Source data, a, Comparison between short-read (Illumina) and long-read single-molecule (Oxford Nanopore) sequencing methods for the six observed mutations in the spike protein. R.K.G., S.A.K., D.A.C., L.E.M., J.A.G.B., E.G.-K., N.T., A. Chandra, C.S., R.D., R.A.G., D.D.P. All trees were visualized with Figtree v.1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/), rooted on the SARS-CoV-2 reference sequence and nodes arranged in descending order. Seow, J. et al. In contrast to the early period of infection, between days 66 and 82, after the first two administrations of convalescent sera, a shift in the virus population was observed, with a variant bearing a D796H substitution in S2 and a ΔH69/ΔV70 deletion in the S1 N-terminal domain (NTD) of spike becoming the dominant population at day 82. Li, H. Minimap2: pairwise alignment for nucleotide sequences. S.A.K. Share to Twitter Share to Facebook Share to Pinterest. Pseudotyped virus was incubated with serial dilutions of purified monoclonal antibodies9 in duplicate for 1 h at 37 °C. 2). The inferred linkage of spike(D796H) and spike(ΔH69/ΔV70) was maintained as evidenced by the highly similar frequencies of the two variants, suggesting that the third unit of convalescent plasma led to the re-emergence of this population under renewed positive selection. b, Variants detected in patient X1 on days 82–101. Data from healthy control individuals are shown as grey circles (n = 15), data from patient X1 at days 71 and 98 are shown as blue and red circles, respectively. The clinical efficacy of convalescent plasma in patients with severe COVID-19 has not been demonstrated21, and its use in different stages of infection and disease remains experimental; as such, we suggest that it should be reserved for use within clinical trials, and with rigorous monitoring of clinical and virological parameters. Written informed consent was obtained from both the patient and his family. Zhou, T. et al. CP, convalescent plasma; RDV, remdesivir. In our phylogenetic analysis, we included sequential sequences from three other local patients identified with persistent viral RNA shedding over a period of 4 weeks or more as well as two recently reported long-term immunosuppressed individuals with SARS-CoV-24,5 (Extended Data Fig. Ravindra GUPTA | Cited by 3,238 | of University of London, London | Read 121 publications | Contact Ravindra GUPTA 217, e20201181 (2020). März 2020 Britische Mediziner haben den zweiten HIV-Patient geheilt Der sogenannte "London-Patient" hat eine spezielle Stammzellentherapie bekommen (…) R.K.G. After clinical deterioration, remdesivir and a unit of convalescent plasma were administered on day 95, but the individual died on day 102 (Supplementary Note). Ravindra Gupta. Y707 is from the neighbouring protomer. This indirect ELISA-based assay uses a recombinant structural spike 1 (S1) protein of SARS-CoV-2 expressed in the human cell line HEK293 for the detection of SARS-CoV-2 IgG. b, Maximum-likelihood phylogenetic tree of patient X1 with the day of sampling indicated. PubMed Central  It should … By contrast, the spike(D796H) single mutant had significantly lower infectivity compared to the wild-type spike protein and the double mutant (spike(D796H, ΔH69/ΔV70)) had a similar infectivity to wild-type spike (Fig. Singer, Patawee Asamaphan, Marc O. Niebel, Lily Tong, Alice Broos, Daniel Mair, Jenna Nichols, Stephen N. Carmichael, Kyriaki Nomikou, Elihu Aranday-Cortes, Natasha Johnson & Seema Nickbakhsh, Matthew D. Parker, Thushan I. de Silva, Dennis Wang, Matthew Wyles, Danielle C. Groves, Peijun Zhang, Marta Gallis, Stavroula F. Louka, Benjamin B. Lindsey, Timothy M. Freeman, Nikki Smith, Alexander J. Keeley, David G. Partridge, Mohammad Raza, Cariad Evans, Kate Johnson, Adrienn Angyal, Luke R. Green, Paul J. Parsons, Rachel M. Tucker, Rebecca Brown & Max Whiteley, Portsmouth Hospitals University NHS Trust, Portsmouth, UK, Sharon Glaysher, Anoop J. Chauhan, Scott Elliott, Kelly Bicknell, Sarah Wyllie, Allyson Lloyd & Robert Impey, School of Pharmacy and Biomedical Sciences, University of Portsmouth (PORT), Portsmouth, UK, Katie F. Loveson, Salman Goudarzi, Christopher Fearn, Kate Cook, Hannah Dent & Hannah Paul, Kate E. Templeton, Martin P. McHugh, Rebecca Dewar & Elizabeth Wastenge, Kate E. Templeton, Andrew Rambaut, Stefan Rooke, Áine O’Toole, Thomas Williams, Verity Hill, Carlos E. Balcazar, Michael D. Gallagher, Kathleen A. Williamson & Thomas D. Stanton, Department of Medicine, University of Oxford, Oxford, UK, Quadram Institute Bioscience, Norwich, UK, Justin O’Grady, Andrew J. Ravindra Kumar Gupta. Nucleotides were then filtered to have a PHRED score of at least 30; reads with fewer than 30 such reads were discarded. HEK293T cells were transfected with a mixture of 11 μl of Fugene HD, 1 μg of pCDNAΔ19Spike–HA, 1 μg of p8.91 HIV-1 gag–pol expression vector45,46 and 1.5 μg of pCSFLW (expressing the firefly luciferase reporter gene with the HIV-1 packaging signal). ISSN 1476-4687 (online). The eight RBD-specific monoclonal antibodies (Extended Data Fig. Richard, M., Herfst, S., Tao, H., Jacobs, N. T. & Lowen, A. C. Influenza A virus reassortment is limited by anatomical compartmentalization following coinfection via distinct routes. COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. C.J.R.I. In a building that has been largely empty for the past three months, Ravi Gupta has been working non-stop alongside other virus experts. Then, freshly trypsinized HeLa ACE2-expressing cells were added to each well. Profile von Personen mit dem Namen Ravindra Ram Gupta anzeigen. J. Med. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. 9). Gupta is known for leading a study that lead to the recovery of Adam Castillejo, the second person to have been saved from the deadly Human Immunodeficiency Virus or HIV. In a final attempt to reduce the viral load, a third course of remdesivir (day 93) and a third dose of convalescent plasma (day 95) were administered. The other, previously reported patient4 showed a similar degree of diversification as patient X1. Struct. Extended Data Fig. PubMed  Google Scholar. and E.G.-K. conceived the study. Honorary staff. Get the most important science stories of the day, free in your inbox. Cryo-EM structures of SARS-CoV-2 spike without and with ACE2 reveal a pH-dependent switch to mediate endosomal positioning of receptor-binding domains. share to linkedin ... including a deletion present in the B.1.1.7 variant, reported Ravindra Gupta, MD, PhD, of University of Cambridge in England, and colleagues. The repeated increase in the frequency of the viral population with convalescent plasma therapy strongly supports the hypothesis that the combination of the deletion and mutation in the spike protein conferred a selective advantage. 9). P rof. Cambridge physician and microbiologist Professor Ravindra Kumar Gupta is one of six persons of Indian-origin on the latest Time 100 Most Influential People 2020 list.. D.A.C. Bioinformatics 34, 3094–3100 (2018). Approximately two weeks after receiving two units of convalescent plasma, viral populations carrying spike(ΔH69/ΔV70) and spike(D796H) increased to frequencies of more than 80% but decreased significantly 4 days later. As this loop is flexible and highly accessible, ΔH69/ΔV70 could in principle affect antibody binding in this region. The 82-year-old protested against the Citizenship Amendment Act (CAA) by dedicatedly taking part in the Shaheen Bagh protests in Delhi. This diagram highlights the considerable diversity of patient X1 (green) compared with three other local patients with prolonged shedding (patients C1–C3 are shown as red, blue and purple sequences, respectively). 3). Mixing of virus from different compartments—for example, via blood or the movement of secretions from lower to upper respiratory tract—could lead to fluctuations in viral populations at particular sampling sites. Contact email address: rkg20@cam.ac.uk. Case study: prolonged infectious SARS-CoV-2 shedding from an asymptomatic immunocompromised cancer patient. of the neutralization of technical replicates (n = 2). He is a popular Indian Film Critic, a Motivational Speaker, and a renowned Leadership Consultant. In his piece about Gupta for Time, Castillejo said, "Through the years, our partnership has developed and strengthened as Gupta has shared his knowledge and his … Combined point-of-care nucleic acid and antibody testing for SARS-CoV-2 following emergence of D614G spike variant. All data are also available from the corresponding author. https://doi.org/10.1038/s41586-021-03291-y, COVID-19 in early 2021: current status and looking forward. The first major changes in the spike genome occurred on day 82, after convalescent plasma was administered on days 63 and 65. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. et al. 2 Blood parameters over time in patient X1. The HotDeals360 team writes about stuff we think you'll like. Articles Cited by Co-authors. Twitter CEO Jack Dorsey’s 1st tweet up for grabs, bid reaches Rs 2 crore. We noted in our analysis signs of compartmentalized viral replication based on the sequences recovered in upper respiratory tract samples. In the last few years, Khurrana has built his own image by doing some unconventional roles perfectly. Libraries were loaded at 15 nM and spiked in 5% PhiX (Illumina) and sequenced on for MiSeq 500 cycle using a Miseq Nano v.2 with 2 × 250 bp paired-end sequencing. All libraries were then pooled in equimolar ratios accordingly. Collier, D. A. et al. (Source: Screen grab) Weeks after Supreme Court’s order on standing up during National Anthem in cinema halls, to “instill a feeling within one a sense of committed patriotism and nationalism”, BJP’s Ravinder Gupta was caught on camera singing the national anthem incorrectly. Psychiatric and medical health care policies in juvenile detention facilities. Ravindra Jadeja injury update: Southpaw completes successful surgery. Virus neutralization assays were performed on HEK293T cells transiently transfected with ACE2 and TMPRSS2 using SARS-CoV-2 spike pseudotyped virus expressing luciferase48. Template RNA was degraded with RNase H (Thermo Fisher Scientific). AIDS 24, 1651–1655 (2010). The Gupta lab has teams in both London and at the Africa Health Research Institute in Durban South Africa. Variant frequencies were validated using custom code as part of the AnCovMulti package (https://github.com/PollockLaboratory/AnCovMulti). Profile von Personen mit dem Namen Ravindra Gupta anzeigen. The authors declare no competing interests. J. Clin. The average Ravindra Gupta is around 60 years of age with around 55% falling in to the age group of 41-60. Commun. The top state of residence is New Jersey, followed by California. The CITIID-NIHR BioResource COVID-19 Collaboration, The COVID-19 Genomics UK (COG-UK) Consortium, https://github.com/PollockLaboratory/AnCovMulti, http://tree.bio.ed.ac.uk/software/figtree/, https://github.com/schrodinger/pymol-open-source/releases, https://github.com/Steven-Kemp/sequence_files, https://doi.org/10.21203/rs.3.rs-105996/v1, https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563, https://doi.org/10.1101/2020.12.14.422555, https://www.cdc.gov/coronavirus/2019-ncov/hcp/disposition-hospitalized-patients.html, https://doi.org/10.1101/2020.11.18.20230599, https://doi.org/10.17504/protocols.io.bbmuik6w, https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html, Extended Data Fig. Shu, Y. The number of single genomes obtained at each time point with the mutations of interest (identified by deep sequencing) are shown. All authors contributed to revising the paper. Professor. Jordan, M. R. et al. Ct values from respiratory samples are indicated on the right y axis (black dashed line and triangles). This research was supported by the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre, the Cambridge Clinical Trials Unit (CCTU) and by the UCL Coronavirus Response Fund and made possible through generous donations from UCL’s supporters, alumni, and friends (to L.E.M.). 6 Sequence analyses and comparisons with other patients with SARS-CoV-2. (2021)Cite this article. Red indicates significant fold changes. The Gupta lab has teams in both London and at the Africa Health Research Institute in Durban South Africa. In vitro, the spike double mutant bearing both ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. A randomized trial of convalescent plasma in COVID-19 severe pneumonia. f, g, Neutralizing potency of the serum of patient X1 against pseudotyped virus bearing spike(D796H), spike(ΔH69/ΔV70) and spike(D796H, ΔH69/ΔV70). Professor Ravi Gupta is an infectious diseases clinician with specific focus on HIV. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. Choi, B. et al. J. Exp. Ravindra Kumar Gupta. 2, 3). Cell 182, 1295–1310 (2020). Xiong, X. et al. RLU, relative light units;  nU, nanounit. People … share to twitter. Lumby, C. K., Zhao, L., Breuer, J. Med. However, owing to the higher reliability of Illumina for low frequency variants, this was used for formal analysis2,3. Extended Data Fig. Convergent antibody responses to SARS-CoV-2 in convalescent individuals. 4). 11, e1004041 (2015). Ravindra GUPTA | Cited by 12 | of Indian Institute of Technology (ISM) Dhanbad, Dhanbād (ISM) | Read 5 publications | Contact Ravindra GUPTA Internet Explorer). Ravindra Gautam. Ravinder Gupta, Mayor of North Delhi Municipal Corporation (NDMC) can … Research in the Gupta lab focusses on host-pathogen and drug-pathogen interactions to inform HIV treatment and curative strategies. A partial gene sequence of spike (encoding amino acids 21–800) was amplified as one continuous length of DNA (the spike gene is approximately 1.8 kb) by nested PCR. 2). 3 Serum antibody levels against SARS-CoV-2. Indian names such as Narendra Modi, Ayushmann Khurrana, Sundar Pichai, Ravindra Gupta, and Bilkis Bano have featured in TIME magazine's list of 100 influential people of 2020. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Biol. Amino acid substitutions described in the text are indicated by labels using the same colouring as the position in the genome (associated proteins are included for each name). Nat. Cell Rep. Med. is supported by a Wellcome Trust Clinical PhD Research Fellowship. Serial samples were collected from the patient periodically from the lower respiratory tract (sputum or endotracheal aspirate), upper respiratory tract (throat and nasal swab) and from stool. 11, 6272 (2020). Viral vectors were prepared by transfection of HEK293T cells using the Fugene HD transfection reagent (Promega). Ravindra Gautam has conceptualized, produced and is associated with many information-laden TV Shows on popular national channels. b, Pairwise distances between samples in the larger clade (black) and between these samples and those collected on days 93 and 95 (red). 13, e1006203 (2017). Shrock, E. et al. c–e, Neutralization potency of convalescent plasma units (CP1–CP3) against pseudotyped viruses bearing spike(D796H), spike(ΔH69/ΔV70) and spike(D796H, ΔH69/ΔV70). 27, 763–767 (2020). Distinct conformational states of SARS-CoV-2 spike protein. 6). The pelleted virions were lysed in Laemmli reducing buffer (1 M Tris-HCl (pH 6.8), SDS, 100% glycerol, β-mercaptoethanol and bromophenol blue). Control patients with SARS-CoV-2 generally showed limited diversity temporally, although the sequences from one of the previous studies4 were highly divergent. The most surprising name on the list is that of Bilkis Bano. On days 86 and 89, viruses obtained from upper respiratory tract samples were characterized by the spike(Y200H, T240I) double mutant, with the mutation–deletion pair (spike(D796H, ΔH69/ΔV70)) observed on day 82 having decreased to frequencies of 10% or less (Figs. Pseudotyped virus was incubated with serial dilutions of heat-inactivated human serum samples or convalescent plasma in duplicate for 1 h at 37 °C. D796H, but not ΔH69/ΔV70, conferred a reduction in susceptibility to polyclonal antibodies in the units of convalescent plasma administered, although we cannot speculate as to their individual effect on sera from other individuals. The deletion was observed contemporaneously with the rare S2 variant spike(D796H) after two separate courses of convalescent plasma, with other viral populations emerging. Investigating the details of macrophage infection in clinical isolates. 2 and Supplementary Table 4). Ravindra Gupta ist bei Facebook. For long-read sequencing, genomes were assembled with reference-based assembly and a curated bioinformatics pipeline with 20× minimum coverage across the whole genome27. 17, 10–12 (2011). 1). a, Variants detected in patient X1 on days 1–82 after the first positive RT–qPCR test for SARS-CoV-2. Dr. Ravindra A Gupta, MD, is an Anesthesiology specialist in Kankakee, Illinois. Dr Ravindra Gupta says new test results likely demonstrate the patient is cured. 1, 100099 (2020). We note that detection of viral RNA in post-mortem tissue was observed previously not only in lung tissue, but also in the spleen, liver, and heart4. I.G.G. Loman, N., Rowe, W. & Rambaut, A. nCoV-2019 novel coronavirus bioinformatics protocol. Twitter; Bone Marrow Transplant Renders Second Patient Free Of HIV. All rights reserved. Computed tomography of the chest showed widespread abnormalities consistent with pneumonia associated with coronavirus disease 2019 (COVID-19) (Supplementary Fig. PubMed  [Epub ahead of print] Prof Gupta presented the work at CROI. eLife 9, e56915 (2020). Microbiol. In addition, we were also able to follow the dynamics of virus populations down to low frequencies during the entire period (Fig. It is likely that both chemotherapy and underlying lymphoma contributed to combined immunodeficiency of B and T cells (Extended Data Figs. Viral RNA extracts were reverse-transcribed from each sample to sufficiently capture the diversity of the viral population without introducing resampling bias. Boshier, F. A. T. et al. Sequencing of these surface viruses showed clustering with those derived from the respiratory tract (Extended Data Fig. All samples tested positive for SARS-CoV-2 by RT–qPCR and there was no sustained change in Ct values throughout the 101 days after the first two courses of remdesivir (days 41 and 54) or the first two units of convalescent plasma with polyclonal antibodies (days 63 and 65) (Extended Data Fig. A representative set of 10 sequences was selected and also sequenced using the Illumina MiSeq platform. Justices L Nageswara Rao, Abdul Nazeer, Hemant Gupta and S Ravindra Bhat. The effects of convalescent plasma on virus evolution found here are unlikely to apply in immunocompetent hosts in whom viral diversity is likely to be lower owing to better immune control. Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. 4). Mol. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. The left-hander also assured his fans that he will soon return to … Amino acid variant and corresponding nucleotide position: spike(W64G), 21752; spike(Δ69), 21765–21770; spike(Y200H), 22160; spike(T240I), 22281; spike(P330S), 22550; spike(D795H), 23948. Understanding the viral dynamics and characterizing the viral evolution in response to different selection pressures in an immunocompromised individual are necessary not only for improved patient management but also for public health benefit. is supported by the Bill and Melinda Gates Foundation via PANGEA grant (OPP1175094). Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. Google Scholar. ADS  In further support of our proposed idea of competition, frequencies of these two variants appeared to mirror changes in the NSP2(I513T) variant (Fig. Although the samples that we obtained on days 93 and 95 of infection are genetically distinct from the other samples, the remaining samples are consistent with arising from a consistent viral population. He also loves to play cricket and badminton. Research Interests: HIV drug resistance, HIV persistence and cure, cellular biology of macrophages. Post-ligation products were cleaned using AMPure beads and eluted in 25 μl. a, White cell (WCC) and lymphocyte counts are expressed as 103 cells per mm3. Environmental samples (the call bell and mobile phone of the patient) are indicated. View the profiles of professionals named "Ravindra Gupta" on LinkedIn. D796 is located near the base of the spike protein, in a surface loop that is structurally disordered in the prefusion conformation and becomes part of a large disordered region in the post-fusion S2 trimer11 (Extended Data Fig. PubMed Google Scholar. the water that can be used for drinking is a bare 0.5% of the total water available on Earth; the rest is either unfit for usage or locked away in glaciers.