From Alpha to Omicron BA.2: New digital RT-PCR approach and challenges for SARS-CoV-2 VOC monitoring and normalization of variant dynamics in wastewater

Wurtzer, Sébastien; Levert, Morgane; Dhenain, Eloïse; Accrombessi, Héberte; Manco, Sandra; Fagour, Nathalie; Goulet, Marion; Boudaud, Nicolas; Gaillard, Lucie; Bertrand, Isabelle; Challant, Julie; Masnada, Sophie; Azimi, Sam; Gillon-Ritz, Miguel; Robin, Alban; Mouchel, Jean-Marie; Sig, Obepine; Moulin, Laurent

doi:10.1016/j.scitotenv.2022.157740

Cited by 18 publications

(12 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…This type of surveillance is high priority within South Africa, especially with the lifting of lockdown restrictions and the implementation of prioritized COVID-19 testing strategies. Hence, we suggest that the national government should embark on a new wastewater-based testing strategy to accurately track and trace SARS-CoV-2 viral loads and detect VOC within communities [ 16 , 17 ].…”

Section: Discussionmentioning

confidence: 99%

Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1–BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

Johnson

Mangwana

Sharma

et al. 2022

The Journal of Infectious Diseases

View full text Add to dashboard Cite

This study was one of the first to detect Omicron sublineages BA.4 and BA.5 in wastewater from South Africa. Spearman rank correlation analysis confirmed a strong positive correlation exists between SARS-CoV-2 viral RNA in wastewater samples and clinical cases (r = 0.7749, p < 0.0001). SARS-CoV-2 viral load detected in wastewater, resulting from the Delta-driven 3rd wave, was significantly higher than during the Omicron-driven 4th wave, p < 0.005. Whole-genome sequencing confirmed the presence of Omicron lineage defining mutations in wastewater with the first occurrence reported on 23 November 2021 (BA.1 predominant). The variant rapidly spread, with the prevalence of Omicron positive wastewater samples rising to >80% by 10 January 2022 with BA.2 as the predominant sub-lineage by 10 March 2022, whilst on 18 April 2022 BA.4 and BA.5 were detected in selected wastewater sites. Taken together, these findings demonstrate the value of WBE to monitor the spatiotemporal spread and potential origination of new Omicron sub-lineages of SARS-CoV-2.

show abstract

Section: Discussionmentioning

confidence: 99%

Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1–BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

Johnson

Mangwana

Sharma

et al. 2022

The Journal of Infectious Diseases

View full text Add to dashboard Cite

show abstract

“…We observe a higher binding interaction of the Alpha and Omicron variants in comparison to the Original variant, suggesting that these variants could be highly transmissible. The high transmissibility of the Alpha variant resulted in the origin of the third wave of COVID-19 encountered in France [ 52 ]. However, the introduction of vaccinations coupled with acquired collective immunity to this allowed the expansion and circulation of a better-adapted variant, Delta, which eventually was monitored with vaccine introduction.…”

Section: Discussionmentioning

confidence: 99%

“…However, the introduction of vaccinations coupled with acquired collective immunity to this allowed the expansion and circulation of a better-adapted variant, Delta, which eventually was monitored with vaccine introduction. Later, the reduced efficacy of vaccinations contributed to the selection of the Omicron variant, which showed a greater temporal shift [ 52 ]…”

Section: Discussionmentioning

confidence: 99%

In Silico Protein Folding Prediction of COVID-19 Mutations and Variants

et al. 2022

View full text Add to dashboard Cite

With its fast-paced mutagenesis, the SARS-CoV-2 Omicron variant has threatened many societies worldwide. Strategies for predicting mutagenesis such as the computational prediction of SARS-CoV-2 structural diversity and its interaction with the human receptor will greatly benefit our understanding of the virus and help develop therapeutics against it. We aim to use protein structure prediction algorithms along with molecular docking to study the effects of various mutations in the Receptor Binding Domain (RBD) of the SARS-CoV-2 and its key interactions with the angiotensin-converting enzyme 2 (ACE-2) receptor. The RBD structures of the naturally occurring variants of SARS-CoV-2 were generated from the WUHAN-Hu-1 using the trRosetta algorithm. Docking (HADDOCK) and binding analysis (PRODIGY) between the predicted RBD sequences and ACE-2 highlighted key interactions at the Receptor-Binding Motif (RBM). Further mutagenesis at conserved residues in the Original, Delta, and Omicron variants (P499S and T500R) demonstrated stronger binding and interactions with the ACE-2 receptor. The predicted T500R mutation underwent some preliminary tests in vitro for its binding and transmissibility in cells; the results correlate with the in-silico analysis. In summary, we suggest conserved residues P499 and T500 as potential mutation sites that could increase the binding affinity and yet do not exist in nature. This work demonstrates the use of the trRosetta algorithm to predict protein structure and future mutations at the RBM of SARS-CoV-2, followed by experimental testing for further efficacy verification. It is important to understand the protein structure and folding to help develop potential therapeutics.

show abstract

“…Cette preuve de concept a démontré la faisabilité de mise en œuvre de ce type de surveillance spécifique des mutations, complémentaire des méthodes de séquençage. Un examen spécifique des variants par RT-qPCR ou PCR digitale permet ainsi une mesure rapide et peu coûteuse de la proportion des mutations, qui pourrait être utilisée comme un « proxy » pour le suivi de la dynamique des variants [ 18 ].…”

Section: L’irba Co-fondateur Du Réseau Obépine Réseau Sentinelle De L...unclassified

L’Institut de recherche biomédicale des armées (IRBA) et l’épidémiologie des eaux usées : intérêt pour les forces armées

Boni

Gorgé²,

Mullot

et al. 2022

Bulletin de l'Académie Nationale de Médecine

View full text Add to dashboard Cite

From Alpha to Omicron BA.2: New digital RT-PCR approach and challenges for SARS-CoV-2 VOC monitoring and normalization of variant dynamics in wastewater

Cited by 18 publications

References 41 publications

Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1–BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

Delineating the Spread and Prevalence of SARS-CoV-2 Omicron Sublineages (BA.1–BA.5) and Deltacron Using Wastewater in the Western Cape, South Africa

In Silico Protein Folding Prediction of COVID-19 Mutations and Variants

L’Institut de recherche biomédicale des armées (IRBA) et l’épidémiologie des eaux usées : intérêt pour les forces armées

Contact Info

Product

Resources

About