Novel SARS-CoV-2 Variant Derived from Clade 19B, France

Fourati, Slim; Decousser, Jean‐Winoc; Khouider, Souraya; N’Debi, Mélissa; Démontant, Vanessa; Trawinski, Elisabeth; Gourgeon, Aurélie; Gangloff, C.; Destras, Grégory; Bal, Antonin; Josset, Laurence; Soulier, Alexandre; Costa, Yannick; Gricourt, Guillaume; Lina, Bruno; Lepeule, R.; Pawlotsky, Jean‐Michel; Rodriguez, Christophe

doi:10.3201/eid2705.210324

Cited by 24 publications

(26 citation statements)

References 4 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…4 ). This lineage had been previously reported in the French overseas department Mayotte, then in Créteil [14] and the detection of this variant in Nice in January may be related to the arrival of travelers from these areas for Christmas. A.27 totally disappeared in February in this neighborhood when B.1.1.7 became prominent.…”

Section: Resultssupporting

confidence: 62%

Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing

Rios

Lacoux

Leclercq³

et al. 2021

The Lancet Regional Health - Europe

View full text Add to dashboard Cite

Background Wastewater surveillance was proposed as an epidemiological tool to define the prevalence and evolution of the SARS-CoV-2 epidemics. However, most implemented SARS-CoV-2 wastewater surveillance projects were based on qPCR measurement of virus titers and did not address the mutational spectrum of SARS-CoV-2 circulating in the population. Methods We have implemented a nanopore RNA sequencing monitoring system in the city of Nice (France, 550,000 inhabitants). Between October 2020 and March 2021, we monthly analyzed the SARS-CoV-2 variants in 113 wastewater samples collected in the main wastewater treatment plant and 20 neighborhoods. Findings We initially detected the lineages predominant in Europe at the end of 2020 (B.1.160, B.1.177, B.1.367, B.1.474, and B.1.221). In January, a localized emergence of a variant (Spike:A522S) of the B.1.1.7 lineage occurred in one neighborhood. It rapidly spread and became dominant all over the city. Other variants of concern (B.1.351, P.1) were also detected in some neighborhoods, but at low frequency. Comparison with individual clinical samples collected during the same week showed that wastewater sequencing correctly identified the same lineages as those found in COVID-19 patients. Interpretation Wastewater sequencing allowed to document the diversity of SARS-CoV-2 sequences within the different neighborhoods of the city of Nice. Our results illustrate how sequencing of sewage samples can be used to track pathogen sequence diversity in the current pandemics and in future infectious disease outbreaks. Translation For the French translation of the abstract see Supplementary Materials section.

show abstract

Section: Resultssupporting

confidence: 62%

Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing

Rios

Lacoux

Leclercq³

et al. 2021

The Lancet Regional Health - Europe

View full text Add to dashboard Cite

show abstract

“…described the variant as Clade 19B. 62 However, the Nextstrain server describes it as the 20C clade. Transmission of this variant is low because the variant does possess a mutation that is not associated with the transmission.…”

Section: Properties Of the Significant Voismentioning

confidence: 99%

Present variants of concern and variants of interest of severe acute respiratory syndrome coronavirus 2: Their significant mutations in S‐glycoprotein, infectivity, re‐infectivity, immune escape and vaccines activity

Chakraborty

Bhattacharya

Sharma

2021

Reviews in Medical Virology

View full text Add to dashboard Cite

Summary Newly arising variants of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) are now a threat to global public health and are creating COVID‐19 surges in different countries. At the same time, there is limited knowledge about these emerging variants. Even if research data are available, it is varyingly scattered. In this review, we have discussed the appearance of significant alarming SARS‐CoV‐2 variants in the entire world. The study also discusses the properties of the substantial variant of concern (VOC) variants such as B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.427 (Epsilon) and B.1.429 (Epsilon). At the same time, the characteristic properties of some significant variant of interest (VOI) variants like B.1.525 (Eta), B.1.526 (Iota) (sublineage B.1.526.1), B.1.617 (sublineages B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.617.3), P.2 (Zeta), P.3 (Theta), B.1.616 and B.1.427 have also been discussed. Here, we have explained some essential mutations for the VOC and VOI variants such as K417T/N, L452R, E484K, N501Y, D614G and P681R. Consecutively, we also highlighted the crucial clinical characteristics of the variants, such as transmissibility, infectivity, re‐infectivity, immune escape, vaccine activity and vaccine escape. Our comprehensive review will provide updated information on the newly appearing variants of SARS‐CoV‐2 and help the researchers to formulate strategies to curtail the COVID‐19 pandemic.

show abstract

“… 42 43 44 A novel SARS-CoV-2 variant derived from clade 19B (HMN.19B variant or Henri Mondor variant) has been recently identified and is actually circulating in France. 45 Whether HMN.19B will be less susceptible to protection by natural, therapeutic, or vaccine-induced immune responses remains to be determined. Some SARS-CoV-2 variants such as the Danish 46 one disappear rapidly, whereas others, like the most recent Indian strain, represent a real threat due to the high transmission rate.…”

Section: Considerations To Improve the Feasibility Of Vaccination Programsmentioning

confidence: 99%

The COVID-19 Pandemic and the Need for an Integrated and Equitable Approach: An International Expert Consensus Paper

et al. 2021

View full text Add to dashboard Cite

One year after the declaration of the COVID-19 pandemic by the World Health Organization (WHO) and despite the implementation of mandatory physical barriers and social distancing, humanity remains challenged by a long-lasting and devastating public health crisis. Non-pharmacological interventions (NPI) are efficient mitigation strategies. The success of these intense NPI is dependent on the approval and commitment of the population. The launch of a mass vaccination program in many countries in late December 2020 with mRNA vaccines, adenovirus-based vaccines, and inactivated virus vaccines has generated hope for the end of the pandemic. Current issues: The continuous appearance of new pathogenic viral strains and the ability of vaccines to prevent infection and transmission raise important concerns as we try to achieve community immunity against SARS-CoV-2 and its variants. The need of a second and even third generation of vaccines and the possibility of potentially harmful side-effects of the vaccines (i.e. venous thromboembolism ) have already been acknowledged. Perspectives: There is a critical and urgent need for a balanced and integrated strategy for the management of the COVID-19 outbreaks organized on three axes: (1) Prevention of the SARS-CoV-2 infection, (2) Detection and early diagnosis of patients at risk of disease worsening, and (3) Anticipation of medical care (PDA). Conclusion: The “PDA strategy” integrated into state policy for the support and expansion of health systems and introduction of digital organization (i.e. telemedicine, artificial intelligence and machine learning technology) is of major importance for the preservation of citizens’ health and life world-wide.

show abstract

Novel SARS-CoV-2 Variant Derived from Clade 19B, France

Cited by 24 publications

References 4 publications

Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing

Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing

Present variants of concern and variants of interest of severe acute respiratory syndrome coronavirus 2: Their significant mutations in S‐glycoprotein, infectivity, re‐infectivity, immune escape and vaccines activity

The COVID-19 Pandemic and the Need for an Integrated and Equitable Approach: An International Expert Consensus Paper

Contact Info

Product

Resources

About