Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

Dudas, Gytis; Hong, Samuel L.; Potter, Barney; Calvignac‐Spencer, Sébastien; Niatou-Singa, Frédéric S.; Tombolomako, Thais B.; Fuh-Neba, Terence; Vickos, Ulrich; Ulrich, Markus; Leendertz, Fabian H.; Khan, Kamran; Huber, Carmen; Watts, Alexander; Olendraitė, Ingrida; Snijder, Joost; Wijnant, Kim N.; Bonvin, Alexandre M. J. J.; Martres, Pascale; Behillil, Sylvie; Ayouba, Ahidjo; Maïdadi‐Foudi, Martin; Djomsi, Dowbiss Meta; Godwe, Celestin; Butel, Christelle; Šimaitis, Aistis; Gabrielaitė, Miglė; Katėnaitė, Monika; Norvilas, Rimvydas; Raugaitė, Ligita; Koyaweda, Giscard Wilfried; Kandou, Jephté Kaleb; Jonikas, Rimvydas; Nasvytienė, Inga; Žemeckienė, Živilė; Gečys, Dovydas; Norkienė, Milda; Vasiliūnaitė, Emilija; Žiogienė, Danguolė; Timinskas, Albertas; Šukys, Marius; Šarauskas, Mantas; Alzbutas, Gediminas; Aziza, Adrienne Amuri; Kinganda-Lusamaki, Eddy; Makangara, Jean-Claude C.; Mawete, Francisca Muyembe; Lofiko, Emmanuel Lokilo; Kingebeni, Placide Mbala; Tamfum, Jean‐Jacques Muyembe; Belizaire, Marie Roseline Darnycka; Essomba, René Ghislain; Assoumou, Marie Claire Okomo; Mboringong, Akenji Blaise; Dieng, Allé Baba; Juozapaitė, Dovilė; Hosch, Salome; Obama, Justino; Ayekaba, Mitoha Ondo’o; Naumovas, Daniel; Pautienius, Arnoldas; Rafaï, Clotaire; Vitkauskienė, Astra; Ugenskienė, Rasa; Gedvilaitė, Alma; Čereškevičius, Darius; Lesauskaitė, Vaiva; Žemaitis, Lukas; Griškevičius, Laimonas; Baele, Guy

doi:10.1038/s41467-021-26055-8

Cited by 64 publications

(44 citation statements)

References 56 publications

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“…The Equato-Guinean Public Health Laboratory located in the Baney district of Bioko Island uses a hybrid approach combining rapidly adaptable spike gene mutationspecific RT-qPCR assays and whole genome sequencing to monitor the emergence, evolution, and spread of SARS-CoV-2 lineages in the country. Selection of samples for whole genome sequencing can be guided by the results of the mutation-specific RT-qPCR assays and has successfully led in the past to the discovery of the novel lineage B.1.620 (21). Additionally, results from mutation-specific RT-qPCR assays can be generated in real-time in standard local diagnostic laboratories and therefore genomic surveillance becomes actionable.…”

Section: Discussionmentioning

confidence: 99%

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

Hosch

Mpina

Nyakurungu³

et al. 2022

Front. Public Health

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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.

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Section: Discussionmentioning

confidence: 99%

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

Hosch

Mpina

Nyakurungu³

et al. 2022

Front. Public Health

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“…11 Omicron's S‐mutations allow it to be discovered by genotyping assays, which produce findings considerably faster than genome sequencing. 9 , 12 …”

Section: Introductionmentioning

confidence: 99%

SARS‐CoV‐2 Omicron variant: A next phase of the COVID‐19 pandemic and a call to arms for system sciences and precision medicine

Mostafavi

Dubey²,

Teodori

et al. 2022

MedComm

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Since early 2020, coronavirus diseases 2019 (COVID‐19) infection pandemic/endemic is constantly surprising health experts because of continuous variations in the structures of severe acute respiratory coronavirus 2 (SARS‐CoV‐2) in the form of newly emerged variants. Such mutations have exhibited high mortality and severity due to the newly emerged more infectious sites of SARS‐CoV‐2, making viral infection more transmissible, infectious, and severe. Recently, SARS‐CoV‐2 mutated to another variant, namely, Omicron (B.1.1.529), which is many times more transmissible and infectious than existed deadly Delta variants of the virus. This severity is closely correlated to a larger number of mutations observed in the receptor‐binding domain of the spike protein of the Omicron‐SARS‐CoV‐2. Considering severity, Omicron has been declared as variant of concerns by the World Health Organization and within days from its emergence, Omicron infection has spread globally, increased hospitalization, exhibited more severity for the young generation, invaded defense mechanism of natural immunity, not responsive to the available vaccines. Such circumstances resonated with the efficiency of available strategies established to manage COVID‐19 intelligently and successfully. To explore these aspects, this perspective article carefully and critically summarizes the Omicron's origin, structure, pathogenesis, impact health along with health systems, and experts’ recommendations to manage it successfully.

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“…11 , 12 VOCs are variants of global concern as they are linked with increased transmissibility, pathogenicity, disease severity (increased hospitalization and death), immune escape, diagnostic failure, and vaccine (therapeutic) escape. 13 …”

Section: Overview Of the Omicron Sars Cov-2 Variantmentioning

confidence: 99%

Mutational Pattern, Impacts and Potential Preventive Strategies of Omicron SARS-CoV-2 Variant Infection

Abebe¹,

G/Medhin²,

T/Mariam³

et al. 2022

IDR

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Since the emergence of COVID 19, the authentic SARS-CoV-2 has evolved into a range of novel variants that are of more global concern. In late November 2021, the Omicron (lineage B.1.1.529) variant was identified as a new variant and considered as the fifth variant of concern. Omicron harbors a genetic profile that is exceedingly unusual, with a huge number of mutations. Above thirty mutations are localized in the S protein, while some are found in other structural and non-structural proteins. Half of the mutations in the S protein are in the RBD, which is a major target of antibodies, showing that Omicron mutations may affect antibody binding affinity to the S protein. The Omicron variant has been found to result in immune escape, therapeutic or vaccine escape, as well as increased transmissibility and reinfection risk, explaining its rapid international spread that sparks a global alarm even more serious than the previously reported variants. Omicron has the capability to bypass at least some of the multi-faceted immune responses induced by prior infection or vaccination. It is shown to extensively escape neutralizing antibodies while evading cell mediated immune defense to a lesser extent. The efficacy of COVID 19 vaccines against Omicron variant is decreased with primary vaccination, showing that the vaccine is less efficient in preventing Omicron infections. However, after receiving a booster vaccine dose, the immunological response to Omicron significantly improved and hold promising results. Despite the mild nature of the disease in most vaccinated people, the rapid spread of Omicron, as well as the increased risk of re-infection, poses yet another major public health concern. Therefore, effort should be devoted to maintaining the existing COVID 19 preventive measures as well as developing new vaccination strategies in order to control the fast dissemination of Omicron.

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Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

Cited by 64 publications

References 56 publications

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

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

SARS‐CoV‐2 Omicron variant: A next phase of the COVID‐19 pandemic and a call to arms for system sciences and precision medicine

Mutational Pattern, Impacts and Potential Preventive Strategies of Omicron SARS-CoV-2 Variant Infection

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