International Expansion of a Novel SARS-CoV-2 Mutant

Wang, Minjin; Li, Mengjiao; Ren, Rui; Li, Lifeng; Chen, En Qiang; Liu, Weimin; Ying, Binwu

doi:10.1128/jvi.00567-20

Cited by 48 publications

(55 citation statements)

References 4 publications

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“…The G614 variant, containing a glycine (G) at residue 614 in the SARS-CoV-2 spike protein, has become the dominant pandemic form globally showing a consistent increase at all national, regional, and local levels, which suggests a possible fitness advantage [ 42 ]. However, no evidence exists yet that any observed changes among SARS-CoV-2 isolates, including G614, have resulted in adaptation to the human host, increased transmissibility, or worsening disease severity [ 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 ]. Other possible explanations for G614 dominance exist such as being caused by purely neutral sampling processes as described for other viruses during previous pandemics [ 54 ].…”

Section: Discussionmentioning

confidence: 99%

“…Apart from establishing an alert system for virus detection by ES, phylogenetic analysis of viral RNA found in sewage [ 14 , 16 ] can also help in understanding virus transmission patterns, tracing virus variants, and detecting virus importations. Analysis of SARS-CoV-2 RNA nucleotide sequences from clinical samples reveals some level of genetic variation including non-synonymous changes observed during the COVID-19 pandemic [ 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 ]. This includes a relevant virus variant containing an amino acid change from aspartate (D) to glycine (G) at residue 614 in the SARS-CoV-2 spike (S) protein, responsible for virus attachment to the Angiotensin-converting enzyme 2 (ACE2) receptor on host cells and subsequent cell entry.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic

Martı́n

Klapsa

Wilton

et al. 2020

Viruses

135

142

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Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), responsible for the ongoing coronavirus disease (COVID-19) pandemic, is frequently shed in faeces during infection, and viral RNA has recently been detected in sewage in some countries. We have investigated the presence of SARS-CoV-2 RNA in wastewater samples from South-East England between 14th January and 12th May 2020. A novel nested RT-PCR approach targeting five different regions of the viral genome improved the sensitivity of RT-qPCR assays and generated nucleotide sequences at sites with known sequence polymorphisms among SARS-CoV-2 isolates. We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. Low levels of viral RNA were detected in a sample from 11th February, 3 days before the first case was reported in the sewage plant catchment area. SARS-CoV-2 RNA concentration increased in March and April, and a sharp reduction was observed in May, showing the effects of lockdown measures. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic

Martı́n

Klapsa

Wilton

et al. 2020

Viruses

135

142

View full text Add to dashboard Cite

show abstract

“…Subsequently, further diversity was recognized as the virus continued to spread, and researchers developed a consensus reference sequence for SARS-CoV-2, to which other sequences may be compared [13]. Researchers have continued to publish studies of the specific variants in the context of localized outbreaks, such as the Diamond Princess cruise ship [14], as well as regional outbreaks and their international connections [12,[15][16][17][18].…”

Section: Introductionmentioning

confidence: 99%

Genetic Grouping of SARS-CoV-2 Coronavirus Sequences using Informative Subtype Markers for Pandemic Spread Visualization

Zhao

Sokhansanj

Malhotra

et al. 2020

Preprint

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We propose an efficient framework for genetic subtyping of SARS-CoV-2, the novel coronavirus that causes the COVID-19 pandemic. Efficient viral subtyping enables visualization and modeling of the geographic distribution and temporal dynamics of disease spread. Subtyping thereby advances the development of effective containment strategies and, potentially, therapeutic and vaccine strategies. However, identifying viral subtypes in real-time is challenging: SARS-CoV-2 is a novel virus, and the pandemic is rapidly expanding. Viral subtypes may be difficult to detect due to rapid evolution; founder effects are more significant than selection pressure; and the clustering threshold for subtyping is not standardized. We propose to identify mutational signatures of available SARS-CoV-2 sequences using a population-based approach: an entropy measure followed by frequency analysis. These signatures, Informative Subtype Markers (ISMs), define a compact set of nucleotide sites that characterize the most variable (and thus most informative) positions in the viral genomes sequenced from different individuals. Through ISM compression, we find that certain distant nucleotide variants covary, including non-coding and ORF1ab sites covarying with the D614G spike protein mutation which has become increasingly prevalent as the pandemic has spread. ISMs are also useful for downstream analyses, such as spatiotemporal visualization of viral dynamics. By analyzing sequence data available in the GISAID database, we validate the utility of ISM-based subtyping by comparing spatiotemporal analyses using ISMs to epidemiological studies of viral transmission in Asia, Europe, and the United States. In addition, we show the relationship of ISMs to phylogenetic reconstructions of SARS-CoV-2 evolution, and therefore, ISMs can play an important complementary role to phylogenetic tree-based analysis, such as is done in the Nextstrain project. The developed pipeline dynamically generates ISMs for newly added SARS-CoV-2 sequences and updates the visualization of pandemic spatiotemporal dynamics, and is available on Github at https://github.com/EESI/ISM and via an interactive website at https://covid19-ism.coe.drexel.edu/.

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“…SARS-CoV-2 has evolved since its initial outbreak by changing its viral genome, which may cause mutations in viral proteins including S protein, resulting in the establishment of better fitness (19,24). We analyzed 1000 full length or near-full length S protein sequences (Supplementary Table 1) through multiple alignment and comparison with the reference S protein sequence to identify potential recurrent mutations and assess the effect on CD8 T cell epitope generation for different HLAs.…”

Section: Mutations On S Protein Of Sars-cov-2mentioning

confidence: 99%

“…Therefore, identifying SARS-CoV-2 S protein specific CD8 T cell epitopes and fully utilizing CD8 T cell immunity in addition to neutralization response are urgently needed for studying anti-COVID-19 immunity and developing effective vaccines. Since its initial outbreak, SARS-CoV-2 has undergone genetic mutations (19). Further, mutations on S proteins that may affect human ACE2 receptor binding, viral transmission and infectivity have been reported (20)(21)(22).…”

Section: Introductionmentioning

confidence: 99%

CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention

Guo¹,

Guo²

2020

Preprint

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The ongoing pandemic of SARS-CoV-2 has brought tremendous crisis on global health care systems and industrial operations that dramatically affect the economic and social life of numerous individuals worldwide. Understanding anti-SARS-CoV-2 immune responses in population with different genetic backgrounds and tracking the viral evolution are crucial for successful vaccine design. In this study, we reported the generation of CD8 T cell epitopes by a total of 80 alleles of three major class I HLAs using NetMHC 4.0 algorithm for the spike protein of SARS-CoV-2, a key antigen that is targeted by both B cells and T cells. We found diverse capacities of S protein specific epitope presentation by different HLA alleles with very limited number of predicted epitopes for HLA-B*2705, HLA-B*4402 and HLA-B*4403 and as high as 132 epitopes for HLA-A*6601. Our analysis of 1000 S protein sequences from field isolates collected globally over the past few months identified three recurrent point mutations including L5F, D614G and G1124V. Differential effects of these mutations on CD8 T cell epitope generation by corresponding HLA alleles were observed. Finally, our multiple alignment analysis indicated the absence of seasonal CoV induced cross-reactive CD8 T cells to drive these mutations. Our findings provided molecular explanations for the observation that individuals with certain HLA alleles such as B*44 are more prone to SARS-CoV-2 infection. Studying anti-S protein specific CD8 T cell immunity in diverse genetic background is critical for better control and prevention of the SARS-CoV-2 pandemic.

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International Expansion of a Novel SARS-CoV-2 Mutant

Abstract: Author order was determined both alphabetically and in order of increasing seniority.

Cited by 48 publications

References 4 publications

Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic

Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic

Genetic Grouping of SARS-CoV-2 Coronavirus Sequences using Informative Subtype Markers for Pandemic Spread Visualization

CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention

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