Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling.
PMID: 34438144
2021
The Science of the total environment
Abstract: We identify four signature mutations in the surface glycoprotein (spike) gene that are associated with the following variants of interest or concern, VOI or VOC (listed in parenthesis): S477N (B.1.526, Iota), T478K (B.1.617.2, Delta), D614G (present in all VOC as of May 2021), and H655Y (P.1, Gamma).
Result: Four mutations in the spike gene were detected that are present in one or more variants of interest (VOI) or variants of concern (VOC), which are listed in parenthesis: S477N (B.1.526, Iota), T478K (B.1.617.2, Delta), D614G (present in all VOC as of May 2021), H655Y (P.1, Gamma).
Table:
An Autochthonous Outbreak of the SARS-CoV-2 P.1 Variant of Concern in Southern Italy, April 2021.
PMID: 34449757
2021
Tropical medicine and infectious disease
Introduction: These amino acid changes are L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I, and V1176F.
Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021.
Result: Fifteen substitutions (10 in the spike protein: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, and T1027I) are P.1 lineage-defining mutations (Figure 1B and Table 2).
Discussion: The VOC P.1 carries three deletions, four synonymous substitutions, a four base-pair nucleotide insertion, and at least 17 other lineage-defining replacements, including 10 missense mutations in the spike protein (L18F, T20N, P26S, D138Y,
Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany.
Result: In total, A.27 harbors 17 lineage-defining mutations (Figure 3A and Figure 4A), seven of which result in non-synonymous nucleotide substitutions in the spike protein: L18F, L452R, N501Y, A653V, H655Y, D796Y, G1219V.
Result: The H655Y substitution adjacent to the S1/S2 cleavage site and also known from P.1 was recently detected in a potential new VOI within the A lineage (temporarily designated A.VOI.V2) identified from three cases of incoming travelers from Tanzania to Angola.
Result: The polymorphic positions are labeled on the S protein structure (Figure 3B), indicating the localization of L452R
Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner.
Result: Sequences from the S1S2 amplicon matched lineage B.1.1.7 with '1841G(D614G) 2042A(P681H) 2147T(T716I)', lineage P.1 with '1841G(D614G) 1963T(H655Y) 2063T(A688V)' or the B.1 lineage with only the now ubiquitous D614G variation (Supplementary 12).
Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants.
Method: We used the following amino acids replacements and deletions in Spike for each lineage-based COG-UK defined changes for each lineage; Beta (B1.351;
Discussion: H655Y has been observed by others in vitro, associated with adaption to cats and hamsters antibody escape and, identified in the sequence of super spreaders as well as arising by convergent evolution in circulating lineages (eg., P1 and A.27 lineages).
Discussion: This is further highlighted by two mutations that arise in vitro; N501T and H655Y, the first within the RDB and the latter outside of the RDB and toward the S1-S2 cleavage site.
Discussion: While the phenotypic importances of H655 mutation is unknown, Braun et al., postulated it is unlikely H655Y improves spike fusion efficiency and entry.
Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity.
Result: Additionally, whereas a convergent A701V mutation is also found in the B.1.526 and S/E484K carrying lineage that was first identified in New York, P681H is found in the S/E484K and S/N501Y carrying P.3 lineage first identified in the Philippines, and both S/H655Y and S/P681H are found in the highly mutated S/E484K carrying A.VOI.V2 lineage first identified in Tanzanian travelers.
Result: Any of H655Y, P681H, A701V, or T716I might directly impact the efficiency of viral entry into host cells.
Result: Whereas sites S/655 and S/681 are also detectably evolvi
Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants.
SARS_CoV_2 mutation literature information.
PMID: 
2021
The Science of the total environment
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