Viral sequencing uncovers new mutations, guiding effective response

VOCs are a very real threat to our people and our current progress on combatting mutations

More then 5,628,545 sequences already published on GISAID as of December 2021

Viruses mutate constantly and SARS-CoV-2 is not any different. The emergence of mutations leads to new variants that have different characteristics. Next generation sequencing for the SARS-CoV-2 virus was key to identifying the more transmissible variants discovered in the UK, South Africa, Brazil, California and more recently New York and India. CDC has initiated a genome surveillance program for sequencing genes in the SARS-CoV-2 virus for the purpose of detecting variants that:

Can spread more quickly among individuals
Cause milder or more severe symptoms
Evade detection by PCR based diagnostic kits
Decreased responsiveness to monoclonal antibody-based therapy
Evade natural or vaccine induced immunity

Ayass BioScience are sequencing positive COVID-19 cases to find new mutations.

SARS-CoV-2 genome sequencing is a fast and efficient method for research on viral replication, packaging, function of terminase, transcription regulation, and metabolism of host cell. Ayass BioScience, LLC delivers high quality sequencing data for SARS-CoV-2 genome.

Without more of this kind of surveillance, much of the country will remain blind to changes in the types of virus circulating in their communities.
Sequencing viral RNA can also describe patterns of infection to help make important decisions about where to steer public health orders and to whom the vaccine needs are delivered. We can apply the sequencing data to show where the highest risks lie for health care providers.

A coordinated sequencing system in the U.S. could help end not only this pandemic, but also the next ones.

The COVID-19 pandemic has devastated health-care systems, shut down schools and communities, dipped the world into an economic recession. Understandably the 2020 was tested all of us, but 2021 looks are presenting with the emergence of multiple variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Positive, negative, neutral mutations during the evolution of coronaviruses:

SARS-CoV-2 variants, if considered to have concerning epidemiological, immunological or pathogenic properties, warranting urgent follow-up investigation.

An unexpected recent rise in reported COVID-19 cases was attributed to the emergence of the new major SARS-CoV-2 variants. System for genomic surveillance and the effort to expand sequencing of all emerging variants will increase the availability of timely U.S. genomic surveillance data.

The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021. The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021. (WHO)

Sub-lineage of: B.1.1. Countries circulating: Botswana (3 genomes), Hong Kong ex S. Africa (1 genome, partial). Currently only 4 sequences so would recommend monitoring for now. Export to Asia implies this might be more widespread than sequences alone would imply. Also the extremely long branch length and incredibly high amount of spike mutations suggest this could be of real concern (predicted escape from most known monoclonal antibodies).

This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage. (WHO)

Conserved Spike mutations – A67V, Δ69-70, T95I, G142D/Δ143-145, Δ211/L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F.

Conserved non-Spike mutations – NSP3 – K38R, V1069I, Δ1265/L1266I, A1892T; NSP4 – T492I; NSP5 – P132H; NSP6 – Δ105-107, A189V; NSP12 – P323L; NSP14 – I42V; E – T9I; M – D3G, Q19E, A63T; N – P13L, Δ31-33, R203K, G204R.

Genomes:
EPI_ISL_6590608 (partial RBD Sanger sequencing from Hong Kong)
EPI_ISL_6640916
EPI_ISL_6640919
EPI_ISL_6640917

Transmissability: Increased risk of reinfection. It is not yet clear whether Omicron is more transmissible (e.g., more easily spread from person to person) compared to other variants, including Delta. The number of people testing positive has risen in areas of South Africa affected by this variant, but epidemiologic studies are underway to understand if it is because of Omicron or other factors. (According to WHO)
Virulence: It is not yet clear whether infection with Omicron causes more severe disease compared to infections with other variants, including Delta. Preliminary data suggests that there are increasing rates of hospitalization in South Africa, but this may be due to increasing overall numbers of people becoming infected, rather than a result of specific infection with Omicron. There is currently no information to suggest that symptoms associated with Omicron are different from those from other variants. Initial reported infections were among university students—younger individuals who tend to have more mild disease—but understanding the level of severity of the Omicron variant will take days to several weeks. All variants of COVID-19, including the Delta variant that is dominant worldwide, can cause severe disease or death, in particular for the most vulnerable people, and thus prevention is always key. (According to WHO)
Antigenicity: Increase in transmissibility or detrimental change in COVID-19 epidemiology; increase in virulence or change in clinical disease presentation; decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics (monoclonal antibodies).
Effectiveness of current tests: The widely used PCR tests continue to detect infection, including infection with Omicron, as we have seen with other variants as well. Studies are ongoing to determine whether there is any impact on other types of tests, including rapid antigen detection tests.
Spread: South_Africa 73.0%, Botswana 11.0%, Hong_Kong 3.0%, Australia 2.0%, Italy 2.0%.

Global Positive Samples Sequenced: 5,628,545

B.1.1.529 Sequenced: 169

% of Global Samples Sequenced: 0%

Most common countries: South_Africa 73.0%, Botswana 11.0%, Hong_Kong 3.0%, Australia 2.0%, Italy 2.0%. (South Africa and Botswana lineage, from pango-designation issue #343)

Summary of B.1.1.529 data

Global Samples Sequencing Data

Updated December 30 2021

Date of designation – VOI – 4 April 2021, VOC –  11 May 2021. In October 2020 B.1.617 emerged in India, causing an rapid increase in COVID-19 cases across the country. The lineage is further divided into three subgroups: B.1.617.1, B.1.617.2, and B.1.617.3; of which the B.1.617.2 variant has been designated as Variant of Concern (VOC) because of significantly increased infectivity.

B.1.617.2 variant contains nine spike mutations, including five mutations in the N-terminal domain (NTD), 2 mutations in the receptor-binding domain (RBD), 1 mutation in the furin-cleavage site, and one mutation in the spike S2 subunit.

Spike Protein Substitutions: T19R, (V70F*), T95I, G142D, E156-, F157-, R158G, (A222V*), (W258L*), (K417N*), L452R, T478K, D614G, P681R, D950N.
(*) = detected in some sequences but not all.

GeneNucleotideAmino acid
ORF1abC14408TP4715L
G15451AG5063S
C16466TP5401L
SpikeC21618GT19R
22029-22034 delAGTTCA
EF 156-157 deletion
G21987AG142D
T22917GL452R
C22995AT478K
A23403GD614G
C23604GP681R
G24410AD950N
ORF3AC25469TS26L
MT26767CI82T
ORF7AT27638CV82A
C27752TT120I
ORF828248-282530 delGATTTCDF 119-120 deletion
NA28461GD63G
G28881TR203M
G29402TD377Y
Transmissability: Increased.
Virulence: Likely Increased.
Antigenicity: B.1.617.2 variant is resistant to therapeutic monoclonal antibodies, natural infection’s or vaccine-induced antibodies.
Spread: Originally was discovered in India and has now spread to more than 60 countries. Variant is dominant in India & UK now (and many other Asian countries where sequence data is not widely available), but prevalence also growing fast in US, as well as many European countries.

Global Positive Samples Sequenced: 5,628,545

B.1.617.2 Sequenced: 135,690

% of Global Samples Sequenced: 2.41%

Most common countries: United States of America 35.0%, United Kingdom 12.0%, India 12.0%, Denmark 6.0%, Germany 5.0% (Predominantly India lineage with several spike mutations, pango-designation issue #49).

Summary of B.1.617.2 data

Global Samples Sequencing Data

Updated December 2021

First samples of the Lambda variant were detected in Peru in December 2020 and by April 2021, over eighty percent of new cases of COVID-19 in Peru were from the new variant. At least 29 countries have reported Lambda cases in recent months, including Chile, Argentina, Peru, Ecuador, Brazil and Colombia as well as the U.S., Canada, Germany, Spain, Israel, France, the U.K. and Zimbabwe, among others. This variant identified to cause significant community transmission or multiple COVID-19 clusters, in multiple countries with increasing relative prevalence alongside increasing number of cases over time, or other apparent epidemiological impacts to suggest an emerging risk to global public health. Lambda carries a number of mutations with suspected phenotypic implications, such as an increased transmissibility and increased resistance to neutralizing antibodies.

The Lambda genome has the following amino acid mutations, all of which are in the virus’s spike protein code: G75V, T76I, Δ246-252, L452Q, F490S, D614G and T859N.

ORF1abC4002TT1246I
C7124TP2287S
T7424GF2387V
T9867CL3201P
C10029TT3255I
G10097AG3278S
11288-11296 delTCTGGTTTTSGF 3675-3677 deletion
C14408TP4715L
SpikeG21786TG75V
C21789TT76I
22299-22319 delGAAGTTATTTGACTCCTGGTGRSYLTPGD246N
T22917AL452Q
T23031CF490S
A23403GD614G
C23731TT859N
NC28311TP13L
GG28881AAR203K
G28883CG204R
G28913TG214C
Transmissability: Increased.
Virulence: Likely Increased.
Antigenicity: C.37 variant is possibly resistant to therapeutic monoclonal antibodies, natural infection’s or vaccine-induced antibodies.
Spread: Originally was discovered in Peru and has now spread to 29 countries. Variant is dominant in Peru, Chile, Mexico, Equador, but prevalence also growing fast in US, as well as some European countries.

Global Positive Samples Sequenced: 5,628,545

C.37 Sequenced: 8,659

% of Global Samples Sequenced: 0.15%

Most common countries: Peru 44.0%, Chile 20.0%, United States of America 13.0%, Argentina 11.0%, Ecuador 3.0% (Alias of B.1.1.1.37, lineage in Peru, Chile, USA and Germany, from pango-designation issue #52).

Global Samples Sequencing Data

Updated December 2021

Mu Variant was first detected in Colombia in January 2021 and designated by the WHO as a variant of interest on August 30, 2021. The WHO indicated the variant has mutations that indicate a risk of resistance to the current vaccines and stressed that further studies were needed to better understand it. Outbreaks of the Mu variant were reported in South America and Europe. The lineage B.1.621 has a sublineage, labeled B.1.621.1 under the PANGO nomenclature, which has already been detected in more than 20 countries worldwide.

The Mu genome has a total number of 21 mutations, including 9 amino acid mutations, all of which are in the virus’s spike protein code: T95I, Y144S, Y145N, R346K, E484K or the escape mutation, N501Y, D614G, P681H, and D109N.

Transmissability: Likely Increased.
Virulence: Likely Increased.
Antigenicity: Mu variant has mutations that have the potential to evade immunity provided by a previous COVID-19 infection or vaccination.
Spread: Outbreaks of the Mu variant were reported in South America and Europe. The lineage B.1.621 has a sublineage, labeled B.1.621.1 under the PANGO nomenclature, which has already been detected in more than 20 countries worldwide.

Global Positive Samples Sequenced: 5,628,545

B.1.621 Sequenced: 9,755

% of Global Samples Sequenced: 0.17%

Most common countries: United States of America 43.0%, Colombia 25.0%, Chile 9.0%, Spain 5.0%, Mexico 4.0% (Lineage predominantly in Colombia with several spike mutations, pango-designation issue #57)

Global Samples Sequencing Data

Updated December 2021

A more highly transmissible variant of SARS-CoV-2, B.1.1.7 (first detected and sequenced in the UK in September 2020), now has been detected in many US States. Modeling data indicate that B.1.1.7 has the potential to increase the U.S. pandemic trajectory in the coming months, because B.1.1.7 has tendency to explode rapidly in new countries where it appears.

This variant has a mutation in the receptor binding domain (RBD) of the spike protein at position 501, where the amino acid asparagine (N) has been replaced with tyrosine (Y). There are three mutations of particular interest in the spike region of the B.1.1.7 genome: N501Y, 69–70del, P681H.

Spike Protein Substitutions: 69del, 70del, 144del, (E484K*), (S494P*), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H (K1191N*).
(*) = detected in some sequences but not all.

GeneNucleotideAmino acid
ORF1abC3267TT1001I
C5388AA1708D
T6954CI2230T
11288–11296 delTCTGGTTTTSGF 3675–3677 deletion
S (S Protein)21765–21770 delTACATGHV 69–70 deletion
21991–21993 delTTAY144 deletion
A23063TN501Y
C23271AA570D
A23403GD614G
C23604AP681H
C23709TT716I
T24506GS982A
G24914CD1118H
ORF8C27972TQ27stop
G28048TR52I
A28111GY73C
N28280 GAT→CTAD3L
C28977TS235F
Transmissability: Increased by 50% (more efficient and rapid transmission).
Virulence: Potentially 30% more lethal. Minimal impact on neutralization by convalescent and post-vaccination sera. No impact on susceptibility to EUA monoclonal antibody treatments.
Antigenicity: Indications of ostensible reduced antigenic activity.
Spread: Global.

Global Positive Samples Sequenced: 5,628,545

B.1.1.7 Sequenced: 1,063,125

% of Global Samples Sequenced: 18.89%

Most common countries: United Kingdom 24.0%, United States of America 20.0%, Germany 10.0%, Sweden 6.0%, Denmark 6.0% (UK lineage of concern, associated with the N501Y mutation).

Summary of B.1.1.7 data

Global Samples Sequencing Data

Updated December 2021

This variant was first detected in South Africa and was first sequenced in December 2020. B.1.351 has a mutation that makes it more transmissible from one person to another and a separate mutation that might make it less responsive to the antibodies we form when we have COVID or get vaccinated. This variant was first detected in US in January 2021.

There are three mutations of particular interest in the spike region of the B.1.351 genome: K417N, E484K, N501Y.

Spike Protein Substitutions: D80A, D215G, 241del, 242del, 243del, K417N, E484K, N501Y, D614G, A701V.
(*) = detected in some sequences but not all.

GeneNucleotideAmino acid
ORF1abC1059TT265I
G5230TK1655N
C8660TH2799Y
C8964TS2900L
A10323GK3353R
G13843TD4527Y
C14408TP4715L
C17999TT5912I
EC26456TP71L
NC28887TT205I
S (S Protein)
C21614TL18F
A21801CD80A
A22206GD215G
G22299TR246I
G22813TK417N
G23012AE484K
A23063TN501Y
A23403GD614G
C23664TA701V
22286-22294 delCTTGCTTTALAL 242-244del
Transmissability: Increased by 50%.
Antigenicity: 21% reduction in antigenicity. Significantly reduced susceptibility to the combination of bamlanivimab and etesevimab monoclonal antibody treatment. Reduced neutralization by convalescent and post-vaccination sera.
Spread: Global.

Global Positive Samples Sequenced: 5,628,545

B.1.351 Sequenced: 31,029

% of Global Samples Sequenced: 0.55%

Most common countries: South Africa 18.0%, United States of America 11.0%, Philippines 10.0%, Sweden 8.0%, Germany 7.0% (Lineage of concern detected in South Africa).

Summary of B.1.351 data

Global Samples Sequencing Data

Updated December 2021

P.2 (descendent of B.1.1.28). This variant was first detected in Brazil and was first sequenced in November 2020.
P.1 (P.1, P.1.1, P.1.2) (descendent of B.1.1.28). This variant was first detected in Japan in travelers from Brazil in January 2021.
Both variants were identified in the United States at the end of January 2021.

There are three mutations of particular interest in the spike region of the P.1/P.2 genome: N501Y, E484K, K417T.

Spike Protein Substitutions: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I.

GeneNucleotideAmino acid
ORF1abC3828TS1188L
A5648CK1795Q
11288–11296 delTCTGGTTTTSGF 3675–3677 deletion
G17259TE5665D
SpikeC21614TL18F
C21621AT20N
C21638TP26S
G21974TD138Y
G22132TR190S
A22812CK417T
G23012AE484K
A23063TN501Y
A23403GD614G
C23525TH655Y
C24642TT1027I
ORF8G28167AE92K
ins28269-28273 AAAC
NC28512GP80R
Transmissability: Likely Increased
Virulence: 10–80% more lethal
Antigenicity: Overall reduction in effective neutralisation. Significantly reduced susceptibility to the combination of bamlanivimab and etesevimab monoclonal antibody treatment. Reduced neutralization by convalescent and post-vaccination sera.
Spread: International.
Both variants contains a set of additional mutations that may affect its ability to be recognized by antibodies.

Global Positive Samples Sequenced: 5,628,545

P.1 Sequenced: 60,077

P.2 Sequenced: 4,929

% of Global Samples Sequenced (P1): 1.07%

% of Global Samples Sequenced (P2): 0.09%

Most common countries P.1: Brazil 55.0%, United States of America 29.0%, Chile 3.0%, Peru 2.0%, Argentina 2.0% (Alias of B.1.1.28.1, Brazilian lineage with a number of spike mutaions with likely functional significance E484K, K417T, and N501Y.) (Description)

Most common countries P.2: Brazil 55.0%, United States of America 26.0%, Canada 4.0%, Argentina 2.0%, Suriname 2.0% (Alias of B.1.1.28.2, Brazilian lineage)

Summary of P.1 data

Global Samples Sequencing Data

Updated December 2021

This variants first emerged in late spring or summer of 2020 before it was first detected by researchers from the University of California, San Francisco, in December 2020. Now they have been found in at least 45 U.S. states and several countries around the world.
This variant is concerning because scientific data shows that it is more contagious, more likely to be associated with severe illness, and at least partially resistant to neutralizing antibodies.

There are five mutations of particular interest in the spike region of this genomes: 4205V and D1183Y in the ORF1ab-gene, and S13I, W152C, L452R in the spike proteins S-gene.

B.1.427

GeneNucleotideAmino acid
ORF1abC1059TT265I
G9738CS3158T
C16394TP5377L
G17014TD5584Y
SpikeT22917GL452R
A23403GD614G
NC28887TT205I
ORF3aG25563TQ57H

B.1.429

GeneNucleotideAmino acid
ORF1abC1059TT265I
A12878GI4205V
C14408TP4715L
G17014TD5584Y
SpikeG21600TS13I
G22018TW152C
T22917GL452R
A23403GD614G
ORF3aG25563TQ57H
NC28887TT205I
Transmissability: Likely Increased
Virulence: Likely Increased
Antigenicity: Likely Increased
Spread: North America, and in Europe, Asia and Australia

B.1.427

Global Positive Samples Sequenced: 5,628,545

B.1.427 Sequenced: 17,734

% of Global Samples Sequenced: 0.32%

Most common countries: United States of America 97.0%, Mexico 1.0%, Aruba 0.0%, Argentina 0.0%, El_Salvador 0.0% (USA lineage (CA)).

B.1.429

Global Positive Samples Sequenced: 5,628,545

B.1.429 Sequenced: 39,495

% of Global Samples Sequenced: 0.07%

Most common countries: United States of America 97.0%, Canada 2.0%, Mexico 1.0%, South_Korea 0.0%, Chile 0.0% (A lineage predominantly circulating in California but with exports to other countries (Characterised by the spike L452R mutation but also has spike:W152C orf1ab:D5584Y and N:T205I.).

Global Samples Sequencing Data

Updated December 2021

The variant first emerged in samples taken in November. By Jan. 2021, the variant represented about 3% of samples analyzed by researchers, rising to 12.3% by mid-February, according to a study by scientists at Columbia University Vagelos College of Physicians and Surgeons that has yet to be peer-reviewed. By mid-February, the Caltech team found that B.1.526 cases had risen to 27 percent of viral sequences in the database.

There are three mutations of particular interest in the spike region of the B.1.526 genome: E484K, S477N, N501Y.
Genetic analysis of B.1.526 variants also revealed several mutations on the spike protein including, L5F, T95I, D253G, D614G, and A701V.
Additional mutations in the S, N, NSP2, NSP3, NSP4, NSP6, NSP8, NSP12 and NSP13 genes.

ProteinNucleotideAmino acid
ORF1abC1059TT265I
T9867CL3201P
11288–11296 delTCTGGTTTTSGF 3675–3677 deletion
C14408TP4715L
A16500CQ5412H
SpikeC21575TL5F
C21846TT95I
A22320GD253G
G23012AE484K
G22992AS477N
A23403GD614G
C23664TA701V
NC28869TP199L
G28975AM234I
ORF3aC25517TP42L
G25563TQ57H
ORF8C27925TT11I
Transmissability: Likely Increased
Virulence: Likely Increased
Antigenicity: Drop in effectiveness of certain monoclonal treatments and some current vaccines. This mutation could evade natural immune responses, causing reinfection in people who were had recovered from earlier variants of the coronavirus.
Spread: Has been reported in some of the most populous areas of New York: Westchester, Bronx, Queens, Manhattan and Brooklyn. When genomic data from public databases was analyzed, approximately 140 genomes was found to be related to the B.1.526 variant spread across the Northeast.

Global Positive Samples Sequenced: 5,628,545

B.1.526 Sequenced: 40,275

% of Global Samples Sequenced: 0.72%

Most common countries: United States of America 97.0%, Ecuador 1.0%, Puerto_Rico 1.0%, Canada 1.0%, Spain 0.0% (A lineage predominantly circulating in New York but with a few exports to other countries. Characterised by spike mutations T95I and D253G, plus others. The most frequent spike mutation pattern is L5F T95I D253G E484K D614G A701V, with a smaller fraction having S477N instead of E484K. Spike mutation E484K is present in about half of this lineage (as of 2021-02-10) – Very possible not all new additions carry T95I and D253G).

Global Samples Sequencing Data

Updated December 2021

B.1.525

International lineage with variants of biological significance E484K, Q677H, F888L and a similar suite of deletions to B.1.1.7.

A.23.1

International lineage with variants of biological significance F157L, V367F, Q613H and P681R, described fully in the preprent: Bugembe et al 2021. Q613H is predicted to be functionally equivalent to the D614G mutation that arose early in 2020.

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