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Article ; Online: SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads.

Cell reports. Medicine

2022 Volume 3, Issue 3, Page(s) 100564

Abstract: We report on the sequencing of 74,348 SARS-CoV-2 positive samples collected across the United States and show that the Delta variant, first detected in the United States in March 2021, made up the majority of SARS-CoV-2 infections by July 1, 2021 and ... ...

Abstract	We report on the sequencing of 74,348 SARS-CoV-2 positive samples collected across the United States and show that the Delta variant, first detected in the United States in March 2021, made up the majority of SARS-CoV-2 infections by July 1, 2021 and accounted for >99.9% of the infections by September 2021. Not only did Delta displace variant Alpha, which was the dominant variant at the time, it also displaced the Gamma, Iota, and Mu variants. Through an analysis of quantification cycle (Cq) values, we demonstrate that Delta infections tend to have a 1.7× higher viral load compared to Alpha infections (a decrease of 0.8 Cq) on average. Our results are consistent with the hypothesis that the increased transmissibility of the Delta variant could be due to the ability of the Delta variant to establish a higher viral load earlier in the infection as compared to the Alpha variant.
MeSH term(s)	COVID-19/epidemiology ; Humans ; SARS-CoV-2/genetics ; United States/epidemiology ; Viral Load/genetics
Language	English
Publishing date	2022-03-15
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ISSN	2666-3791
ISSN (online)	2666-3791
DOI	10.1016/j.xcrm.2022.100564
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A Method for Variant Agnostic Detection of SARS-CoV-2, Rapid Monitoring of Circulating Variants, and Early Detection of Emergent Variants Such as Omicron.

Lai, Eric / Kennedy, Emily B / Lozach, Jean / Hayashibara, Kathleen / Davis-Turak, Jeremy / Becker, David / Brzoska, Pius / Cassens, Tyler / Diamond, Evan / Gandhi, Manoj / Greninger, Alexander L / Hajian, Pooneh / Leonetti, Nicole A / Nguyen, Jason M / O'Donovan, K M Clair / Peck, Troy / Ramirez, Jimmy M / Roychoudhury, Pavitra / Sandoval, Efren /

Wesselman, Cassandra / Wesselman, Timothy / White, Simon / Williams, Stephen / Wong, David / Yu, Yufei / Creager, Richard S

Journal of clinical microbiology

2022 Volume 60, Issue 7, Page(s) e0034222

Abstract: The rapid emergence of SARS-CoV-2 variants raised public health questions concerning the capability of diagnostic tests to detect new strains, the efficacy of vaccines, and how to map the geographical distribution of variants to understand transmission ... ...

Abstract	The rapid emergence of SARS-CoV-2 variants raised public health questions concerning the capability of diagnostic tests to detect new strains, the efficacy of vaccines, and how to map the geographical distribution of variants to understand transmission patterns and loads on healthcare resources. Next-generation sequencing (NGS) is the primary method for detecting and tracing new variants, but it is expensive, and it can take weeks before sequence data are available in public repositories. This article describes a customizable reverse transcription PCR (RT-PCR)-based genotyping approach which is significantly less expensive, accelerates reporting, and can be implemented in any lab that performs RT-PCR. Specific single-nucleotide polymorphisms (SNPs) and indels were identified which had high positive-percent agreement (PPA) and negative-percent agreement (NPA) compared to NGS for the major genotypes that circulated through September 11, 2021. Using a 48-marker panel, testing on 1,031 retrospective SARS-CoV-2 positive samples yielded a PPA and NPA ranging from 96.3 to 100% and 99.2 to 100%, respectively, for the top 10 most prevalent World Health Organization (WHO) lineages during that time. The effect of reducing the quantity of panel markers was explored, and a 16-marker panel was determined to be nearly as effective as the 48-marker panel at lineage assignment. Responding to the emergence of Omicron, a genotyping panel was developed which distinguishes Delta and Omicron using four highly specific SNPs. The results demonstrate the utility of the condensed panel to rapidly track the growing prevalence of Omicron across the US in December 2021 and January 2022.
MeSH term(s)	COVID-19/diagnosis ; Humans ; Nucleic Acid Amplification Techniques ; Retrospective Studies ; SARS-CoV-2/genetics
Language	English
Publishing date	2022-06-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/jcm.00342-22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Rapid displacement of SARS-CoV-2 variant B.1.1.7 by B.1.617.2 and P.1 in the United States

Bolze, Alexandre / Cirulli, Elizabeth T / Luo, Shishi / White, Simon / Cassens, Tyler / Jacobs, Sharoni / Nguyen, Jason / Ramirez, Jimmy M. / Sandoval, Efren / Wang, Xueqing / Wong, David / Becker, David / Laurent, Marc / Lu, James / Isaksson, Magnus / Washington, Nicole L / Lee, William

medRxiv

Abstract: The SARS-CoV-2 variant of concern B.1.617.2 displaced B.1.1.7 as the dominant variant in England and other countries. This study aimed to determine whether B.1.617.2 was also displacing B.1.1.7 in the United States. We analyzed PCR testing results and ... ...

Abstract	The SARS-CoV-2 variant of concern B.1.617.2 displaced B.1.1.7 as the dominant variant in England and other countries. This study aimed to determine whether B.1.617.2 was also displacing B.1.1.7 in the United States. We analyzed PCR testing results and viral sequencing results of samples collected across the United States, and showed that B.1.1.7 was rapidly being displaced and is no longer responsible for the majority of new cases. The percentage of SARS-CoV-2 positive cases that are B.1.1.7 dropped from 70% in April 2021 to 42% in just 6 weeks. Our analysis showed rapid growth of variants B.1.617.2 and P.1 as the primary drivers for this displacement. Currently, the growth rate of B.1.617.2 was higher than P.1 in the US (0.61 vs. 0.22), which is consistent with reports from other countries. Lastly, we showed that B.1.617.2 was growing faster in counties with a lower vaccination rate.
Keywords	covid19
Language	English
Publishing date	2021-06-21
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.06.20.21259195
Database	COVID19

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Article ; Online: Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility.

van Blokland, Irene V / Lanting, Pauline / Ori, Anil P S / Vonk, Judith M / Warmerdam, Robert C A / Herkert, Johanna C / Boulogne, Floranne / Claringbould, Annique / Lopera-Maya, Esteban A / Bartels, Meike / Hottenga, Jouke-Jan / Ganna, Andrea / Karjalainen, Juha / Hayward, Caroline / Fawns-Ritchie, Chloe / Campbell, Archie / Porteous, David / Cirulli, Elizabeth T / Schiabor Barrett, Kelly M /

Riffle, Stephen / Bolze, Alexandre / White, Simon / Tanudjaja, Francisco / Wang, Xueqing / Ramirez, Jimmy M / Lim, Yan Wei / Lu, James T / Washington, Nicole L / de Geus, Eco J C / Deelen, Patrick / Boezen, H Marike / Franke, Lude H

PloS one

2021 Volume 16, Issue 8, Page(s) e0255402

Abstract: Epidemiological and genetic studies on COVID-19 are currently hindered by inconsistent and limited testing policies to confirm SARS-CoV-2 infection. Recently, it was shown that it is possible to predict COVID-19 cases using cross-sectional self-reported ... ...

Abstract	Epidemiological and genetic studies on COVID-19 are currently hindered by inconsistent and limited testing policies to confirm SARS-CoV-2 infection. Recently, it was shown that it is possible to predict COVID-19 cases using cross-sectional self-reported disease-related symptoms. Here, we demonstrate that this COVID-19 prediction model has reasonable and consistent performance across multiple independent cohorts and that our attempt to improve upon this model did not result in improved predictions. Using the existing COVID-19 prediction model, we then conducted a GWAS on the predicted phenotype using a total of 1,865 predicted cases and 29,174 controls. While we did not find any common, large-effect variants that reached genome-wide significance, we do observe suggestive genetic associations at two SNPs (rs11844522, p = 1.9x10-7; rs5798227, p = 2.2x10-7). Explorative analyses furthermore suggest that genetic variants associated with other viral infectious diseases do not overlap with COVID-19 susceptibility and that severity of COVID-19 may have a different genetic architecture compared to COVID-19 susceptibility. This study represents a first effort that uses a symptom-based predicted phenotype as a proxy for COVID-19 in our pursuit of understanding the genetic susceptibility of the disease. We conclude that the inclusion of symptom-based predicted cases could be a useful strategy in a scenario of limited testing, either during the current COVID-19 pandemic or any future viral outbreak.
MeSH term(s)	Area Under Curve ; COVID-19/genetics ; COVID-19/pathology ; COVID-19/virology ; Cross-Sectional Studies ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Phenotype ; Polymorphism, Single Nucleotide ; ROC Curve ; SARS-CoV-2/isolation & purification
Language	English
Publishing date	2021-08-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0255402
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.

Washington, Nicole L / Gangavarapu, Karthik / Zeller, Mark / Bolze, Alexandre / Cirulli, Elizabeth T / Schiabor Barrett, Kelly M / 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 / De Hoff, Peter / Seaver, Phoebe / Sathe, Shashank / Gietzen, Kimberly / Sickler, Brad / Antico, Jay / Hoon, Kelly / Liu, Jingtao / Harding, Aaron / Bakhtar, Omid / Basler, Tracy / Austin, Brett / MacCannell, Duncan / Isaksson, Magnus / Febbo, Phillip G / Becker, David / Laurent, Marc / McDonald, Eric / Yeo, Gene W / Knight, Rob / Laurent, Louise C / de Feo, Eileen / Worobey, Michael / Chiu, Charles Y / Suchard, Marc A / Lu, James T / Lee, William / Andersen, Kristian G

Cell

2021 Volume 184, Issue 10, Page(s) 2587–2594.e7

Abstract: The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing, we investigated the prevalence and dynamics of ... ...

Abstract	The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing, we investigated the prevalence and dynamics of this variant in the United States (US), tracking it back to its early emergence. We found that, while the fraction of B.1.1.7 varied by state, the variant increased at a logistic rate with a roughly weekly doubling rate and an increased transmission of 40%-50%. We revealed several independent introductions of B.1.1.7 into the US as early as late November 2020, with community transmission spreading it to most states within months. We show that the US is on a similar trajectory as other countries where B.1.1.7 became dominant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.
MeSH term(s)	COVID-19/genetics ; COVID-19/mortality ; COVID-19/transmission ; Female ; Humans ; Male ; Models, Biological ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; SARS-CoV-2/pathogenicity ; United States/epidemiology
Language	English
Publishing date	2021-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.03.052
Database	MEDical Literature Analysis and Retrieval System OnLINE

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

Washington, Nicole L / Gangavarapu, Karthik / Zeller, Mark / Bolze, Alexandre / Cirulli, Elizabeth T / Barrett, Kelly M Schiabor / 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 / De Hoff, Peter / Seaver, Phoebe / Sathe, Shashank / Gietzen, Kimberly / Sickler, Brad / Antico, Jay / Hoon, Kelly / Liu, Jingtao / Harding, Aaron / Bakhtar, Omid / Basler, Tracy / Austin, Brett / Isaksson, Magnus / Febbo, Phillip G / Becker, David / Laurent, Marc / McDonald, Eric / Yeo, Gene W / Knight, Rob / Laurent, Louise C / de Feo, Eileen / Worobey, Michael / Chiu, Charles / Suchard, Marc A / Lu, James T / Lee, William / Andersen, Kristian G

medRxiv : the preprint server for health sciences

2021

Abstract: As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the ... ...

Abstract	As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.
Language	English
Publishing date	2021-02-07
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.02.06.21251159
Database	MEDical Literature Analysis and Retrieval System OnLINE

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

Washington, Nicole L. / Gangavarapu, Karthik / Zeller, Mark / Bolze, Alexandre / Cirulli, Elizabeth T. / Schiabor Barrett, Kelly M. / 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 / De Hoff, Peter / Seaver, Phoebe / Sathe, Shashank / Gietzen, Kimberly / Sickler, Brad / Antico, Jay / Hoon, Kelly / Liu, Jingtao / Harding, Aaron / Bakhtar, Omid / Basler, Tracy / Austin, Brett / Isaksson, Magnus / Febbo, Phil / Becker, David / Laurent, Marc / McDonald, Eric / Yeo, Gene W. / Knight, Rob / Laurent, Louise C. / de Feo, Eileen / Worobey, Michael / Chiu, Charles / Suchard, Marc A. / Lu, James T. / Lee, William / Andersen, Kristian G.

medRxiv

Abstract	As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.
Keywords	covid19
Language	English
Publishing date	2021-02-07
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.02.06.21251159
Database	COVID19

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Article ; Online: Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility

van Blokland, Irene V / Lanting, Pauline / Ori, Anil PS / Vonk, Judith M / Warmerdam, Robert CA / Herkert, Johanna C / Boulogne, Floranne / Claringbould, Annique / Lopera-Maya, Esteban A / Bartels, Meike / Hottenga, Jouke-Jan / Ganna, Andrea / Karjalainen, Juha / Lifelines COVID-19 cohort study / The COVID-19 Host Genetics Initiative / Hayward, Caroline / Fawns-Ritchie, Chloe / Campbell, Archie / Porteous, David /

Cirulli, Elizabeth T / Schiabor Barrett, Kelly M / Riffle, Stephen / Bolze, Alexandre / White, Simon / Tanudjaja, Francisco / Wang, Xueqing / Ramirez, Jimmy M / Lim, Yan Wei / Lu, James T / Washington, Nicole L / de Geus, Eco JC / Deelen, Patrick / Boezen, H Marike / Franke, Lude H

medRxiv

Abstract: Epidemiological and genetic studies on COVID-19 are hindered by inconsistent and limited testing policies to confirm SARS-CoV-2 infection. Recently, it was shown that it is possible to predict potential COVID-19 cases using cross-sectional self-reported ... ...

Abstract	Epidemiological and genetic studies on COVID-19 are hindered by inconsistent and limited testing policies to confirm SARS-CoV-2 infection. Recently, it was shown that it is possible to predict potential COVID-19 cases using cross-sectional self-reported disease-related symptoms. Using a previously reported COVID-19 prediction model, we show that it is possible to conduct a GWAS on predicted COVID-19 which benefits from a larger sample size in order to gain new insights into the genetic susceptibility of the disease. Furthermore, we find suggestive evidence that genetic variants for other viral infectious diseases do not overlap with COVID-19 susceptibility and that severity of COVID-19 may have a different genetic architecture compared to COVID-19 susceptibility. Our findings demonstrate the added value of using self-reported symptom assessments to quickly monitor novel endemic viral outbreaks in a scenario of limited testing. Should there be another outbreak of a novel infectious disease, then we recommend repeatedly collecting data of disease-related symptoms.
Keywords	covid19
Language	English
Publishing date	2020-08-24
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.08.21.20177246
Database	COVID19

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Article ; Online: SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads.

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Article ; Online: A Method for Variant Agnostic Detection of SARS-CoV-2, Rapid Monitoring of Circulating Variants, and Early Detection of Emergent Variants Such as Omicron.

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Article ; Online: Rapid displacement of SARS-CoV-2 variant B.1.1.7 by B.1.617.2 and P.1 in the United States

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Article ; Online: Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility.

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Article ; Online: Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.

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

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

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Article ; Online: Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility

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