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Case Reports
. 2022 Jan 4:9:818401.
doi: 10.3389/fpubh.2021.818401. eCollection 2021.

Genomic Surveillance Enables the Identification of Co-infections With Multiple SARS-CoV-2 Lineages in Equatorial Guinea

Salome Hosch  1   2 , Maxmillian Mpina  1   2   3 , Elizabeth Nyakurungu  3 , Nelson Silochi Borico  3 , Teodora Mikumu Alogo Obama  3 , Maria Carmen Ovona  3 , Philipp Wagner  1   2 , Sarah E Rubin  1   2 , Ulrich Vickos  4   5 , Diosdado Vicente Nsue Milang  6 , Mitoha Ondo'o Ayekaba  6 , Wonder P Phiri  7 , Claudia A Daubenberger  1   2 , Tobias Schindler  1   2
Affiliations
Case Reports

Genomic Surveillance Enables the Identification of Co-infections With Multiple SARS-CoV-2 Lineages in Equatorial Guinea

Salome Hosch et al. Front Public Health. .

Abstract

COVID-19 disease caused by SARS-CoV-2 represents an ongoing global public health emergency. Rapid identification of emergence, evolution, and spread of SARS-CoV-2 variants of concern (VOC) would enable timely and tailored responses by public health decision-making bodies. Yet, global disparities in current SARS-CoV-2 genomic surveillance activities reveal serious geographical gaps. Here, we discuss the experiences and lessons learned from the SARS-CoV-2 monitoring and surveillance program at the Public Health Laboratory on Bioko Island, Equatorial Guinea that was implemented as part of the national COVID-19 response and monitoring activities. We report how three distinct SARS-CoV-2 variants have dominated the epidemiological situation in Equatorial Guinea since March 2020. In addition, a case of co-infection of two SARS-CoV-2 VOC, Beta and Delta, in a clinically asymptomatic and fully COVID-19 vaccinated man living in Equatorial Guinea is presented. To our knowledge, this is the first report of a person co-infected with Beta and Delta VOC globally. Rapid identification of co-infections is relevant since these might provide an opportunity for genetic recombination resulting in emergence of novel SARS-CoV-2 lineages with enhanced transmission or immune evasion potential.

Keywords: Central-Africa; SARS-CoV-2; co-infection; genomic surveillance; variant of concern.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
(A) Number of COVID-19 patient hospitalizations per month. (B) SARS-CoV-2 lineages identified in Equatorial Guinea over time. (C) Surveillance of SARS-CoV-2 VOC-associated spike gene mutations. RT-qPCR results for the spike gene mutations L452R, E484K, and N501Y and the spike gene deletion HV69/70Δ indicative of a co-infection are marked with “x”.
Figure 2
Figure 2
(A) Timeline of vaccination, diagnostic testing and whole genome sequencing. RT-qPCR results for the spike gene mutations (B) L452R, (C) E484K, and (D) N501Y. Orange represents the curves matching Beta VOC (L452, 484K, and 501Y) and purple represents the curves matching Delta VOC (452R, E484, and N501) defining SNPs. (E) Proportion of sequencing reads matching Beta or Delta VOC for the lineage defining mutations. Orange bars represent Beta VOC and purple bars represent Delta VOC. White bars represent the proportion of reads matching neither Beta nor Delta VOC.
See this image and copyright information in PMC

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