Published on 05/27/2021
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
-
Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants
M Yuan et al, Science, May 20, 2021Neutralizing antibodies (nAbs) elicited against the receptor-binding site (RBS) of the spike protein of wild-type SARS-CoV-2 are generally less effective against recent variants of concern. RBS residues E484, K417 and N501 are mutated in variants first described in South Africa (B.1.351) and Brazil (P.1). We analyzed their effects on ACE2 binding and K417N and E484K mutations on nAbs isolated from COVID-19 patients. Binding and neutralization of the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2), which can both bind the RBS in alternate binding modes, are abrogated by K417N, E484K, or both. -
Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa
OS Okoh et al, MEDRXIV, May 19, 2021We show that after almost one year of the COVID-19 pandemic, only 143 out of the 782 Pango lineages found worldwide circulated in Africa, with five different lineages dominating in distinct periods of the pandemic. Analysis of the number of reported deaths in Africa also revealed large heterogeneity across the continent. Phylogenetic analysis revealed that African viruses cluster closely with those from all continents but more notably with viruses from Europe. However, the extent of viral diversity observed among African genomes is closest to that of the Oceania outbreak, most likely due to genomic under-surveillance in Africa. -
ACE2 and SARS-CoV-2 Infection Risk: Insights From Patients With Two Rare Genetic Tubulopathies, Gitelman's and Bartter's Syndromes.
Calò Lorenzo A et al. Frontiers in medicine 2021 5 647319 -
SARS-CoV-2 B.1.1.7 and B.1.351 spike variants bind human ACE2 with increased affinity.
Ramanathan Muthukumar et al. The Lancet. Infectious diseases 2021 5 -
Identification and trajectory of growth of concerning SARS-CoV-2 variants in Houston, Texas, January through April 2021 based on 11,568 genome sequences
RJ Olsen et al, MEDRXIV, May 23, 2021The SARS-CoV-2 variant designated UK B.1.1.7 increased very rapidly, and now causes 75%-90% of all new cases in the Houston area. Five of the 2,543 B.1.1.7 genomes had an E484K change in spike protein. Compared with non-B.1.1.7 patients, individuals infected with B.1.1.7 had a significantly lower cycle threshold value (considered to be a proxy for higher virus load) and higher rate of hospitalization. Other variants (e.g., B.1.429, B.1.427, P.1, P.2, and R.1) also increased rapidly in frequency, although the magnitude was less than for B.1.1.7. -
Effectiveness of COVID-19 vaccines against the B.1.617.2 variant
JL Bernard et al, MEDRXIV, May 24, 2021After 2 doses of either vaccine there were only modest differences in vaccine effectiveness with the B.1.617.2 variant. Absolute differences in vaccine effectiveness were more marked with dose 1. This would support maximising vaccine uptake with two doses among vulnerable groups. -
Emergence of SARS-CoV-2 variants of concern in the pediatric population of the United States
JD Bard et al, MEDRXIV, May 24, 2021We report data from a genomic surveillance program that includes 9 U.S. children's hospitals. Analysis of SARS-CoV-2 genome from 2119 patients <19 years old between 03/20 to 04/21 identified 252 VOCs and 560 VOC signature mutations, most from 10/20 onwards. From 02/21 to 04/21, B.1.1.7 prevalence increased from 3.85% to 72.22% corresponding with the decline of B.1.429/B.1.427 from 51.82% to 16.67% at one institution. 71.74% of the VOC signature mutations detected were in children <12 years old, including 33 cases of B.1.1.7 and 119 of B.1.429/B.1.427. -
COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence
FJ Naveca et al, Nature Medicine, May 25, 2021Through a genomic epidemiology study based on 250?severe acute respiratory syndrome coronavirus?2 (SARS-CoV-2) genomes from different Amazonas municipalities sampled between March 2020 and January 2021, we reveal that the first exponential growth phase was driven mostly by the dissemination of lineage B.1.195, which was gradually replaced by lineage B.1.1.28 between May and June 2020. The second wave coincides with the emergence of the variant of concern (VOC) P.1, which evolved from a local B.1.1.28 clade in late November 2020 and replaced the parental lineage in <2?months. -
Variants of concern are overrepresented among post-vaccination breakthrough infections of SARS-CoV-2 in Washington State
AE McEwen et al, MEDRXIV, May 25, 2021Across 20 vaccine breakthrough cases detected at our institution, all 20 (100%) infections were due to variants of concern (VOC) and had a median Ct of 20.2 (IQR=17.1-23.3). When compared to 5174 contemporaneous samples sequenced in our laboratory, VOC were significantly enriched among breakthrough infections (p < .05).
Non-Genomics Precision Health Studies
-
Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants
M Yuan et al, Science, May 20, 2021Neutralizing antibodies (nAbs) elicited against the receptor-binding site (RBS) of the spike protein of wild-type SARS-CoV-2 are generally less effective against recent variants of concern. RBS residues E484, K417 and N501 are mutated in variants first described in South Africa (B.1.351) and Brazil (P.1). We analyzed their effects on ACE2 binding and K417N and E484K mutations on nAbs isolated from COVID-19 patients. Binding and neutralization of the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2), which can both bind the RBS in alternate binding modes, are abrogated by K417N, E484K, or both. -
Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa
OS Okoh et al, MEDRXIV, May 19, 2021We show that after almost one year of the COVID-19 pandemic, only 143 out of the 782 Pango lineages found worldwide circulated in Africa, with five different lineages dominating in distinct periods of the pandemic. Analysis of the number of reported deaths in Africa also revealed large heterogeneity across the continent. Phylogenetic analysis revealed that African viruses cluster closely with those from all continents but more notably with viruses from Europe. However, the extent of viral diversity observed among African genomes is closest to that of the Oceania outbreak, most likely due to genomic under-surveillance in Africa. -
ACE2 and SARS-CoV-2 Infection Risk: Insights From Patients With Two Rare Genetic Tubulopathies, Gitelman's and Bartter's Syndromes.
Calò Lorenzo A et al. Frontiers in medicine 2021 5 647319 -
SARS-CoV-2 B.1.1.7 and B.1.351 spike variants bind human ACE2 with increased affinity.
Ramanathan Muthukumar et al. The Lancet. Infectious diseases 2021 5 -
Identification and trajectory of growth of concerning SARS-CoV-2 variants in Houston, Texas, January through April 2021 based on 11,568 genome sequences
RJ Olsen et al, MEDRXIV, May 23, 2021The SARS-CoV-2 variant designated UK B.1.1.7 increased very rapidly, and now causes 75%-90% of all new cases in the Houston area. Five of the 2,543 B.1.1.7 genomes had an E484K change in spike protein. Compared with non-B.1.1.7 patients, individuals infected with B.1.1.7 had a significantly lower cycle threshold value (considered to be a proxy for higher virus load) and higher rate of hospitalization. Other variants (e.g., B.1.429, B.1.427, P.1, P.2, and R.1) also increased rapidly in frequency, although the magnitude was less than for B.1.1.7. -
Effectiveness of COVID-19 vaccines against the B.1.617.2 variant
JL Bernard et al, MEDRXIV, May 24, 2021After 2 doses of either vaccine there were only modest differences in vaccine effectiveness with the B.1.617.2 variant. Absolute differences in vaccine effectiveness were more marked with dose 1. This would support maximising vaccine uptake with two doses among vulnerable groups. -
Emergence of SARS-CoV-2 variants of concern in the pediatric population of the United States
JD Bard et al, MEDRXIV, May 24, 2021We report data from a genomic surveillance program that includes 9 U.S. children's hospitals. Analysis of SARS-CoV-2 genome from 2119 patients <19 years old between 03/20 to 04/21 identified 252 VOCs and 560 VOC signature mutations, most from 10/20 onwards. From 02/21 to 04/21, B.1.1.7 prevalence increased from 3.85% to 72.22% corresponding with the decline of B.1.429/B.1.427 from 51.82% to 16.67% at one institution. 71.74% of the VOC signature mutations detected were in children <12 years old, including 33 cases of B.1.1.7 and 119 of B.1.429/B.1.427. -
COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence
FJ Naveca et al, Nature Medicine, May 25, 2021Through a genomic epidemiology study based on 250?severe acute respiratory syndrome coronavirus?2 (SARS-CoV-2) genomes from different Amazonas municipalities sampled between March 2020 and January 2021, we reveal that the first exponential growth phase was driven mostly by the dissemination of lineage B.1.195, which was gradually replaced by lineage B.1.1.28 between May and June 2020. The second wave coincides with the emergence of the variant of concern (VOC) P.1, which evolved from a local B.1.1.28 clade in late November 2020 and replaced the parental lineage in <2?months. -
Variants of concern are overrepresented among post-vaccination breakthrough infections of SARS-CoV-2 in Washington State
AE McEwen et al, MEDRXIV, May 25, 2021Across 20 vaccine breakthrough cases detected at our institution, all 20 (100%) infections were due to variants of concern (VOC) and had a median Ct of 20.2 (IQR=17.1-23.3). When compared to 5174 contemporaneous samples sequenced in our laboratory, VOC were significantly enriched among breakthrough infections (p < .05).
News, Reviews and Commentaries
-
Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants
M Yuan et al, Science, May 20, 2021Neutralizing antibodies (nAbs) elicited against the receptor-binding site (RBS) of the spike protein of wild-type SARS-CoV-2 are generally less effective against recent variants of concern. RBS residues E484, K417 and N501 are mutated in variants first described in South Africa (B.1.351) and Brazil (P.1). We analyzed their effects on ACE2 binding and K417N and E484K mutations on nAbs isolated from COVID-19 patients. Binding and neutralization of the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2), which can both bind the RBS in alternate binding modes, are abrogated by K417N, E484K, or both. -
Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa
OS Okoh et al, MEDRXIV, May 19, 2021We show that after almost one year of the COVID-19 pandemic, only 143 out of the 782 Pango lineages found worldwide circulated in Africa, with five different lineages dominating in distinct periods of the pandemic. Analysis of the number of reported deaths in Africa also revealed large heterogeneity across the continent. Phylogenetic analysis revealed that African viruses cluster closely with those from all continents but more notably with viruses from Europe. However, the extent of viral diversity observed among African genomes is closest to that of the Oceania outbreak, most likely due to genomic under-surveillance in Africa. -
ACE2 and SARS-CoV-2 Infection Risk: Insights From Patients With Two Rare Genetic Tubulopathies, Gitelman's and Bartter's Syndromes.
Calò Lorenzo A et al. Frontiers in medicine 2021 5 647319 -
SARS-CoV-2 B.1.1.7 and B.1.351 spike variants bind human ACE2 with increased affinity.
Ramanathan Muthukumar et al. The Lancet. Infectious diseases 2021 5 -
Identification and trajectory of growth of concerning SARS-CoV-2 variants in Houston, Texas, January through April 2021 based on 11,568 genome sequences
RJ Olsen et al, MEDRXIV, May 23, 2021The SARS-CoV-2 variant designated UK B.1.1.7 increased very rapidly, and now causes 75%-90% of all new cases in the Houston area. Five of the 2,543 B.1.1.7 genomes had an E484K change in spike protein. Compared with non-B.1.1.7 patients, individuals infected with B.1.1.7 had a significantly lower cycle threshold value (considered to be a proxy for higher virus load) and higher rate of hospitalization. Other variants (e.g., B.1.429, B.1.427, P.1, P.2, and R.1) also increased rapidly in frequency, although the magnitude was less than for B.1.1.7. -
Effectiveness of COVID-19 vaccines against the B.1.617.2 variant
JL Bernard et al, MEDRXIV, May 24, 2021After 2 doses of either vaccine there were only modest differences in vaccine effectiveness with the B.1.617.2 variant. Absolute differences in vaccine effectiveness were more marked with dose 1. This would support maximising vaccine uptake with two doses among vulnerable groups. -
Emergence of SARS-CoV-2 variants of concern in the pediatric population of the United States
JD Bard et al, MEDRXIV, May 24, 2021We report data from a genomic surveillance program that includes 9 U.S. children's hospitals. Analysis of SARS-CoV-2 genome from 2119 patients <19 years old between 03/20 to 04/21 identified 252 VOCs and 560 VOC signature mutations, most from 10/20 onwards. From 02/21 to 04/21, B.1.1.7 prevalence increased from 3.85% to 72.22% corresponding with the decline of B.1.429/B.1.427 from 51.82% to 16.67% at one institution. 71.74% of the VOC signature mutations detected were in children <12 years old, including 33 cases of B.1.1.7 and 119 of B.1.429/B.1.427. -
COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence
FJ Naveca et al, Nature Medicine, May 25, 2021Through a genomic epidemiology study based on 250?severe acute respiratory syndrome coronavirus?2 (SARS-CoV-2) genomes from different Amazonas municipalities sampled between March 2020 and January 2021, we reveal that the first exponential growth phase was driven mostly by the dissemination of lineage B.1.195, which was gradually replaced by lineage B.1.1.28 between May and June 2020. The second wave coincides with the emergence of the variant of concern (VOC) P.1, which evolved from a local B.1.1.28 clade in late November 2020 and replaced the parental lineage in <2?months. -
Variants of concern are overrepresented among post-vaccination breakthrough infections of SARS-CoV-2 in Washington State
AE McEwen et al, MEDRXIV, May 25, 2021Across 20 vaccine breakthrough cases detected at our institution, all 20 (100%) infections were due to variants of concern (VOC) and had a median Ct of 20.2 (IQR=17.1-23.3). When compared to 5174 contemporaneous samples sequenced in our laboratory, VOC were significantly enriched among breakthrough infections (p < .05).
- Page last reviewed:Feb 1, 2024
- Page last updated:Apr 25, 2024
- Content source: