Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany

Abstract

Here, we report on the increasing frequency of the SARS-CoV-2 lineage A.27 in Germany during the first months of 2021. Genomic surveillance identified 710 A.27 genomes in Germany as of 2 May 2021, with a vast majority identified in laboratories from a single German state (Baden-Wuerttemberg, n = 572; 80.5%). Baden-Wuerttemberg is located near the border with France, from where most A.27 sequences were entered into public databases until May 2021. The first appearance of this lineage based on sequencing in a laboratory in Baden-Wuerttemberg can be dated to early January ’21. From then on, the relative abundance of A.27 increased until the end of February but has since declined—meanwhile, the abundance of B.1.1.7 increased in the region. The A.27 lineage shows a mutational pattern typical of VOIs/VOCs, including an accumulation of amino acid substitutions in the Spike glycoprotein. Among those, L18F, L452R and N501Y are located in the epitope regions of the N-terminal- (NTD) or receptor binding domain (RBD) and have been suggested to result in immune escape and higher transmissibility. In addition, A.27 does not show the D614G mutation typical for all VOIs/VOCs from the B lineage. Overall, A.27 should continue to be monitored nationally and internationally, even though the observed trend in Germany was initially displaced by B.1.1.7 (Alpha), while now B.1.617.2 (Delta) is on the rise.

CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance

“…We downloaded the complete time series data for C284T from the mutation distribution plot via the web app to perform an additional trend analysis. We compared the proportion of the alternative nucleotide T at position 284 between CWs using a Fisher exact test (adjusted p-value < 0.01, Table S3, see [18] for details on the method). We found that in two time periods (CW21-34 and CW 47-52), the proportion of samples with the alternative nucleotide T at position 284 increased significantly between consecutive weeks (Fig.…”

“…Based on the underlying time series data downloaded from CovRadar, we calculated a significant increase of T95I in two time periods (CW21–34 and CW 47–52). Significant increases between consecutive CWs are marked by an asterisk and were calculated as described before [18].…”

“…To further investigate in which geographic location the first significant rise in L452R can be observed, we downloaded the selected time series data per location. We tested for significant differences in the proportion within the single postal code areas compared between calendar weeks (Fisher exact test, adjusted p-value < 0.01, Table S4, see [18] for details). We excluded data from February 2021 to rule out fluctuation effects due to increased sequencing capacity starting from January 25, 2021 in Germany.…”

SARS-CoV-2 Lineage A.27: New Data from African Countries and Dynamics in the Context of the COVID-19 Pandemic

“…A.27 is a SARS-CoV-2 variant that was reported in late 2020 [ 7 , 8 , 9 , 10 , 11 , 12 ]. Its genome holds several mutations along the viral genome, some of which are shared with other VOCs and VOIs [ 7 , 8 ].…”

“…These variants are subject to attentive surveillance, to better understand how easily they might be transmitted and the effectiveness of currently authorized vaccines against them. The A.27 lineage was first classified as a VUM by the eCDC and the COG-UK [ 7 , 8 ] and as a VOI by the French Society of Microbiology [ 9 ] since it shows a mutational pattern similar to VOCs and VOIs, with several amino acid substitutions along the viral genome, especially in the S gene [ 10 , 11 , 12 , 13 ]. Among these amino acid substitutions, L18F, L452R and N501Y are located in the N-terminal (NTD) or receptor binding domain (RBD) regions and have been suggested to result in immune escape and higher transmissibility [ 14 , 15 , 16 , 17 ].…”