Genome sequencing of severe acute respiratory syndrome COVID-19 EF.1 variant strain obtained from a Moroccan patient

TL;DR

This paper reports the genome sequence of a SARS-CoV-2 strain from a Moroccan patient, identified as the EF.1 subvariant of BA.5 Omicron.

Contribution

The study provides a new genome sequence of the EF.1 subvariant of the BA.5 Omicron variant of SARS-CoV-2.

Findings

The identified strain EF.1 belongs to the BQ1.1 subvariant of the BA.5 Omicron variant.

The complete coding genome sequence of the strain was obtained from a Moroccan patient.

Abstract

Here, we report the identification and coding-complete genome sequence of a severe acute respiratory syndrome COVID-19 (SARS-CoV-2) strain obtained from a Moroccan patient. The detected strain EF.1 belongs to the BQ1.1 subvariant of the BA.5 Omicron variant.

Figures

Phylogenetic tree displaying the sequenced SARS-CoV-2 strain (with reference to the global GISAID data set), according to the clades assigned to the virus in the phylogenetic analysis using the Augur toolkit (with default settings) run by the Nextstrain server. The red dot marking the location of the strain hCoV-19/Morocco/117/2023 is part of the 22E Omicron clade. However, it shows a high number of mutations compared to the closely related strains.

Tables

TABLE 1. Amino acids changes of SARS-CoV-2 strain hCoV-19/Morocco/117/2023 in comparison to the reference strain (GenBank accession number NC_045512.2)

Protein	Amino acids changes
NSP1	S135R
NSP2	Q376K
NSP3	T24I, G489S
NSP4	L264F, T327I, T492I
NSP5	P132H
NSP6	F108del, G107del, L260F, S106del
NSP12	P323L, Y273H
NSP13	M233I, N268S, R392C
NSP14	I42V
NSP15	T112I
Spike	A27S, D405N, D614G, D796Y, E484A, F486V, G142D, G339D, H69del, H655Y, K417N, K444T, L24del, L452R, N440K, N460K, N679K, N764K, N969K, P25del, P26del, P681H, Q954H, S371F, S373P, S375F, S477N, T19I, T376A, T478K, V70del, V213G, Y144del
NS3	A72T, T223I
E	T9I, V62F
M	A63T, D3N, Q19E
N	E31del, E136D, G204R, P13L, R32del, R203K, S33del, S413R

Full text

ANNOUNCEMENT

Severe acute respiratory syndrome COVID-19 (SARS-CoV-2 virus; genus: Betacoronavirus; family: Coronaviridae), responsible for COVID-19 pandemic, remains a substantial concern due to the mutations in variants that could cause a resurgence (1, 2). Two prominent variants, BQ.1 and BQ.1.1, were initially detected in Nigeria in July 2022 and quickly considered variants of interest (VOIs) (3) due to their increasing complexity of spike mutations which enhance their ability to evade neutralizing antibodies, even in individuals who have received a bivalent mRNA booster or have previously encountered breakthrough Omicron infections (4).

In the evolution monitoring of the SARS-CoV-2 virus, a sample was obtained from an asymptomatic patient from Rabat (Morocco) on 2023-05-01. The viral RNA was extracted using a MagPurix viral RNA extraction kit (Zinexts Life Science, China). Reverse transcription (SARS-CoV-2-specific primers) was performed using SuperScript VILO cDNA synthesis kit (Invitrogen, Thermo Fisher Scientific, USA) and a library was prepared according to the instruction of Ion AmpliSeq SARS-CoV-2 research panel (Thermo Fisher, USA). Template preparation and chip loading were performed using the Ion Chef system, and sequenced by the Ion S5 sequencer (Thermo-fisher Scientific, USA). In all, 1,927,688 reads (Average length: 188.38 bp; GC content: 37.83%) were obtained and aligned to the Wuhan-Hu-1 reference sequence (GenBank accession number NC_045512.2) using Unipro UGENE V.45 to generate a consensus sequence. Default parameters were used.

The obtained genome (hCoV-19/Morocco/117/2023) presented a length of 29,841 bp, which covered 99.6288% of the reference genome (average coverage depth: 11916.9×). The missing portions were the 5′ and 3′ UTRs. Sequence quality check was performed using Nextclade web tool v2.14.0 (https://clades.nextstrain.org) and mutation identification was carried out using the web application Cov-GLUE (http://cov-glue.cvr.gla.ac.uk/). Lineage and sublineage were obtained using the Pangolin web application v4.0 (https://pangolin.cog-uk.io/).

According to the Pangolin web application, the sample belongs to the sublineage BQ1.1 of the Omicron variant. According to Nextclade, on the other hand, it was part of the clade 22E. The viral genome presented a total of 74 mutations (Table 1), and their locations in the global diversity of SARS-CoV-2 are illustrated in Fig. 1. Notably, 27 of the total mutations were located at the level of the S Protein gene, and contained well-known mutations such as D614G, which is also present in most variants including alpha and delta (5). Other substitutions observed were characteristic of BQ1.1, such as E484A (6). This latter mutation is extensively investigated for its impact on the binding affinity of the spike to the ACE2 receptor, whose increase helps viral entry into host cells (2, 7). Moreover, it was linked to a reduction in the neutralization potency of antibodies, suggesting a potential immune evasion mechanism (2).

Phylogenetic tree displaying the sequenced SARS-CoV-2 strain (with reference to the global GISAID data set), according to the clades assigned to the virus in the phylogenetic analysis using the Augur toolkit (with default settings) run by the Nextstrain server. The red dot marking the location of the strain hCoV-19/Morocco/117/2023 is part of the 22E Omicron clade. However, it shows a high number of mutations compared to the closely related strains.

Other interesting mutations were observed, such as S477N of the Receptor-Binding Domain (RBD) of the Spike protein (8), N679K and P681H between the S1 and S2 subunits (9, 10), as well as G142D in the NTD region (a crucial binding site for antibody 4A8) (11, 12).

The subvariant BQ1.1 and its emergence is a significant challenge in the fight against COVID-19. It shows an ability to evade immune responses and alter the virus biology, which raises concerns about vaccine effectiveness and current control measures. This only helps emphasize the importance of continued research and a better understanding of the prevalence, transmissibility, and clinical impact of the Omicron EF.1 variant.