SARS‐CoV‐2 AY.4.2 variant circulating in Italy: Genomic preliminary insight

Abstract

The appearance of emerging variants of SARS-CoV-2 carrying mutations into the spike protein has recently raised concern with respect to tracking their transmission and mitigating the impact in the evolving pandemic across countries. AY.4.2, a recently detected Delta variant sublineage, is considered a new variant under investigation (VUI) as it carries specific genetic signatures present in the spike protein, called Y145H and A222V. Here, using genomic epidemiology, we provide the first preliminary insight regarding the circulation of this emerging VUI in Italy.

Interpretable and Predictive Deep Modeling of the SARS-CoV-2 Spike Protein Sequence

“…We see a more complicated picture for position 222, as the A222V mutation emerged late in 2021 in the Delta AY.4.2 sublineage. [121] The A222V mutation, however, had also been found in mid-2020, which corresponds to the earlier peak in Fig. 4B.…”

“…The overlap between B.1.617.2 (Delta) and AY.4 is also expected, as AY.4 lineages (e.g., AY.4.2) are recognized as Delta sublineages which have emerged during the Delta outbreak. [121] In sum, Fig. 2 shows that, without doing 1) further alignment, 2) phylogenetic tree-building, or 3) classification based on sequence polymorphisms, we can replicate SARS-CoV-2 lineages and predict the date of emergence of a sequence.…”

Impact of SARS-CoV-2 omicron BA.1 and delta AY.4.2 variants on the neutralization by sera of patients treated with different authorized monoclonal antibodies

“…The study was conducted in accordance with the Declaration of Helsinki and approved by the local Ethics Committee (Neutro-COVID observational study, protocol number 4069/21); written informed consent was obtained by all the patients enrolled. The efficacy of the mAbs was assessed by a live virus neutralization assay against wild type (GISAID accession number EPI_ISL_2472896), delta (EPI_ISL_2840619), omicron (EPI_ISL_6777160) and the delta sublineage AY.4.2 (EPI_ISL_6943992), recently detected in Italy [ 6 ] and carrying the additional Y145H and A222V spike substitutions (details of each viral stock are indicated in Supplementary table S1 ). Neutralizing antibody (NtAb) titers were determined by a microneutralization live virus assay [ 7 ] and defined as the reciprocal value of the sample dilution that showed a 50% protection of virus-induced cytopathic effect (ID 50 ).…”

COVID-19 Genetic Variants and Their Potential Impact in Vaccine Development

“…Five key mutations were detected in the spike region of “Delta Plus”, which were more prominent than those in the Delta variant, including T95I, A222V, Y145H, G142D, R158G, and K417N [ 64 ]. Y145H and A222V mutations may also have an impact on viral functions, such as immune escape and a higher transmissibility [ 65 ]. AY.4.2 was found to have slightly higher transmissibility than the original Delta variant.…”