A Mathematical Modeling Approach

González-Parra

Martínez‐Rodríguez

Micó

2021

MCA

View full text Add to dashboard Cite

Several SARS-CoV-2 variants have emerged around the world, and the appearance of other variants depends on many factors. These new variants might have different characteristics that can affect the transmissibility and death rate. The administration of vaccines against the coronavirus disease 2019 (COVID-19) started in early December of 2020 and in some countries the vaccines will not soon be widely available. For this article, we studied the impact of a new more transmissible SARS-CoV-2 strain on prevalence, hospitalizations, and deaths related to the SARS-CoV-2 virus. We studied different scenarios regarding the transmissibility in order to provide a scientific support for public health policies and bring awareness of potential future situations related to the COVID-19 pandemic. We constructed a compartmental mathematical model based on differential equations to study these different scenarios. In this way, we are able to understand how a new, more infectious strain of the virus can impact the dynamics of the COVID-19 pandemic. We studied several metrics related to the possible outcomes of the COVID-19 pandemic in order to assess the impact of a higher transmissibility of a new SARS-CoV-2 strain on these metrics. We found that, even if the new variant has the same death rate, its high transmissibility can increase the number of infected people, those hospitalized, and deaths. The simulation results show that health institutions need to focus on increasing non-pharmaceutical interventions and the pace of vaccine inoculation since a new variant with higher transmissibility, such as, for example, VOC-202012/01 of lineage B.1.1.7, may cause more devastating outcomes in the population.

show abstract

Section: Discussionmentioning

confidence: 99%

Impact of a New SARS-CoV-2 Variant on the Population: A Mathematical Modeling Approach

González-Parra

Martínez‐Rodríguez

Micó

2021

MCA

View full text Add to dashboard Cite

show abstract

“…In late 2020, two SARS-CoV-2 lineages of concern were discovered through genomic surveillance, both characterised by sets of significant mutations: lineage B.1.351, first reported in South Africa (12) and lineage B.1.1.7, detected in the United Kingdom (13). Both variants have transmitted rapidly in the countries where they were discovered and spread to other regions (14,15). Analyses indicate B.1.1.7 has higher transmissibility than previously circulating lineages in the UK (13).…”

Section: Identification and Nomenclature Of A Novel P1 Lineage In Mamentioning

confidence: 99%

“…AmpureXP beads (Beckman Coulter, United Kingdom) were used for PCR product purification and fluorimetry-based quantification was carried out using the Qubit dsDNA High Sensitivity assay on the Qubit 3.0 (Life Technologies, USA). To ensure uniform sequencing of samples, equimolar normalisation of 10 ng per sample was performed followed by barcoding using the EXP-NBD104 (1-12) and EXP-NBD114 (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24) Native Barcoding Kits (Oxford Nanopore Technologies, UK). Finally, barcoded samples were pooled followed by library preparation using the SQK-LSK109 Kit (Oxford Nanopore Technologies, UK).…”

Section: Pcr Amplification and Virus Nanopore Sequencingmentioning

confidence: 99%

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil

Faria

Mellan

Whittaker

et al. 2021

Preprint

Self Cite

225

237

View full text Add to dashboard Cite

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4–2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.One-Sentence SummaryWe report the evolution and emergence of a SARS-CoV-2 lineage of concern associated with rapid transmission in Manaus.

show abstract

“…Despite accounting for roughly 25% of globally recorded COVID-19 cases, and approximately 20% of the available SARS-CoV-2 genome data, relatively few studies have detailed the introduction and emergence of SARS-CoV-2 lineages in the United States (Rochman et al, 2020;Worobey et al, 2020;Washington et al, 2021;Zeller et al, 2021). Furthermore, seroprevalence surveys indicate that between 1 in 10 and 1 in 3 people in the USA have already been infected with SARS-CoV-2, potentially high enough that selection for immune evasion may be present (Angulo, Finelli and Swerdlow, 2021;Bubar et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677

Hodcroft

Domman

Snyder³

et al. 2021

Preprint

122

116

View full text Add to dashboard Cite

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) plays critical roles in host cell entry. Non-synonymous substitutions affecting S are not uncommon and have become fixed in a number of SARS-CoV-2 lineages. A subset of such mutations enable escape from neutralizing antibodies or are thought to enhance transmission through mechanisms such as increased affinity for the cell entry receptor, angiotensin-converting enzyme 2 (ACE2). Independent genomic surveillance programs based in New Mexico and Louisiana contemporaneously detected the rapid rise of numerous clade 20G (lineage B.1.2) infections carrying a Q677P substitution in S. The variant was first detected in the US on October 23, yet between 01 Dec 2020 and 19 Jan 2021 it rose to represent 27.8% and 11.3% of all SARS-CoV-2 genomes sequenced from Louisiana and New Mexico, respectively. Q677P cases have been detected predominantly in the south central and southwest United States; as of 03 Feb 2021, GISAID data show 499 viral sequences of this variant from the USA. Phylogenetic analyses revealed the independent evolution and spread of at least six distinct Q677H sub-lineages, with first collection dates ranging from mid-August to late November 2020. Four 677H clades from clade 20G (B.1.2), 20A (B.1.234), and 20B (B.1.1.220, and B.1.1.222) each contain roughly 100 or fewer sequenced cases, while a distinct pair of clade 20G clusters are represented by 754 and 298 cases, respectively. Although sampling bias and founder effects may have contributed to the rise of S:677 polymorphic variants, the proximity of this position to the polybasic cleavage site at the S1/S2 boundary are consistent with its potential functional relevance during cell entry, suggesting parallel evolution of a trait that may confer an advantage in spread or transmission. Taken together, our findings demonstrate simultaneous convergent evolution, thus providing an impetus to further evaluate S:677 polymorphisms for effects on proteolytic processing, cell tropism, and transmissibility.

show abstract

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

Cited by 91 publications

References 22 publications

Impact of a New SARS-CoV-2 Variant on the Population: A Mathematical Modeling Approach

Impact of a New SARS-CoV-2 Variant on the Population: A Mathematical Modeling Approach

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil

Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677

Contact Info

Product

Resources

About