Mutations Associated with SARS-CoV-2 Variants of Concern, Benin, Early 2021

Intense transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Africa might promote emergence of variants. We describe 10 SARS-CoV-2 lineages in Benin during early 2021 that harbored mutations associated with variants of concern. Benin-derived SARS-CoV-2 strains were more efficiently neutralized by antibodies derived from vaccinees than patients, warranting accelerated vaccination in Africa.

Intense transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Africa might promote emergence of variants. We describe 10 SARS-CoV-2 lineages in Benin during early 2021 that harbored mutations associated with variants of concern. Benin-derived SARS-CoV-2 strains were more effi ciently neutralized by antibodies derived from vaccinees than patients, warranting accelerated vaccination in Africa. Definite lineage designation relies on the full genome sequence. We selected 68 (9 typeable and 59 nontypeable) samples according to unique mutational patterns covering the complete period of the study for a NimaGen/Illumina-based whole-genome sequencing workflow (Appendix Table 1). All near-full genomes generated within this study were deposited into GISAID (https://www.gisaid.org; accession nos. EPI_ISL_2932532-84 and EPI_ISL_2958658-72). Lineage assignment using the Pangolin COVID-19 Lineage Assigner version 3.0.2 (https://pangolin. cog-uk.io) confirmed SNP-based lineage prediction in all 9 typeable samples selected for whole-genome sequencing (Appendix Table 2). Despite robust lineage prediction based on unambiguous SNP-based results, our data demonstrate the limited use of VirSNiP assays for strain designation; however, these assays can detect relevant mutations of currently circulating variants. The 68 Benin-derived near-complete genomes were designated to 10 unique lineages, suggesting higher genetic diversity in Benin than ≈1 year before (3  Table 3). Despite presence of the mutation P681R (associated with the Delta VOC) in 1 sequence, that strain was typed as A.23.1, and no Delta variant was found.
No data x P681R No data x *SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; SNP single-nucleotide polymorphism. †Variants of concern according to the World Health Organization. ‡G. Hahn et al., unpub. data, https://www.biorxiv.org/content/10.1101/2020.11.17.386714v2.  Putative higher fitness mediated by genomic change was consistent with more mutations in predominant lineages than in lineages found at lower frequencies ( Figure 1, panel B).
Because S mutations, individually or in combination, have been shown to afford viral escape to antibody-mediated immune responses, the high prevalence of variants with large numbers of these mutations circulating in Benin was cause for concern. To investigate whether and to what extent

SARS-CoV-2 variants circulating in Benin and West
Africa (5) Figure  2). Additional isolation attempts of strains belonging to the frequently detected B.1.525 and B.1.318 lineages failed, likely because of degradation after repeated freeze-thaw cycles under tropical conditions. We tested neutralization potency of 6 serum samples from patients in Benin taken ≈8 days after RT-PCRconfirmed SARS-CoV-2 infection during early 2020 (6) and another 7 serum samples from persons in Europe 4 weeks after receiving the second dose of the Pfizer/BioNTech vaccine (BNT162b2; https:// www.pfizer.com) (Appendix Table 4). Sampling was approved by the ethics committee of the Benin Ministry of Health (approval no. 030/MS/DC/SGM/ DNSP/CJ/SA/027SGG2020) and of Charité-Universitätsmedizin Berlin (approval nos. EA1/068/20 and EA4/245/20). We compared neutralization titers with a SARS-CoV-2 strain (B.1.153) from January 2020 and the Beta strain (B.1.351) known to evade antibody-mediated neutralization (7). Despite the early sampling time after RT-PCR confirmation of SARS-CoV-2 infection, all 6 serum specimens from patients in Benin efficiently neutralized the early SARS-CoV-2 isolate carrying only the D614G mutation. In contrast, only 3 of those 6 serum specimens neutralized the B.1 isolate, the only isolate with the E484K mutation (Figure 2, panel A). Among the serum specimens from vaccinated persons, all neutralized the B.1 isolate, albeit at 1.5-fold lower titers than the early lineage B.1.153 isolate (by Friedman test and Dunn's multiple comparisons test; p>0.99) (Figure 2, panel B). Those data were consistent with a recent report describing efficient neutralization of a B.1.525 strain from Nigeria by vaccinee-derived serum specimens (8). Of note, another strain classified as B.1.214.2 was neutralized more efficiently than all other tested lineages ( Figure  2), highlighting that not every mutation in circulating lineages affords reduced antibody-mediated neutralization. Other hypothetically present fitness advantages of such strains will require detailed virologic investigation.
Our study is limited by patient-derived samples taken an average of 8 days after infection (7), which could imply incomplete maturation of antibodies. However, similar neutralization patterns between patient-derived and vaccinee-derived serum specimens suggest robustness of our data. Another limitation is that vaccinee-derived serum samples originated exclusively from Europe. Vaccine responses vary between populations, possibly influenced by genetic background and immune-modulating diseases (e.g., malaria or HIV) (9), highlighting the importance of testing serum samples from vaccinees in Africa for future studies. Of note, the efficacy trial of the Pfizer/ BioNTech vaccine enrolled ≈40,000 participants, only ≈800 of whom were from Africa, and all of those from South Africa (10).

Conclusions
Our data highlight the importance of ongoing monitoring of population immunity to emerging SARS-CoV-2 variants in Africa and of using serum specimens from local settings for phenotypic characterizations. Vaccination programs in Africa should be accelerated urgently, emphasizing the importance of global access to vaccines.