One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages

Gónzález-Candelas, Fernando; Shaw, Marie; Phan, Tung; Kulkarni‐Kale, Urmila; Paraskevis, Dimitrios; Luciani, Fabio; Kimura, Hirokazu; Sironi, Manuela

doi:10.1016/j.meegid.2021.104869

Cited by 54 publications

(58 citation statements)

References 166 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Patients infected with this virus shed more viral nucleic acid compared with those infected with the wild-type (D614) Wuhan-Hu-1 strain and showed significantly higher infectious titers in vitro as a consequence of higher affinity for ACE2 ( 6 ). During the summer of 2020, the dynamic tracking of the SARS-CoV-2 mutants in the global pandemic highlighted a rapid evolution of the virus with an increase in the frequency of mutations and an epidemic pattern characterized by the generation of new variants including the Marseille 4 variant Nextclade 20A.EU2 ( 7 ), the UK variant 20I/501Y.V1 ( 8 ), the South African variant 20H/501Y.V2 ( 9 ), the Brazilian variant 484K.V2 ( 25 ), and others ( 10 ). These variants can be associated with different clinical features of COVID-19 and increased frequency of death ( 26 , 27 ).…”

Section: Discussionmentioning

confidence: 99%

“…During the spring of 2020, a non-synonymous mutation leading to a spike protein substitution D614G became dominant in the reported sequences of SARS-CoV-2 and was found to enhance viral replication as a result of higher affinity for the ACE2 receptor (5,6). Since the summer of 2020, the emergence of major viral variants has been observed (7)(8)(9)(10). These variants have been found to be responsible for juxtaposed or successive epidemics in various geographic areas.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time

et al. 2021

View full text Add to dashboard Cite

Since the start of COVID-19 pandemic the Republic of Djibouti, in the horn of Africa, has experienced two epidemic waves of the virus between April and August 2020 and between February and May 2021. By May 2021, COVID-19 had affected 1.18% of the Djiboutian population and caused 152 deaths. Djibouti hosts several foreign military bases which makes it a potential hot-spot for the introduction of different SARS-CoV-2 strains. We genotyped fifty three viruses that have spread during the two epidemic waves. Next, using spike sequencing of twenty-eight strains and whole genome sequencing of thirteen strains, we found that Nexstrain clades 20A and 20B with a typically European D614G substitution in the spike and a frequent P2633L substitution in nsp16 were the dominant viruses during the first epidemic wave, while the clade 20H South African variants spread during the second wave characterized by an increase in the number of severe forms of COVID-19.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Despite the unprecedented achievement of having approved vaccines in one year, it is still early to establish the durability and extent of the protection; recent data on the vaccines which first received approval, like BNT162b2, from Pfizer-BioNTech, point to a diminished efficacy already six months after vaccination [6,7]. Most importantly, the way to optimize the existing vaccines to protect against the prevalent SARS-CoV-2 variants of concern (VOC) that are spreading globally it is still unclear [8]. These VOC have multiple mutations in Spike, mainly in the RBM region and N-terminal domain, that differ substantially from the Spike variants encoded by the already approved vaccines.…”

Section: Introductionmentioning

confidence: 99%

A Single Dose of a Hybrid hAdV5-Based Anti-COVID-19 Vaccine Induces a Long-Lasting Immune Response and Broad Coverage against VOC

et al. 2021

View full text Add to dashboard Cite

Most approved vaccines against COVID-19 have to be administered in a prime/boost regimen. We engineered a novel vaccine based on a chimeric human adenovirus 5 (hAdV5) vector. The vaccine (named CoroVaxG.3) is based on three pillars: (i) high expression of Spike to enhance its immunodominance by using a potent promoter and an mRNA stabilizer; (ii) enhanced infection of muscle and dendritic cells by replacing the fiber knob domain of hAdV5 by hAdV3; (iii) use of Spike stabilized in a prefusion conformation. The transduction with CoroVaxG.3-expressing Spike (D614G) dramatically enhanced the Spike expression in human muscle cells, monocytes and dendritic cells compared to CoroVaxG.5 that expressed the native fiber knob domain. A single dose of CoroVaxG.3 induced a potent humoral immunity with a balanced Th1/Th2 ratio and potent T-cell immunity, both lasting for at least 5 months. Sera from CoroVaxG.3-vaccinated mice was able to neutralize pseudoviruses expressing B.1 (wild type D614G), B.1.117 (alpha), P.1 (gamma) and B.1.617.2 (delta) Spikes, as well as an authentic P.1 SARS-CoV-2 isolate. Neutralizing antibodies did not wane even after 5 months, making this kind of vaccine a likely candidate to enter clinical trials.

show abstract

“…Despite the unprecedented achievement of having approved vaccines in one year it is still early to establish the durability and extent of the protection, and recent data on the vaccines which first received approval, like BNT162b2 from Pfizer-BioNTech, point to a diminished efficacy already six months after vaccination 6,7 . Most importantly, it is still unclear the way to optimize the existing vaccines to protect against the prevalent SARS-CoV-2 variants of concern (VOC) that are spreading globally 8 . These VOC have multiple mutations in Spike, mainly in the RBM region and N-terminal domain, that differ substantially from the Spike variants encoded by the already approved vaccines.…”

Section: Introductionmentioning

confidence: 99%

A single shot of a hybrid hAdV5-based anti-COVID-19 vaccine induces a long-lasting immune response and broad coverage against VOC

López

Vinzón

Cafferata

et al. 2021

Preprint

View full text Add to dashboard Cite

Most approved vaccines against COVID-19 have to be administered in a prime/boost regimen. We engineered a novel vaccine based on a chimeric hAdV5 vector. The vaccine (named CoroVaxG.3) is based on three pillars: i) high expression of Spike to enhance its immunodominance by using a potent promoter and a mRNA stabilizer; ii) enhanced infection of muscle and dendritic cells by replacing the fiber knob domain of hAdV5 by hAdV3; iii) use of Spike stabilized in a prefusion conformation. Transduction with CoroVaxG.3 expressing Spike (D614G) dramatically enhanced Spike expression in human muscle cells, monocytes and dendritic cells compared to CoroVaxG.5 that expressed the native fiber knob domain. A single dose of CoroVaxG.3 induced potent humoral immunity with a balanced Th1/Th2 ratio and potent T-cell immunity, both lasting for at least 5 months. Sera from CoroVaxG.3 vaccinated mice was able to neutralize pseudoviruses expressing B.1 (wild type D614G), B.1.117 (alpha) and P.1 (gamma) Spikes, as well as an authentic WT and P.1 SARS-CoV-2 isolates. Neutralizing antibodies did not wane even after 5 months making this kind of vaccine a likely candidate to enter clinical trials.

show abstract

One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages

Cited by 54 publications

References 166 publications

Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time

Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time

A Single Dose of a Hybrid hAdV5-Based Anti-COVID-19 Vaccine Induces a Long-Lasting Immune Response and Broad Coverage against VOC

A single shot of a hybrid hAdV5-based anti-COVID-19 vaccine induces a long-lasting immune response and broad coverage against VOC

Contact Info

Product

Resources

About