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Kattoor JJ, Mlalazi-Oyinloye M, Nemser SM, Wilkes RP. Development of a Targeted NGS Assay for the Detection of Respiratory Pathogens including SARS-CoV-2 in Felines. Pathogens 2024; 13:335. [PMID: 38668290 PMCID: PMC11055025 DOI: 10.3390/pathogens13040335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 04/29/2024] Open
Abstract
Acute respiratory diseases in felines can be attributed to a diverse range of pathogens. The recent emergence of novel viruses, particularly SARS-CoV-2 and its variants, has also been associated with respiratory ailments in cats and other pets, underscoring the need for a highly sensitive diagnostic assay capable of concurrently detecting multiple respiratory pathogens. In this study, we developed a targeted next generation sequencing panel using Ion Torrent Ampliseq technology to detect multiple respiratory pathogens, including recent SARS-CoV-2 variants and Feline herpesvirus-1, Feline calicivirus, Bordetella bronchiseptica, Mycoplasmopsis (previously Mycoplasma) felis, and Chlamydia felis. A PCR amplification-based library preparation, employing primers designed for pathogen target regions, was synthesized and divided into two pools, followed by sequencing and assembly to a repertoire of target pathogen genomes. Analytical sensitivity was assessed based on Ct values from real-time PCR for the corresponding pathogens, indicating an equivalent detection limit. Most of the pathogens under study were positively identified to a limit of approximately Ct 36, whereas for Feline herpesvirus-1 and SARS-CoV-2, positive reads were observed in samples with a Ct of 37. Based on a limited number of samples, the diagnostic sensitivity values for the SARS-CoV-2, Feline herpesvirus-1, and M. felis samples were 100% with no false negative results. The diagnostic specificity of SARS-CoV-2, Feline herpesvirus-1, Feline calicivirus, and C. felis were 100%. Importantly, none of the target primers exhibited non-specific amplification, ensuring the absence of false positive results for other pathogens within the study. Additionally, the assay's specificity was validated by cross-referencing the raw sequencing data with established databases like BLAST, affirming the high specificity of the targeted Next-Generation Sequencing (tNGS) assay. Variations in the sequencing reads of different pathogens were observed when subjected to diverse extraction methods. Rigorous assessment of the assay's reliability involved reproducibility across testing personnel and repeated runs. The developed assay's clinical applicability was tested using samples submitted to the diagnostic laboratory from cat shelters and suspected cases. The developed targeted next-generation sequencing methodology empowers the detection of multiple respiratory pathogens manifesting similar clinical symptoms while offering confirmation of results through genome sequencing.
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Affiliation(s)
- Jobin J. Kattoor
- Animal Disease Diagnostic Laboratory, Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA;
| | - Mothomang Mlalazi-Oyinloye
- Center for Veterinary Medicine, Vet-LIRN, Food and Drug Administration, Laurel, MD 20708, USA; (M.M.-O.); (S.M.N.)
| | - Sarah M. Nemser
- Center for Veterinary Medicine, Vet-LIRN, Food and Drug Administration, Laurel, MD 20708, USA; (M.M.-O.); (S.M.N.)
| | - Rebecca P. Wilkes
- Animal Disease Diagnostic Laboratory, Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA;
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Fokam J, Gouissi Anguechia DH, Takou D, Jagni Semengue EN, Chenwi C, Beloumou G, Djupsa S, Nka AD, Togna Pabo WLR, Abba A, Ka'e AC, Kengni A, Etame NK, Moko LG, Molimbou E, Nayang Mundo RA, Tommo M, Fainguem N, Fotsing LM, Colagrossi L, Alteri C, Ngono D, Otshudiema JO, Ndongmo C, Boum Y, Etoundi GM, Halle EG, Eben-Moussi E, Montesano C, Marcelin AG, Colizzi V, Perno CF, Ndjolo A, Ndembi N. SARS-CoV-2 genomic surveillance and reliability of PCR single point mutation assay ( SNPsig® SARS-CoV-2 EscapePLEX CE) for the rapid detection of variants of concern in Cameroon. Heliyon 2024; 10:e29243. [PMID: 38623229 PMCID: PMC11016732 DOI: 10.1016/j.heliyon.2024.e29243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024] Open
Abstract
Background Surveillance of SARS-CoV-2 variants of concern (VOCs) and lineages is crucial for decision-making. Our objective was to study the SARS-CoV-2 clade dynamics across epidemiological waves and evaluate the reliability of SNPsig® SARS-CoV-2 EscapePLEX CE in detecting VOCs in Cameroon. Material and methods A laboratory-based study was conducted on SARS-CoV-2 positive nasopharyngeal specimens cycle threshold (Ct)≤30 at the Chantal BIYA International Reference Centre in Yaoundé-Cameroon, between April-2020 to August-2022. Samples were analyzed in parallel with Sanger sequencing and (SNPsig® SARS-CoV-2 EscapePLEX CE), and performance characteristics were evaluated by Cohen's coefficient and McNemar test. Results Of the 130 sequences generated, SARS-CoV-2 clades during wave-1 (April-November 2020) showed 97 % (30/31) wild-type lineages and 3 % (1/31) Gamma-variant; wave-2 (December-2020 to May-2021), 25 % (4/16) Alpha-variant, 25 % (4/16) Beta-variant, 44 % (7/16) wild-type and 6 % (1/16) mu; wave-3 (June-October 2021), 94 % (27/29) Delta-variant, 3 % (1/29) Alpha-variant, 3 % (1/29) wild-type; wave-4 (November-2021 to August-2022), 98 % (53/54) Omicron-variant and 2 % (1/54) Delta-variant. Omicron sub-variants were BA.1 (47 %), BA.5 (34 %), BA.2 (13 %) and BA.4 (6 %). Globally, the two genotyping methods accurately identified the SARS-CoV-2 VOCs (P = 0.17, McNemar test; Ka = 0.67). Conclusion Genomic surveillance reveals a rapid dynamic in SARS-CoV-2 strains between epidemiological waves in Cameroon. For wide-spread variant surveillance in resource-limited settings, SNPsig® SARS-CoV-2 EscapePLEX CEkit represents a suitable tool, pending upgrading for distinguishing Omicron sub-lineages.
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Affiliation(s)
- Joseph Fokam
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Faculty of Health Sciences, University of Buea, Buea, Cameroon
- National Public Health Emergency Operations Centre, Ministry of Public Health, Yaounde, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon
- Central Technical Group, National AIDS Control Committee, Yaounde, Cameroon
| | - Davy-Hyacinthe Gouissi Anguechia
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon
| | - Desire Takou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Ezechiel Ngoufack Jagni Semengue
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Rome “Tor Vergata”, Rome, Italy
- Faculty of Science and Technology, Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Collins Chenwi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Mvangan District Hospital, Mvangan, Cameroon
| | - Grace Beloumou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Sandrine Djupsa
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Alex Durand Nka
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Rome “Tor Vergata”, Rome, Italy
- Faculty of Science and Technology, Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Willy Le Roi Togna Pabo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Aissatou Abba
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Aude Christelle Ka'e
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Rome “Tor Vergata”, Rome, Italy
| | - Aurelie Kengni
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Naomi Karell Etame
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Larissa Gaelle Moko
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon
| | - Evariste Molimbou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Faculty of Science and Technology, Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Rachel Audrey Nayang Mundo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Michel Tommo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | - Nadine Fainguem
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Rome “Tor Vergata”, Rome, Italy
- Faculty of Science and Technology, Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Lionele Mba Fotsing
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | | | | | - Dorine Ngono
- World Health Organisation Afro, Country Office, Yaoundé, Cameroon
| | | | - Clement Ndongmo
- Centres for Disease Control and Prevention, Yaoundé, Cameroon
| | - Yap Boum
- National Public Health Emergency Operations Centre, Ministry of Public Health, Yaounde, Cameroon
| | - Georges Mballa Etoundi
- National Public Health Emergency Operations Centre, Ministry of Public Health, Yaounde, Cameroon
| | - Edie G.E. Halle
- Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | - Emmanuel Eben-Moussi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
| | | | | | - Vittorio Colizzi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- University of Rome “Tor Vergata”, Rome, Italy
| | | | - Alexis Ndjolo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaounde, Cameroon
- Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | - Nicaise Ndembi
- Africa Centres for Disease Control and Prevention, Abbis Ababa, Ethiopia
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Oktavianthi S, Lages AC, Kusuma R, Kurniasih TS, Trimarsanto H, Andriani F, Rustandi D, Meriyanti T, Yusuf I, Malik SG, Jo J, Suriapranata I. Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia. Pathogens 2024; 13:279. [PMID: 38668234 PMCID: PMC11053823 DOI: 10.3390/pathogens13040279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/12/2024] [Accepted: 03/07/2024] [Indexed: 04/29/2024] Open
Abstract
The SARS-CoV-2 infection that caused the COVID-19 pandemic has become a significant public health concern. New variants with distinct mutations have emerged, potentially impacting its infectivity, immune evasion capacity, and vaccine response. A whole-genome sequencing study of 292 SARS-CoV-2 isolates collected from selected regions of Indonesia between January and October 2021 was performed to identify the distribution of SARS-CoV-2 variants and common mutations in Indonesia. During January-April 2021, Indonesian lineages B.1.466.2 and B.1.470 dominated, but from May 2021, Delta's AY.23 lineage outcompeted them. An analysis of 7515 published sequences from January 2021 to June 2022 revealed a decline in Delta in November 2021, followed by the emergence of Omicron variants in December 2021. We identified C241T (5'UTR), P314L (NSP12b), F106F (NSP3), and D614G (Spike) mutations in all sequences. The other common substitutions included P681R (76.4%) and T478K (60%) in Spike, D377Y in Nucleocapsid (61%), and I82T in Membrane (60%) proteins. Breakthrough infection and prolonged viral shedding cases were associated with Delta variants carrying the Spike T19R, G142D, L452R, T478K, D614G, P681R, D950N, and V1264L mutations. The dynamic of SARS-CoV-2 variants in Indonesia highlights the importance of continuous genomic surveillance in monitoring and identifying potential strains leading to disease outbreaks.
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Affiliation(s)
- Sukma Oktavianthi
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Aksar Chair Lages
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Rinaldy Kusuma
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Tri Shinta Kurniasih
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
- Menzies School of Health Research, Charles Darwin University, Darwin 0811, Australia
| | - Febi Andriani
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - David Rustandi
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Tandry Meriyanti
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Irawan Yusuf
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Safarina G. Malik
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Juandy Jo
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Ivet Suriapranata
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
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Chang YJ, Huang CG, Shie SS, Lin JJ, Chen CJ. Clinical features and virologic lineages of COVID-19-associated encephalitis in Taiwanese children during early epidemic wave of omicron in 2022: Report from a medical center. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024; 57:48-54. [PMID: 37926632 DOI: 10.1016/j.jmii.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 09/08/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND A surge of encephalitis was reported in children during the early wave of the omicron epidemic in Taiwan. Information on the COVID-19-associated encephalitis, including epidemiologic features and factors of unfavorable outcomes, remained unclear. METHODS A total of 128 hospitalized Taiwanese children with laboratory-confirmed COVID-19 were enrolled between April 01, 2022, and May 31, 2022. The information on demographics and clinical features was abstracted from the medical records. Virologic lineages were determined by sequences of the spike protein. Factors associated with encephalitis and unfavorable outcomes were identified by comparisons to children without encephalitis and with favorable outcomes, respectively. RESULTS The leading syndromes associated with COVID-19 in hospitalized children were febrile seizure (20, 15.7%), fever as the solitary symptom (18, 14.1%), and croup syndrome (14, 10.9%). Encephalitis was diagnosed in nine (7.03%) children. When compared to the three leading syndromes, children with encephalitis were at older ages, had greater rates of hypotension, PICU admissions, use of inotropic agents (P < .001 for all above comparisons), mortality (P = .008), and longer hospital stays (P = .016), but not the underlying comorbidities (P = .376). Unfavorable outcomes were identified in 3 (33.3%) of 9 encephalitis cases and associated with a lower Glasgow coma scale, hypotension, and higher C-reactive protein (P < .05 for all). BA.2.3.7 was the dominant sublineage in children with or without encephalitis. CONCLUSIONS Omicron BA.2.3.7 can cause fulminant and lethal encephalitis in healthy children. Depressed consciousness and hypotension at presentation were significant risks of unfavorable outcomes for pediatric COVID-19-associated encephalitis.
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Affiliation(s)
- Yi-Jung Chang
- Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, 333 Taoyuan, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chung-Guei Huang
- Department of Laboratory Medicine, Linkou-Chang Gung Memorial Hospital, Taiwan; Department of Medical Biotechnology and Laboratory Science, Graduate Institute of Biomedical Sciences, Chang Gung University, Taiwan
| | - Shian-Sen Shie
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jainn-Jim Lin
- Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, 333 Taoyuan, Taiwan
| | - Chih-Jung Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; School of Medicine, College of Medicine, Chang Gung University, 333 Taoyuan, Taiwan.
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Lowry K, Bauer MJ, Buckley C, Wang C, Bordin A, Badman S, Harris PNA, Mackay I, Whiley D. Evaluation of Illumina® COVIDSeq™ as a tool for Omicron SARS-CoV-2 characterisation. J Virol Methods 2023; 322:114827. [PMID: 37778540 DOI: 10.1016/j.jviromet.2023.114827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
The continued emergence and transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants requires ongoing genetic surveillance to support public health responses. The expansion of reliable next generation sequence (NGS) platforms has enabled the rapid characterisation of the constant emergence of new SARS-CoV-2 variants using nasopharyngeal swab specimens. Several studies have assessed the ability of COVIDSeq to type earlier SARS-CoV-2 strains (pre-Delta) rapidly and successfully, however, there is limited data showing suitability against Omicron variants. In the present study, we evaluated the performance of the Illumina COVIDSeq Assay as a streamlined amplicon-based NGS platform for detection and typing of Omicron variants. Our results demonstrate the high performance of SARS-CoV-2 sequencing using the COVIDSeq approach, with good repeatability, reproducibility and sensitivity for samples approaching CT 31. The COVIDSeq approach was 100% concordant with samples previously characterized by sequencing methods. The quick library preparation process and high throughput kit made it ideal for reflex testing, with a total time required for sequencing and analysis of approximately two days. This study demonstrates the effectiveness and versatility of the amplicon-based NGS characterisation method for SARS-CoV-2, providing a foundation for further research and development of custom-designed amplicon panels targeting different microorganisms.
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Affiliation(s)
- Kym Lowry
- The Queensland Paediatric Infectious Diseases (QPID) Sakzewski Laboratory, Queensland Children's Hospital, Brisbane, Queensland, Australia; The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | - Michelle J Bauer
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Cameron Buckley
- Infectious Diseases Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Claire Wang
- The Queensland Paediatric Infectious Diseases (QPID) Sakzewski Laboratory, Queensland Children's Hospital, Brisbane, Queensland, Australia; Infectious Diseases Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Amanda Bordin
- The Queensland Paediatric Infectious Diseases (QPID) Sakzewski Laboratory, Queensland Children's Hospital, Brisbane, Queensland, Australia; The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Infectious Diseases Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Steven Badman
- Kirby Institute for Infection and Immunity in Society, University of New South Wales (UNSW) Medicine, UNSW Sydney, Kensington, NSW, Australia
| | - Patrick N A Harris
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Infectious Diseases Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Ian Mackay
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Infectious Diseases Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - David Whiley
- The Queensland Paediatric Infectious Diseases (QPID) Sakzewski Laboratory, Queensland Children's Hospital, Brisbane, Queensland, Australia; The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Infectious Diseases Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
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Nilsson PH, Al-Majdoub M, Ibrahim A, Aseel O, Suriyanarayanan S, Andersson L, Fostock S, Aastrup T, Tjernberg I, Rydén I, Nicholls IA. Quartz Crystal Microbalance Platform for SARS-CoV-2 Immuno-Diagnostics. Int J Mol Sci 2023; 24:16705. [PMID: 38069027 PMCID: PMC10705953 DOI: 10.3390/ijms242316705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Rapid and accurate serological analysis of SARS-CoV-2 antibodies is important for assessing immune protection from vaccination or infection of individuals and for projecting virus spread within a population. The quartz crystal microbalance (QCM) is a label-free flow-based sensor platform that offers an opportunity to detect the binding of a fluid-phase ligand to an immobilized target molecule in real time. A QCM-based assay was developed for the detection of SARS-CoV-2 antibody binding and evaluated for assay reproducibility. The assay was cross-compared to the Roche electrochemiluminescence assay (ECLIA) Elecsys® Anti-SARS-CoV-2 serology test kit and YHLO's chemiluminescence immunoassay (CLIA). The day-to-day reproducibility of the assay had a correlation of r2 = 0.99, p < 0.001. The assay linearity was r2 = 0.96, p < 0.001, for dilution in both serum and buffer. In the cross-comparison analysis of 119 human serum samples, 59 were positive in the Roche, 52 in the YHLO, and 48 in the QCM immunoassay. Despite differences in the detection method and antigen used for antibody capture, there was good coherence between the assays, 80-100% for positive and 96-100% for negative test results. In summation, the QCM-based SARS-CoV-2 IgG immunoassay showed high reproducibility and linearity, along with good coherence with the ELISA-based assays. Still, factors including antibody titer and antigen-binding affinity may differentially affect the various assays' responses.
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Affiliation(s)
- Per H. Nilsson
- Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry and Biomedical Sciences, Linnaeus University, SE-39182 Kalmar, Sweden; (P.H.N.); (S.S.); (L.A.)
- Department of Immunology, University of Oslo and Oslo University Hospital Rikshospitalet, Sognsvannsveien 20, NO-0372 Oslo, Norway
| | - Mahmoud Al-Majdoub
- Attana AB, Greta Arwidssons Väg 21, SE-11419 Stockholm, Sweden; (M.A.-M.); (A.I.); (S.F.); (T.A.)
| | - Ahmed Ibrahim
- Attana AB, Greta Arwidssons Väg 21, SE-11419 Stockholm, Sweden; (M.A.-M.); (A.I.); (S.F.); (T.A.)
| | - Obaidullah Aseel
- Medical Programme, Faculty of Medicine and Health Sciences, Linköping University, SE-58225 Linköping, Sweden;
| | - Subramanian Suriyanarayanan
- Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry and Biomedical Sciences, Linnaeus University, SE-39182 Kalmar, Sweden; (P.H.N.); (S.S.); (L.A.)
| | - Linnea Andersson
- Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry and Biomedical Sciences, Linnaeus University, SE-39182 Kalmar, Sweden; (P.H.N.); (S.S.); (L.A.)
| | - Samir Fostock
- Attana AB, Greta Arwidssons Väg 21, SE-11419 Stockholm, Sweden; (M.A.-M.); (A.I.); (S.F.); (T.A.)
| | - Teodor Aastrup
- Attana AB, Greta Arwidssons Väg 21, SE-11419 Stockholm, Sweden; (M.A.-M.); (A.I.); (S.F.); (T.A.)
| | - Ivar Tjernberg
- Department of Clinical Chemistry and Transfusion Medicine, Region Kalmar County, SE-39185 Kalmar, Sweden;
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, SE-58183 Linköping, Sweden
| | - Ingvar Rydén
- Department of Research, Region Kalmar County, SE-39185 Kalmar, Sweden;
- Department of Biomedical and Clinical Sciences, Division of Clinical Chemistry and Pharmacology, Linköping University, SE-58183 Linköping, Sweden
| | - Ian A. Nicholls
- Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry and Biomedical Sciences, Linnaeus University, SE-39182 Kalmar, Sweden; (P.H.N.); (S.S.); (L.A.)
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Murakami K, Kubota SI, Tanaka K, Tanaka H, Akabane K, Suzuki R, Shinohara Y, Takei H, Hashimoto S, Tanaka Y, Hojyo S, Sakamoto O, Naono N, Takaai T, Sato K, Kojima Y, Harada T, Hattori T, Fuke S, Yokota I, Konno S, Washio T, Fukuhara T, Teshima T, Taniguchi M, Murakami M. High-precision rapid testing of omicron SARS-CoV-2 variants in clinical samples using AI-nanopore. LAB ON A CHIP 2023; 23:4909-4918. [PMID: 37877206 DOI: 10.1039/d3lc00572k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
A digital platform that can rapidly and accurately diagnose pathogenic viral variants, including SARS-CoV-2, will minimize pandemics, public anxiety, and economic losses. We recently reported an artificial intelligence (AI)-nanopore platform that enables testing for Wuhan SARS-CoV-2 with high sensitivity and specificity within five minutes. However, which parts of the virus are recognized by the platform are unknown. Similarly, whether the platform can detect SARS-CoV-2 variants or the presence of the virus in clinical samples needs further study. Here, we demonstrated the platform can distinguish SARS-CoV-2 variants. Further, it identified mutated Wuhan SARS-CoV-2 expressing spike proteins of the delta and omicron variants, indicating it discriminates spike proteins. Finally, we used the platform to identify omicron variants with a sensitivity and specificity of 100% and 94%, respectively, in saliva specimens from COVID-19 patients. Thus, our results demonstrate the AI-nanopore platform is an effective diagnostic tool for SARS-CoV-2 variants.
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Affiliation(s)
- Kaoru Murakami
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Shimpei I Kubota
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Kumiko Tanaka
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Hiroki Tanaka
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Keiichiroh Akabane
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Yuta Shinohara
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Hiroyasu Takei
- Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Shigeru Hashimoto
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Yuki Tanaka
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Shintaro Hojyo
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Osamu Sakamoto
- Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Norihiko Naono
- Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Takayui Takaai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047, Osaka, Japan
| | - Kazuki Sato
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Yuichi Kojima
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Toshiyuki Harada
- Department of Respiratory Medicine, Japan Community Healthcare Organization Hokkaido Hospital, Sapporo, 062-8618, Japan
| | - Takeshi Hattori
- Department of Respiratory Medicine, Hokkaido Medical Center, National Hospital Organization, Sapporo, 063-0005, Japan
| | - Satoshi Fuke
- Department of Respiratory Medicine, KKR Sapporo Medical Center, Sapporo, 062-0931, Japan
| | - Isao Yokota
- Department of Biostatistics, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Satoshi Konno
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Takashi Washio
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047, Osaka, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Takanori Teshima
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, 060-8638, Japan
- Department of Hematology, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047, Osaka, Japan
| | - Masaaki Murakami
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0020, Japan
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8
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Curini V, Ancora M, Jurisic L, Di Lollo V, Secondini B, Mincarelli LF, Caporale M, Puglia I, Di Gialleonardo L, Mangone I, Di Domenico M, Di Pasquale A, Lorusso A, Marcacci M, Cammà C. Evaluation of next generation sequencing approaches for SARS-CoV-2. Heliyon 2023; 9:e21101. [PMID: 38027571 PMCID: PMC10643093 DOI: 10.1016/j.heliyon.2023.e21101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/14/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Within public health control strategies for SARS-CoV-2, whole genome sequencing (WGS) is essential for tracking viral spread and monitoring the emergence of variants which may impair the effectiveness of vaccines, diagnostic methods, and therapeutics. In this manuscript different strategies for SARS-CoV-2 WGS including metagenomic shotgun (SG), library enrichment by myBaits® Expert Virus-SARS-CoV-2 (Arbor Biosciences), nCoV-2019 sequencing protocol, ampliseq approach by Swift Amplicon® SARS-CoV-2 Panel kit (Swift Biosciences), and Illumina COVIDSeq Test (Illumina Inc.), were evaluated in order to identify the best approach in terms of results, labour, and costs. The analysis revealed that Illumina COVIDSeq Test (Illumina Inc.) is the best choice for a cost-effective, time-consuming production of consensus sequences.
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Affiliation(s)
- Valentina Curini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Lucija Jurisic
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
- Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Valeria Di Lollo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Barbara Secondini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | | | | | - Ilaria Puglia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | | | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Adriano Di Pasquale
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
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9
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Oyola S. Characterization of SARS-CoV-2 genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population. RESEARCH SQUARE 2023:rs.3.rs-3457875. [PMID: 37961584 PMCID: PMC10635312 DOI: 10.21203/rs.3.rs-3457875/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Vaccination is a key control measure of COVID-19 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing herd immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2, largely through vaccine-induced immune pressure. Here we investigated the recombination events and single nucleotide polymorphisms (SNPs) on SARS-CoV-2 genome in non-vaccinated and vaccinated patients in the Kenyan population. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within-wave and inter-wave recombination events from the beginning of the pandemic (June 2020) to (October 2022) in Kenya. An in-depth analysis of (SNPs) on the S, ORf1a/b, and N genes identified previously unreported mutations. We detected a minority variant in non-vaccinated patients in Kenya, that contained immune escape mutation S255F of the spike gene and showing a differential recombination pattern within the non-vaccinated patients. Detailed analysis of recombination between waves suggested an association between increased population immunity and declining risk of emergence of variants of concern. Overall, this work identified unique mutations in SARS-CoV-2 which could have significant implications for virus evolution, virulence, and immune escape.
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10
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Yousif M, Rachida S, Taukobong S, Ndlovu N, Iwu-Jaja C, Howard W, Moonsamy S, Mhlambi N, Gwala S, Levy JI, Andersen KG, Scheepers C, von Gottberg A, Wolter N, Bhiman JN, Amoako DG, Ismail A, Suchard M, McCarthy K. SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses. Nat Commun 2023; 14:6325. [PMID: 37816740 PMCID: PMC10564906 DOI: 10.1038/s41467-023-41369-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/30/2023] [Indexed: 10/12/2023] Open
Abstract
As global SARS-CoV-2 burden and testing frequency have decreased, wastewater surveillance has emerged as a key tool to support clinical surveillance efforts. The aims of this study were to identify and characterize SARS-CoV-2 variants in wastewater samples collected from urban centers across South Africa. Here we show that wastewater sequencing analyses are temporally concordant with clinical genomic surveillance and reveal the presence of multiple lineages not detected by clinical surveillance. We show that wastewater genomics can support SARS-CoV-2 epidemiological investigations by reliably recovering the prevalence of local circulating variants, even when clinical samples are not available. Further, we find that analysis of mutations observed in wastewater can provide a signal of upcoming lineage transitions. Our study demonstrates the utility of wastewater genomics to monitor evolution and spread of endemic viruses.
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Affiliation(s)
- Mukhlid Yousif
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa.
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Said Rachida
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Setshaba Taukobong
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nkosenhle Ndlovu
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Chinwe Iwu-Jaja
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Wayne Howard
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Shelina Moonsamy
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nompilo Mhlambi
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sipho Gwala
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Cathrine Scheepers
- SAMRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel Gyamfi Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou, South Africa
| | - Melinda Suchard
- Department of Chemical Pathology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Kerrigan McCarthy
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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11
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Tanaka H, Namkoong H, Chubachi S, Irie S, Uwamino Y, Lee H, Azekawa S, Otake S, Nakagawara K, Fukushima T, Watase M, Kusumoto T, Masaki K, Kamata H, Ishii M, Okada Y, Takano T, Imoto S, Koike R, Kimura A, Miyano S, Ogawa S, Kanai T, Sato TA, Fukunaga K. Clinical characteristics of patients with COVID-19 harboring detectable intracellular SARS-CoV-2 RNA in peripheral blood cells. Int J Infect Dis 2023; 135:41-44. [PMID: 37541421 DOI: 10.1016/j.ijid.2023.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
OBJECTIVES Although SARS-CoV-2 RNAemia has been reported to strongly impact patients with severe COVID-19, the clinical characteristics of patients with COVID-19 harboring detectable intracellular SARS-CoV-2 RNA remain unknown. METHODS We included adult patients who had developed COVID-19 between February and September 2020. Total white blood cells derived from the buffy coat of peripheral whole blood were used to detect SARS-CoV-2 RNA using the Illumina COVIDSeq test. We compared the clinical characteristics between patients with and without detected viral RNA (detected and undetected groups). RESULTS Among the 390 patients included, 17 harbored SARS-CoV-2 RNA in peripheral white blood cells. All 17 patients required oxygen support during the disease course and had higher intensive care unit admission (52.9% vs 28.9%, P = 0.035), mortality (17.7% vs 3.5%, P = 0.004), kidney dysfunction (severe, 23.5% vs 6.4%, P = 0.029), and corticosteroid treatment rates (76.5% vs 46.5%, P = 0.016) than those of patients in the undetected group. CONCLUSION We propose that patients with circulating intracellular SARS-CoV-2 RNA in the peripheral blood exhibited the most severe disease course.
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Affiliation(s)
- Hiromu Tanaka
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan.
| | - Shotaro Chubachi
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | | | - Yoshifumi Uwamino
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Ho Lee
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shuhei Azekawa
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shiro Otake
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kensuke Nakagawara
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Takahiro Fukushima
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Mayuko Watase
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tatsuya Kusumoto
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Katsunori Masaki
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Hirofumi Kamata
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Makoto Ishii
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan; Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Tomomi Takano
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ryuji Koike
- Clinical Research Center, Tokyo Medical and Dental University Hospital of Medicine, Tokyo, Japan
| | - Akinori Kimura
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Taka-Aki Sato
- iLAC Co., Ltd., Tsukuba, Ibaraki, Japan; Research and Development Center for Precision Medicine, University of Tsukuba, Ibaraki, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
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12
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de Prost N, Audureau E, Préau S, Favory R, Guigon A, Bay P, Heming N, Gault E, Pham T, Chaghouri A, Voiriot G, Morand-Joubert L, Jochmans S, Pitsch A, Meireles S, Contou D, Henry A, Joseph A, Chaix ML, Uhel F, Descamps D, Emery M, Garcia-Sanchez C, Luyt CE, Marot S, Pène F, Lhonneur AS, Gaudry S, Brichler S, Picard L, Mekontso Dessap A, Rodriguez C, Pawlotsky JM, Fourati S. Clinical phenotypes and outcomes associated with SARS-CoV-2 Omicron variants BA.2, BA.5 and BQ.1.1 in critically ill patients with COVID-19: a prospective, multicenter cohort study. Intensive Care Med Exp 2023; 11:48. [PMID: 37544942 PMCID: PMC10404579 DOI: 10.1186/s40635-023-00536-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Despite current broad natural and vaccine-induced protection, a substantial number of patients infected with emerging SARS-CoV-2 variants (e.g., BF.7 and BQ.1.1) still experience severe COVID-19. Real-life studies investigating the impact of these variants on clinical outcomes of severe cases are currently not available. We performed a prospective multicenter observational cohort study. Adult patients with acute respiratory failure admitted between December 7, 2021 and December 15, 2022, in one of the 20 participating intensive care units (17 from the Greater Paris area and 3 from the North of France) were eligible for inclusion if they had SARS-CoV-2 infection confirmed by a positive reverse transcriptase-polymerase chain reaction (RT-PCR). Full-length SARS-CoV-2 genomes from all included patients were sequenced by means of next-generation sequencing. The primary endpoint of the study was day-28 mortality. RESULTS The study included 158 patients infected with three groups of Omicron sublineages, including (i) BA.2 variants and their early sublineages referred as "BA.2" (n = 50), (ii) early BA.4 and BA.5 sublineages (including BA.5.1 and BA.5.2, n = 61) referred as "BA.4/BA.5", and (iii) recent emerging BA.5 sublineages (including BQ.1, BQ.1.1, BF.7, BE.1 and CE.1, n = 47) referred as "BQ.1.1". The clinical phenotype of BQ1.1-infected patients compared to earlier BA.2 and BA.4/BA.5 sublineages, showed more frequent obesity and less frequent immunosuppression. There was no significant difference between Omicron sublineage groups regarding the severity of the disease at ICU admission, need for organ failure support during ICU stay, nor day 28 mortality (21.7%, n = 10/47 in BQ.1.1 group vs 26.7%, n = 16/61 in BA.4/BA.5 vs 22.0%, n = 11/50 in BA.2, p = 0.791). No significant relationship was found between any SARS-CoV-2 substitution and/or deletion on the one hand and survival on the other hand over hospital follow-up. CONCLUSIONS Critically-ill patients with Omicron BQ.1.1 infection showed a different clinical phenotype than other patients infected with earlier Omicron sublineage but no day-28 mortality difference.
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Affiliation(s)
- Nicolas de Prost
- Service de Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris (AP-HP), Créteil, France.
- Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France.
- Université Paris-Est-Créteil (UPEC), Créteil, France.
| | - Etienne Audureau
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Public Health, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris (AP-HP), Créteil, France
- IMRB INSERM U955, Team CEpiA, Créteil, France
| | - Sébastien Préau
- U1167, RID-AGE Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, 59000, Lille, France
| | - Raphaël Favory
- U1167, RID-AGE Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, 59000, Lille, France
| | - Aurélie Guigon
- Service de Virologie, CHU de Lille, 59000, Lille, France
| | - Pierre Bay
- Service de Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris (AP-HP), Créteil, France
- Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Nicholas Heming
- Médecine Intensive Réanimation, Hôpital Raymond Poincaré, Assistance Publique, Hôpitaux de Paris (AP-HP), Garches, France
| | - Elyanne Gault
- Laboratoire de Virologie, Hôpital Ambroise Paré, Assistance Publique, Hôpitaux de Paris (AP-HP), Boulogne, France
| | - Tài Pham
- Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France
- Service de Médecine Intensive-Réanimation, Assistance Publique, Hôpitaux de Paris, Hôpital de Bicêtre, DMU 4 CORREVE Maladies du Cœur et Des Vaisseaux, FHU Sepsis, Le Kremlin-Bicêtre, France
- Inserm U1018, Equipe d'Epidémiologie Respiratoire Intégrative, CESP, 94807, Villejuif, France
| | - Amal Chaghouri
- Laboratoire de Virologie, Hôpital Paul Brousse, Assistance Publique, Hôpitaux de Paris, Villejuif, France
| | - Guillaume Voiriot
- Sorbonne Université, Centre de Recherche Saint-Antoine INSERM, Médecine Intensive Réanimation, Hôpital Tenon, Assistance Publique, Hôpitaux de Paris, Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
- Laboratoire de Virologie, Hôpital Saint-Antoine, Assistance Publique, Hôpitaux de Paris, 75012, Paris, France
| | | | - Aurélia Pitsch
- Laboratoire de Microbiologie, Hôpital Marc Jacquet, Melun, France
| | - Sylvie Meireles
- Service de Réanimation Médico-Chirurgicale, Assistance Publique, Hôpitaux de Paris, Hôpital Ambroise Paré, Boulogne, France
| | - Damien Contou
- Service de Réanimation, Hôpital Victor Dupouy, Argenteuil, France
| | - Amandine Henry
- Service de Virologie, Hôpital Victor Dupouy, Argenteuil, France
| | - Adrien Joseph
- Médecine Intensive Réanimation, Hôpital Saint-Louis, Assistance Publique, Hôpitaux de Paris, Paris, France
| | - Marie-Laure Chaix
- Université de Paris, Inserm HIPI, 75010, Paris, France
- Laboratoire de Virologie, Hôpital Saint-Louis, Assistance Publique, Hôpitaux de Paris, 75010, Paris, France
| | - Fabrice Uhel
- n, Université de Paris, APHP, Hôpital Louis Mourier, DMU ESPRIT, Service de Médecine Intensive Réanimatio, Colombes, France
- INSERM U1151, CNRS UMR 8253, Institut Necker-Enfants Malades (INEM), Department of Immunology, Infectiology and Hematology, Paris, France
| | - Diane Descamps
- Université de Paris, IAME INSERM UMR 1137, Service de Virologie, Hôpital Bichat-Claude Bernard, Assistance Publique, Hôpitaux de Paris, Paris, France
| | - Malo Emery
- Service de Réanimation, Hôpital Saint-Camille, Bry-Sur-Marne, France
| | | | - Charles-Edouard Luyt
- Sorbonne Université, Assistance Publique, Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Médecine Intensive Réanimation, Paris, France
- INSERM UMRS_1166-iCAN, Institute of Cardiometabolism and Nutrition, Paris, France
| | - Stéphane Marot
- Département de Virologie, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Frédéric Pène
- Médecine Intensive Réanimation, Hôpital Cochin, Assistance Publique, Hôpitaux de Paris, Paris, France
| | - Anne-Sophie Lhonneur
- Laboratoire de Virologie, Hôpital Cochin, Assistance Publique, Hôpitaux de Paris, Paris, France
| | - Stéphane Gaudry
- Service de Réanimation, Hôpital Avicenne, Assistance Publique, Hôpitaux de Paris, Bobigny, France
| | - Ségolène Brichler
- Laboratoire de Virologie, Hôpital Avicenne, Assistance Publique, Hôpitaux de Paris, Bobigny, France
| | - Lucile Picard
- Département d'Anesthésie Réanimations Chirurgicales, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris (AP-HP), Créteil, France
| | - Armand Mekontso Dessap
- Service de Médecine Intensive Réanimation, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris (AP-HP), Créteil, France
- Groupe de Recherche Clinique CARMAS, Université Paris-Est-Créteil (UPEC), Créteil, France
- Université Paris-Est-Créteil (UPEC), Créteil, France
| | - Christophe Rodriguez
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris, Créteil, France
- INSERM U955, Team "Viruses, Hepatology, Cancer", Créteil, France
| | - Jean-Michel Pawlotsky
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris, Créteil, France
- INSERM U955, Team "Viruses, Hepatology, Cancer", Créteil, France
| | - Slim Fourati
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique, Hôpitaux de Paris, Créteil, France
- INSERM U955, Team "Viruses, Hepatology, Cancer", Créteil, France
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Satam H, Joshi K, Mangrolia U, Waghoo S, Zaidi G, Rawool S, Thakare RP, Banday S, Mishra AK, Das G, Malonia SK. Next-Generation Sequencing Technology: Current Trends and Advancements. BIOLOGY 2023; 12:997. [PMID: 37508427 PMCID: PMC10376292 DOI: 10.3390/biology12070997] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
The advent of next-generation sequencing (NGS) has brought about a paradigm shift in genomics research, offering unparalleled capabilities for analyzing DNA and RNA molecules in a high-throughput and cost-effective manner. This transformative technology has swiftly propelled genomics advancements across diverse domains. NGS allows for the rapid sequencing of millions of DNA fragments simultaneously, providing comprehensive insights into genome structure, genetic variations, gene expression profiles, and epigenetic modifications. The versatility of NGS platforms has expanded the scope of genomics research, facilitating studies on rare genetic diseases, cancer genomics, microbiome analysis, infectious diseases, and population genetics. Moreover, NGS has enabled the development of targeted therapies, precision medicine approaches, and improved diagnostic methods. This review provides an insightful overview of the current trends and recent advancements in NGS technology, highlighting its potential impact on diverse areas of genomic research. Moreover, the review delves into the challenges encountered and future directions of NGS technology, including endeavors to enhance the accuracy and sensitivity of sequencing data, the development of novel algorithms for data analysis, and the pursuit of more efficient, scalable, and cost-effective solutions that lie ahead.
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Affiliation(s)
- Heena Satam
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Kandarp Joshi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Upasana Mangrolia
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sanober Waghoo
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Gulnaz Zaidi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Shravani Rawool
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Ritesh P. Thakare
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Shahid Banday
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Alok K. Mishra
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Gautam Das
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sunil K. Malonia
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
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14
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Chen HC. A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level. Front Mol Biosci 2023; 10:1141534. [PMID: 37496777 PMCID: PMC10366608 DOI: 10.3389/fmolb.2023.1141534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/30/2023] [Indexed: 07/28/2023] Open
Abstract
The outbreak of SARS-CoV-2 has made us more alert to the importance of viral diagnostics at a population level to rapidly control the spread of the disease. The critical question would be how to scale up testing capacity and perform a diagnostic test in a high-throughput manner with robust results and affordable costs. Here, the latest 26 articles using barcoding technology for COVID-19 diagnostics and biologically-relevant studies are reviewed. Barcodes are molecular tags, that allow proceeding an array of samples at once. To date, barcoding technology followed by high-throughput sequencing has been made for molecular diagnostics for SARS-CoV-2 infections because it can synchronously analyze up to tens of thousands of clinical samples within a short diagnostic time. Essentially, this technology can also be used together with different biotechnologies, allowing for investigation with resolution of single molecules. In this Mini-Review, I first explain the general principle of the barcoding strategy and then put forward recent studies using this technology to accomplish COVID-19 diagnostics and basic research. In the meantime, I provide the viewpoint to improve the current COVID-19 diagnostic strategy with potential solutions. Finally, and importantly, two practical ideas about how barcodes can be further applied in studying SARS-CoV-2 to accelerate our understanding of this virus are proposed.
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15
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Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
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Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
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Di Lorenzo A, Mangone I, Colangeli P, Cioci D, Curini V, Vincifori G, Mercante MT, Di Pasquale A, Iannetti S. One health system supporting surveillance during COVID-19 epidemic in Abruzzo region, southern Italy. One Health 2023; 16:100471. [PMID: 36507072 PMCID: PMC9726647 DOI: 10.1016/j.onehlt.2022.100471] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022] Open
Abstract
The Istituti Zooprofilattici Sperimentali (IZSs) are public health institutes dealing with the aetiology and pathogenesis of infectious diseases of domestic and wild animals. During Coronavirus Disease 2019 epidemic, the Italian Ministry of Health appointed the IZSs to carry out diagnostic tests for the detection of SARS-CoV-2 in human samples. In particular, the IZS of Abruzzo and Molise (IZS-Teramo) was involved in the diagnosis of SARS-CoV-2 through testing nasopharyngeal swabs by Real Time RT-PCR. Activities and infrastructures were reorganised to the new priorities, in a "One Health" framework, based on interdisciplinary, laboratory promptness, accreditation of the test for the detection of the RNA of SARS-CoV-2 in human samples, and management of confidentiality of sensitive data. The laboratory information system - SILAB - was implemented with a One Health module for managing data of human origin, with tools for the automatic registration of information improving the quality of the data. Moreover, the "National Reference Centre for Whole Genome Sequencing of microbial pathogens - database and bioinformatics analysis" - GENPAT - formally established at the IZS-Teramo, developed bioinformatics workflows and IT dashboard with ad hoc surveillance tools to support the metagenomics-based SARS-CoV-2 surveillance, providing molecular sequencing analysis to quickly intercept the variants circulating in the area. This manuscript describes the One Health system developed by adapting and integrating both SILAB and GENPAT tools for supporting surveillance during COVID-19 epidemic in the Abruzzo region, southern Italy. The developed dashboard permits the health authorities to observe the SARS-CoV-2 spread in the region, and by combining spatio-temporal information with metagenomics provides early evidence for the identification of emerging space-time clusters of variants at the municipality level. The implementation of the One Health module was designed to be easily modelled and adapted for the management of other diseases and future hypothetical events of pandemic nature.
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17
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Pillay S, San JE, Tshiabuila D, Naidoo Y, Pillay Y, Maharaj A, Anyaneji UJ, Wilkinson E, Tegally H, Lessells RJ, Baxter C, de Oliveira T, Giandhari J. Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing. PLoS One 2023; 18:e0283219. [PMID: 37099540 PMCID: PMC10132692 DOI: 10.1371/journal.pone.0283219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/03/2023] [Indexed: 04/27/2023] Open
Abstract
The global pandemic caused by SARS-CoV-2 has increased the demand for scalable sequencing and diagnostic methods, especially for genomic surveillance. Although next-generation sequencing has enabled large-scale genomic surveillance, the ability to sequence SARS-CoV-2 in some settings has been limited by the cost of sequencing kits and the time-consuming preparations of sequencing libraries. We compared the sequencing outcomes, cost and turn-around times obtained using the standard Illumina DNA Prep kit protocol to three modified protocols with fewer clean-up steps and different reagent volumes (full volume, half volume, one-tenth volume). We processed a single run of 47 samples under each protocol and compared the yield and mean sequence coverage. The sequencing success rate and quality for the four different reactions were as follows: the full reaction was 98.2%, the one-tenth reaction was 98.0%, the full rapid reaction was 97.5% and the half-reaction, was 97.1%. As a result, uniformity of sequence quality indicated that libraries were not affected by the change in protocol. The cost of sequencing was reduced approximately seven-fold and the time taken to prepare the library was reduced from 6.5 hours to 3 hours. The sequencing results obtained using the miniaturised volumes showed comparability to the results obtained using full volumes as described by the manufacturer. The adaptation of the protocol represents a lower-cost, streamlined approach for SARS-CoV-2 sequencing, which can be used to produce genomic data quickly and more affordably, especially in resource-constrained settings.
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Affiliation(s)
- Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Yusasha Pillay
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Akhil Maharaj
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Richard J. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Center for AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Center for AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Center for AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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Padilha DA, Souza DSM, Kawagoe EK, Filho VB, Amorim AN, Barazzetti FH, Schörner MA, Fernandes SB, Coelho BK, Rovaris DB, Dos Anjos MPD, Moser JR, Melo FR, De Souza BB, Bessa DDC, Mendes FHDPES, Boing AC, Boing AF, Lacerda JTD, Moura GV, Bastiani DCD, Moraes MHD, De Oliveira LFV, Moreira RS, Stoco PH, Bazzo ML, Fongaro G, Wagner G. Genomic Surveillance of SARS-CoV-2 in Healthcare Workers: A Critical Sentinel Group for Monitoring the SARS-CoV-2 Variant Shift. Viruses 2023; 15:v15040984. [PMID: 37112964 PMCID: PMC10146896 DOI: 10.3390/v15040984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
SARS-CoV-2 genome surveillance is important for monitoring risk groups and health workers as well as data on new cases and mortality rate due to COVID-19. We characterized the circulation of SARS-CoV-2 variants from May 2021 to April 2022 in the state of Santa Catarina, southern Brazil, and evaluated the similarity between variants present in the population and healthcare workers (HCW). A total of 5291 sequenced genomes demonstrated the circulation of 55 strains and four variants of concern (Alpha, Delta, Gamma and Omicron-sublineages BA.1 and BA.2). The number of cases was relatively low in May 2021, but the number of deaths was higher with the Gamma variant. There was a significant increase in both numbers between December 2021 and February 2022, peaking in mid-January 2022, when the Omicron variant dominated. After May 2021, two distinct variant groups (Delta and Omicron) were observed, equally distributed among the five Santa Catarina mesoregions. Moreover, from November 2021 to February 2022, similar variant profiles between HCW and the general population were observed, and a quicker shift from Delta to Omicron in HCW than in the general population. This demonstrates the importance of HCW as a sentinel group for monitoring disease trends in the general population.
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Affiliation(s)
- Dayane Azevedo Padilha
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Doris Sobral Marques Souza
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Eric Kazuo Kawagoe
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Vilmar Benetti Filho
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Ariane Nicaretta Amorim
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Fernando Hartmann Barazzetti
- Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis 88040-370, Santa Catarina, Brazil
| | - Marcos André Schörner
- Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis 88040-370, Santa Catarina, Brazil
| | - Sandra Bianchini Fernandes
- Laboratório Central do Estado da Saúde de Santa Catarina, Florianópolis 88010-001, Santa Catarina, Brazil
| | - Bruna Kellet Coelho
- Laboratório Central do Estado da Saúde de Santa Catarina, Florianópolis 88010-001, Santa Catarina, Brazil
| | - Darcita Buerger Rovaris
- Laboratório Central do Estado da Saúde de Santa Catarina, Florianópolis 88010-001, Santa Catarina, Brazil
| | | | - Juliana Righetto Moser
- Diretoria de Vigilância Epidemiológica de Santa Catarina, Florianópolis 88015-130, Santa Catarina, Brazil
| | - Fernanda Rosene Melo
- Diretoria de Vigilância Epidemiológica de Santa Catarina, Florianópolis 88015-130, Santa Catarina, Brazil
| | | | - Dimitri da Costa Bessa
- Diretoria de Vigilância Epidemiológica de Santa Catarina, Florianópolis 88015-130, Santa Catarina, Brazil
| | | | - Alexandra Crispim Boing
- Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis 88040-370, Santa Catarina, Brazil
| | - Antonio Fernando Boing
- Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis 88040-370, Santa Catarina, Brazil
| | - Josimari Telino de Lacerda
- Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis 88040-370, Santa Catarina, Brazil
| | - Guilherme Valle Moura
- Centro de Sócio Econômico, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | | | | | | | | | - Patricia Hermes Stoco
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Maria Luiza Bazzo
- Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis 88040-370, Santa Catarina, Brazil
| | - Gislaine Fongaro
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Glauber Wagner
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Santa Catarina, Brazil
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Lamba S, Ganesan S, Daroch N, Paul K, Joshi SG, Sreenivas D, Nataraj A, Srikantaiah V, Mishra R, Ramakrishnan U, Ishtiaq F. SARS-CoV-2 infection dynamics and genomic surveillance to detect variants in wastewater - a longitudinal study in Bengaluru, India. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2023; 11:100151. [PMID: 36688230 PMCID: PMC9847225 DOI: 10.1016/j.lansea.2023.100151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/01/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023]
Abstract
Background Environmental surveillance (ES) of a pathogen is crucial for understanding the community load of disease. As an early warning system, ES for SARS-CoV-2 has complemented routine diagnostic surveillance by capturing near real-time virus circulation at a population level. Methods In this longitudinal study conducted between January 2022 and June 2022 in 28 sewershed sites in Bengaluru city (∼11 million inhabitants), we quantified weekly SARS-CoV-2 RNA concentrations to track infection dynamics and provide evidence of change in the relative abundance of emerging variants. Findings We describe an early warning system using the exponentially weighted moving average control chart and demonstrate how SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 8-14 days earlier in wastewater than in clinical data. This was further corroborated by showing that the estimated number of infections is strongly correlated with SARS-CoV-2 RNA copies detected in the wastewater. Using a deconvolution matrix, we detected emerging variants of concern up to two months earlier in wastewater samples. In addition, we found a huge diversity in variants detected in wastewater compared to clinical samples. The findings from this study have been discussed regularly with local authorities to inform policy-making decisions. Interpretation Our study highlights that quantifying viral titre, correlating it with a known number of cases in the area, and combined with genomic surveillance helps in tracking variants of concern (VOC) over time and space, enabling timely and making informed policy decisions. Funding This work has been supported by funding from the Rockefeller Foundation grant to National Centre for Biological Sciences, TIFR) and the Indian Council of Medical Research grant to (FI) Tata Institute for Genetics and Society and Tata Trusts.
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Affiliation(s)
- Sanjay Lamba
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Sutharsan Ganesan
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Namrta Daroch
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Kiran Paul
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Soumya Gopal Joshi
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Darshan Sreenivas
- National Centre for Biological Sciences, TIFR, Bellary Road, Bengaluru, 560065, India
| | - Annamalai Nataraj
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | | | - Rakesh Mishra
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, Bellary Road, Bengaluru, 560065, India
| | - Farah Ishtiaq
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India,Corresponding author. Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
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Ong'era EM, Mohammed KS, Makori TO, Bejon P, Ocholla-Oyier LI, Nokes DJ, Agoti CN, Githinji G. High-throughput sequencing approaches applied to SARS-CoV-2. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18701.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
High-throughput sequencing is crucial for surveillance and control of viral outbreaks. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, advances in the high-throughput sequencing technology resources have enhanced diagnosis, surveillance, and vaccine discovery. From the onset of the pandemic in December 2019, several genome-sequencing approaches have been developed and supported across the major sequencing platforms such as Illumina, Oxford Nanopore, PacBio, MGI DNBSEQTM and Ion Torrent. Here, we share insights from the sequencing approaches developed for sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between December 2019 and October 2022.
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21
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Li X, Wang J, Geng J, Xiao L, Wang H. Emerging Landscape of SARS-CoV-2 Variants and Detection Technologies. Mol Diagn Ther 2023; 27:159-177. [PMID: 36577887 PMCID: PMC9797111 DOI: 10.1007/s40291-022-00631-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2022] [Indexed: 12/29/2022]
Abstract
In 2019, a new coronavirus was identified that has caused significant morbidity and mortality worldwide. Like all RNA viruses, severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) evolves over time through random mutation resulting in genetic variations in the population. Although the currently approved coronavirus disease 2019 vaccines can be given to those over 5 years of age and older in most countries, strikingly, the number of people diagnosed positive for SARS-Cov-2 is still increasing. Therefore, to prevent and control this epidemic, early diagnosis of infected individuals is of great importance. The current detection of SARS-Cov-2 coronavirus variants are mainly based on reverse transcription-polymerase chain reaction. Although the sensitivity of reverse transcription-polymerase chain reaction is high, it has some disadvantages, for example, multiple temperature changes, long detection time, complicated operation, expensive instruments, and the need for professional personnel, which brings considerable inconvenience to the early diagnosis of this virus. This review comprehensively summarizes the development and application of various current detection technologies for novel coronaviruses, including isothermal amplification, CRISPR-Cas detection, serological detection, biosensor, ensemble, and microfluidic technology, along with next-generation sequencing. Those findings offer us a great potential to replace or combine with reverse transcription-polymerase chain reaction detection to achieve the purpose of allowing predictive diagnostics and targeted prevention of SARS-Cov-2 in the future.
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Affiliation(s)
- Xianghui Li
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang, 443002, China
| | - Jing Wang
- Institute of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jingping Geng
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang, 443002, China
| | - Liming Xiao
- Institute of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Hu Wang
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang, 443002, China.
- Institute of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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22
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The genome sequence of lumpy skin disease virus from an outbreak in India suggests a distinct lineage of the virus. Arch Virol 2023; 168:81. [PMID: 36740645 DOI: 10.1007/s00705-023-05705-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/14/2022] [Indexed: 02/06/2023]
Abstract
Although previously confined to regions within Africa, lumpy skin disease virus (LSDV) infections have caused significantly large outbreaks in several regions of the world in recent years. In 2019, an outbreak of the disease was reported in India with low rates of morbidity and no reported mortality. However, in 2022, an ongoing outbreak of LSDV spanning over seven states in India resulted in the loss of over 80,000 cattle over a period of three months. Here, we report complete genome sequences of six isolates of LSDV collected from affected cattle during an ongoing outbreak of the disease in Rajasthan, India. Analysis of these sequences showed that the genome isolates from the 2022 outbreak have a large number of genetic variations compared to the reference strain and that they form a distinct genetic lineage. This report thus highlights the importance of genome sequencing and surveillance of transboundary infectious agents to track the prevalence and emergence of variants.
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23
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Pei XM, Yeung MHY, Wong ANN, Tsang HF, Yu ACS, Yim AKY, Wong SCC. Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases. Cells 2023; 12:493. [PMID: 36766834 PMCID: PMC9913990 DOI: 10.3390/cells12030493] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The outbreak of COVID-19 has positively impacted the NGS market recently. Targeted sequencing (TS) has become an important routine technique in both clinical and research settings, with advantages including high confidence and accuracy, a reasonable turnaround time, relatively low cost, and fewer data burdens with the level of bioinformatics or computational demand. Since there are no clear consensus guidelines on the wide range of next-generation sequencing (NGS) platforms and techniques, there is a vital need for researchers and clinicians to develop efficient approaches, especially for the molecular diagnosis of diseases in the emergency of the disease and the global pandemic outbreak of COVID-19. In this review, we aim to summarize different methods of TS, demonstrate parameters for TS assay designs, illustrate different TS panels, discuss their limitations, and present the challenges of TS concerning their clinical application for the molecular diagnosis of human diseases.
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Affiliation(s)
- Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Alex Ngai Nick Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Allen Chi Shing Yu
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Aldrin Kay Yuen Yim
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
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24
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Nicot F, Trémeaux P, Latour J, Carcenac R, Demmou S, Jeanne N, Ranger N, De Smet C, Raymond S, Dimeglio C, Izopet J. Whole-genome single molecule real-time sequencing of SARS-CoV-2 Omicron. J Med Virol 2023; 95:e28564. [PMID: 36756931 DOI: 10.1002/jmv.28564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
New variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can only be identified using accurate sequencing methods. Single molecule real-time (SMRT) sequencing has been used to characterize Alpha and Delta variants, but not Omicron variants harboring numerous mutations in the SARS-CoV-2 genome. This study assesses the performance of a target capture SMRT sequencing protocol for whole genome sequencing (WGS) of SARS-CoV-2 Omicron variants and compared it to that of an amplicon SMRT sequencing protocol optimized for Omicron variants. The failure rate of the target capture protocol (6%) was lower than that of the amplicon protocol (34%, p < 0.001) on our data set, and the median genome coverage with the target capture protocol (98.6% [interquartile range (IQR): 86-99.4]) was greater than that with the amplicon protocol (76.6% [IQR: 66-89.6], [p < 0.001]). The percentages of samples with >95% whole genome coverage were 64% with the target capture protocol and 19% with the amplicon protocol (p < 0.05). The clades of 96 samples determined with both protocols were 93% concordant and the lineages of 59 samples were 100% concordant. Thus, target capture SMRT sequencing appears to be an efficient method for WGS, genotyping and detecting mutations of SARS-CoV-2 Omicron variants.
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Affiliation(s)
- Florence Nicot
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Pauline Trémeaux
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Justine Latour
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Romain Carcenac
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Sofia Demmou
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Nicolas Jeanne
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Noémie Ranger
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | | | - Stéphanie Raymond
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Chloé Dimeglio
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Jacques Izopet
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
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25
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Outbreak investigation in a COVID-19 designated hospital: The combination of phylogenetic analysis and field epidemiology study suggesting airborne transmission. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2023:S1684-1182(23)00002-6. [PMID: 36690516 PMCID: PMC9841729 DOI: 10.1016/j.jmii.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 12/06/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023]
Abstract
BACKGROUND Healthcare-associated COVID-19 infections caused by SARS-CoV-2 have increased morbidity and mortality. Hospitals and skilled nursing facilities (SNFs) have been challenged by infection control and management. METHODS This case study presents an outbreak investigation in a COVID-19-designated hospital and a hospital-based SNF. Real-time polymerase chain reaction (PCR) and other studies were performed on samples obtained from SNF residents, hospital patients, and healthcare workers (HCWs). The results of the laboratory tests and field epidemiological data were analyzed. Genome sequencing and phylogenetic analysis of SARS-CoV-2 were performed to identify the associations between cases. The tracer gas was released and recorded by a thermal imaging camera to investigate the spatial relations within clusters. RESULTS During the outbreak, 29 COVID-19 infections in 3 clusters were identified through hospital-wide, risk-guided, and symptom-driven PCR tests. This included 12 HCWs, 5 patients, and 12 SNF residents who had been hospitalized for at least 14 days. Serology tests did not identify any cases among the PCR-negative individuals. The phylogenetic analysis revealed that viral strains from the 3 clusters shared a common mutation of G3994T and were phylogenetically related, which suggested that this outbreak had a common source rather than multiple introductions from the community. Linked cases exhibited vertical spatial distribution, and the sulfur hexafluoride release test confirmed a potential airborne transmission. CONCLUSIONS This report addressed the advantage of a multi-disciplinary team in outbreak investigation. Identifying an airborne transmission within an outbreak highlighted the importance of regular maintenance of ventilation systems.
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26
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Bhattacharya S, Chatterji S, Chandy M, Mahajan AY, Goel G, Mishra D, Vivek P, Das P, Mandal S, Chugani A, Mittal A, Perumal RC, Ramprasad VL, Gupta R. Molecular epidemiology of SARS-CoV-2 in healthcare workers and identification of viral genomic correlates of transmissibility and vaccine break through infection: A retrospective observational study from a cancer hospital in eastern India. Indian J Med Microbiol 2023; 41:104-110. [PMID: 36244851 PMCID: PMC9558092 DOI: 10.1016/j.ijmmb.2022.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 09/01/2022] [Accepted: 09/25/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE Despite COVID vaccination with ChAdOx1 ncov-19 (COVISHIELD®) (ChAdOx1 ncov-19) a large number of healthcare workers (HCWs) were getting infected in wave-2 of the pandemic in a cancer hospital of India. It was important therefore to determine the genotypes responsible for vaccine breakthrough infections. METHODS & OBJECTIVES Retrospective observational study of HCWs. Whole genome sequencing of SARS CoV-2 using Illumina NovaSeq was done. Mutations from both waves were compared to identify genomic correlates of transmissibility and vaccine breakthrough infections. RESULTS Vaccine breakthrough infections were seen in 127 HCWs out of 1806 fully vaccinated staff (7.03%). Median number of HCWs infected per day in wave-1 was 0.92 versus 3.25 in wave-2. Majority of wave-1 samples belonged to B.1 and B.1.1 lineage. Variant of concern- Delta variant (90%), and variant of interest- Kappa variant (10%), was seen in only wave-2 samples. Total mutation observed in wave-2 samples (median = 44) was 1.8 times than wave-1 sample (median = 24). Spike protein in wave-2 samples had 13 non-synonymous mutation as compared to 8 seen in wave-1 samples. E484Q-vaccine escape mutant was detected in five samples of wave-2; T478K - highly infectious mutation was seen in 31 samples of wave-2. We identified a novelcoding disruptive in-frame deletion (c.467_472delAGTTCA, p. Glu156_Arg158delinsGly) in the Spike protein. This mutation was seen only in wave-2 (78%, n = 39) samples. CONCLUSION The circulating virus strains in wave-2 infections demonstrated a greater degree of infectivity. There was a significant change in the genotypes observed in wave-1 and wave-2 infections along with almost twice the number of mutations. We noted that vaccine breakthrough infections (although mostly mild).
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Affiliation(s)
- Sanjay Bhattacharya
- Department of Microbiology, Tata Medical Center, 14 MAR, Kolkata, 700160, India
| | - Soumyadip Chatterji
- Department of Infectious Diseases, Tata Medical Center, 14 MAR, Kolkata, 700160, India.
| | - Mammen Chandy
- Department of Clinical Hematology, Tata Medical Center, 14 MAR, Kolkata, 700160, India
| | | | - Gaurav Goel
- Department of Microbiology, Tata Medical Center, 14 MAR, Kolkata, 700160, India
| | - Deepak Mishra
- Department of Laboratory Sciences, Tata Medical Center, Kolkata, India
| | - Priyanka Vivek
- Department of Staff Health, Tata Medical Center, 14 MAR, Kolkata, 700160, India
| | - Parijat Das
- Department of Microbiology, Tata Medical Center, 14 MAR, Kolkata, 700160, India
| | - Sudipto Mandal
- Department of Microbiology, Tata Medical Center, 14 MAR, Kolkata, 700160, India
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27
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Panzera Y, Cortinas MN, Marandino A, Calleros L, Bormida V, Goñi N, Techera C, Grecco S, Williman J, Ramas V, Coppola L, Mogdasy C, Chiparelli H, Pérez R. Emergence and spreading of the largest SARS-CoV-2 deletion in the Delta AY.20 lineage from Uruguay. GENE REPORTS 2022; 29:101703. [PMID: 36338321 PMCID: PMC9617655 DOI: 10.1016/j.genrep.2022.101703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
The genetic variability of SARS-CoV-2 (genus Betacoronavirus, family Coronaviridae) has been scrutinized since its first detection in December 2019. Although the role of structural variants, particularly deletions, in virus evolution is little explored, these genome changes are extremely frequent. They are associated with relevant processes, including immune escape and attenuation. Deletions commonly occur in accessory ORFs and might even lead to the complete loss of one or more ORFs. This scenario poses an interesting question about the origin and spreading of extreme structural rearrangements that persist without compromising virus viability. Here, we analyze the genome of SARS-CoV-2 in late 2021 in Uruguay and identify a Delta lineage (AY.20) that experienced a large deletion (872 nucleotides according to the reference Wuhan strain) that removes the 7a, 7b, and 8 ORFs. Deleted viruses coexist with wild-type (without deletion) AY.20 and AY.43 strains. The Uruguayan deletion is like those identified in Delta strains from Poland and Japan but occurs in a different Delta clade. Besides providing proof of the circulation of this large deletion in America, we infer that the 872-deletion arises by the consecutive occurrence of a 6-nucleotide deletion, characteristic of delta strains, and an 866-nucleotide deletion that arose independently in the AY.20 Uruguayan lineage. The largest deletion occurs adjacent to transcription regulatory sequences needed to synthesize the nested set of subgenomic mRNAs that serve as templates for transcription. Our findings support the role of transcription sequences as a hotspot for copy-choice recombination and highlight the remarkable dynamic of SARS-CoV-2 genomes.
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Affiliation(s)
- Yanina Panzera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - María Noel Cortinas
- Genómica, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Lucía Calleros
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Victoria Bormida
- Genómica, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Natalia Goñi
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Claudia Techera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Sofía Grecco
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Joaquín Williman
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Viviana Ramas
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Leticia Coppola
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Cristina Mogdasy
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Héctor Chiparelli
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
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28
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Yadav PD, Kumar G, Mukherjee A, Nyayanit DA, Shete AM, Sahay RR, Kumar A, Majumdar T, Patil S, Pandit P, Joshi Y, Dudhmal M, Panda S, Sharma LK, Yadav Ml K, Shastri J, Gangwar M, Munivenkattapa A, Potdar V, Nagamani K, Goyal K, Gadepalli R, Thomas M, Shukla S, Nagraj P, Gupta V, Dalela G, Umar N, Patel SM. Delta variant SARS-CoV-2 infections in pediatric cases during the second wave in India. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1060-1068. [PMID: 35843834 PMCID: PMC9250235 DOI: 10.1016/j.jmii.2022.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/26/2022] [Accepted: 06/16/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND During October 2020, Delta variant was detected for the first time in India and rampantly spread across the globe. It also led to second wave of pandemic in India which affected millions of people. However, there is limited information pertaining to the SARS-CoV-2 strain infecting the children in India. METHODS Here, we assessed the SARS-CoV-2 lineages circulating in the pediatric population of India during the second wave of the pandemic. Clinical and demographic details linked with the nasopharyngeal/oropharyngeal swabs (NPS/OPS) collected from SARS-CoV-2 cases (n = 583) aged 0-18 year and tested positive by real-time RT-PCR were retrieved from March to June 2021. RESULTS Symptoms were reported among 37.2% of patients and 14.8% reported to be hospitalized. The E gene CT value had significant statistical difference at the point of sample collection when compared to that observed in the sequencing laboratory. Out of these 512 sequences 372 were VOCs, 51 were VOIs. Most common lineages observed were Delta, followed by Kappa, Alpha and B.1.36, seen in 65.82%, 9.96%, 6.83% and 4.68%, respectively in the study population. CONCLUSION Overall, it was observed that Delta strain was the leading cause of SARS-CoV-2 infection in Indian children during the second wave of the pandemic. We emphasize on the need of continuous genomic surveillance in SARS-CoV-2 infection even amongst children.
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Affiliation(s)
- Pragya D. Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India,Corresponding author
| | - Gunjan Kumar
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Aparna Mukherjee
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Dimpal A. Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Anita M. Shete
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Rima R. Sahay
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Priyanka Pandit
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Manisha Dudhmal
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - Samiran Panda
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Lokesh Kumar Sharma
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi 110029, India
| | - Kala Yadav Ml
- Bowring and Lady Curzon Medical College, Bangalore 560001, Karnataka, India
| | - Jayanthi Shastri
- Kasturba Hospital of Infectious Diseases, Mumbai 400011, Maharashtra, India
| | - Mayank Gangwar
- Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Ashok Munivenkattapa
- Indian Council of Medical Research-National Institute of Virology, Bangalore 560029, India
| | - Varsha Potdar
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India
| | - K. Nagamani
- Gandhi Hospital, Secunderabad, Telangana 500003, India
| | - Kapil Goyal
- Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | | | - Maria Thomas
- Christian Medical College, Ludhiana, Punjab 141008, India
| | - Suruchi Shukla
- King George Medical University, Lucknow 226003, Uttar Pradesh, India
| | - P. Nagraj
- Gandhi Medical College, Bhopal 462001, Madhya Pradesh, India
| | - Vivek Gupta
- Government Institute of Medical Sciences, Noida 201310, Uttar Pradesh, India
| | - Gaurav Dalela
- Sawai Man Singh Medical College, Jaipur 302004, Rajasthan, India
| | - Nawaz Umar
- Gulbarga Institute of Medical Sciences, Rajiv Gandhi University of Health Sciences, Gulbarga 585105, Karnataka, India
| | - Sweety M. Patel
- Smt. NHL Municipal Medical College, Ahmedabad 380006, Gujarat, India
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29
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Yu CY, Wong SY, Liew NWC, Joseph N, Zakaria Z, Nurulfiza I, Soe HJ, Kairon R, Amin-Nordin S, Chee HY. Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: From alpha to Omicron. Front Med (Lausanne) 2022; 9:1001022. [PMID: 36213636 PMCID: PMC9537942 DOI: 10.3389/fmed.2022.1001022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Countries around the world are gearing for the transition of the coronavirus disease 2019 (COVID-19) from pandemic to endemic phase but the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants could lead to a prolonged pandemic. SARS-CoV-2 has continued to evolve as it optimizes its adaptation to the human host and the successive waves of COVID-19 have been linked to the explosion of particular variant of concern. As the genetic diversity and epidemiological landscape of SARS-CoV-2 differ from country to country, this study aims to provide insights into the variants that are circulating in Malaysia. Whole genome sequencing was performed for 204 SARS-CoV-2 from COVID-19 cases and an additional 18,667 SARS-CoV-2 genome sequences were retrieved from the GISAID EpiCoV database for clade, lineage and genetic variation analyses. Complete genome sequences with high coverage were then used for phylogeny investigation and the resulting phylogenetic tree was constructed from 8,716 sequences. We found that the different waves of COVID-19 in Malaysia were dominated by different clades with the L and O clade for first and second wave, respectively, whereas the progressive replacement by G, GH, and GK of the GRA clade were observed in the subsequence waves. Continuous monitoring of the genetic diversity of SARS-CoV-2 is important to identify the emergence and dominance of new variant in different locality so that the appropriate countermeasures can be taken to effectively contain the spread of SARS-CoV-2.
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Affiliation(s)
- Choo Yee Yu
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Sie Yeng Wong
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nancy Woan Charn Liew
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Narcisse Joseph
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Zunita Zakaria
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Isa Nurulfiza
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | | | | | - Syafinaz Amin-Nordin
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Hui Yee Chee
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- *Correspondence: Hui Yee Chee,
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30
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Transcriptomics and RNA-Based Therapeutics as Potential Approaches to Manage SARS-CoV-2 Infection. Int J Mol Sci 2022; 23:ijms231911058. [PMID: 36232363 PMCID: PMC9570475 DOI: 10.3390/ijms231911058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
SARS-CoV-2 is a coronavirus family member that appeared in China in December 2019 and caused the disease called COVID-19, which was declared a pandemic in 2020 by the World Health Organization. In recent months, great efforts have been made in the field of basic and clinical research to understand the biology and infection processes of SARS-CoV-2. In particular, transcriptome analysis has contributed to generating new knowledge of the viral sequences and intracellular signaling pathways that regulate the infection and pathogenesis of SARS-CoV-2, generating new information about its biology. Furthermore, transcriptomics approaches including spatial transcriptomics, single-cell transcriptomics and direct RNA sequencing have been used for clinical applications in monitoring, detection, diagnosis, and treatment to generate new clinical predictive models for SARS-CoV-2. Consequently, RNA-based therapeutics and their relationship with SARS-CoV-2 have emerged as promising strategies to battle the SARS-CoV-2 pandemic with the assistance of novel approaches such as CRISPR-CAS, ASOs, and siRNA systems. Lastly, we discuss the importance of precision public health in the management of patients infected with SARS-CoV-2 and establish that the fusion of transcriptomics, RNA-based therapeutics, and precision public health will allow a linkage for developing health systems that facilitate the acquisition of relevant clinical strategies for rapid decision making to assist in the management and treatment of the SARS-CoV-2-infected population to combat this global public health problem.
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31
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Simultaneous SARS-CoV-2 Genome Sequencing of 384 Samples on an Illumina MiSeq Instrument through Protocol Optimization. Genes (Basel) 2022; 13:genes13091648. [PMID: 36140815 PMCID: PMC9498777 DOI: 10.3390/genes13091648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
In the present study, we propose a high-throughput sequencing protocol using aNextera XT Library DNA kit on an Illumina MiSeq instrument. We made major modifications to this library preparation in order to multiplex 384 samples in a single Illumina flow cell. To validate our protocol, we compared the sequences obtained with the modified Illumina protocol to those obtained with the GridION Nanopore protocol. For the modified Illumina protocol, our results showed that 94.9% (357/376) of the sequences were interpretable, with a viral genome coverage between 50.5% and 99.9% and an average depth of 421×. For the GridION Nanopore protocol, 94.6% (356/376) of the sequences were interpretable, with a viral genome coverage between 7.0% and 98.6% and an average depth of 2123×. The modified Illumina protocol allows for gaining EUR 4744 and returning results of 384 samples in 53.5 h versus four times 55.5 h with the standard Illumina protocol. Our modified MiSeq protocol yields similar genome sequence data as the GridION Nanopore protocol and has the advantage of being able to handle four times more samples simultaneously and hence is much less expensive.
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32
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Nicot F, Trémeaux P, Latour J, Jeanne N, Ranger N, Raymond S, Dimeglio C, Salin G, Donnadieu C, Izopet J. Whole-genome sequencing of SARS-CoV-2: Comparison of target capture and amplicon single molecule real-time sequencing protocols. J Med Virol 2022; 95:e28123. [PMID: 36056719 PMCID: PMC9539136 DOI: 10.1002/jmv.28123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 01/11/2023]
Abstract
Fast, accurate sequencing methods are needed to identify new variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Single-molecule real-time (SMRT) Pacific Biosciences (PacBio) provides long, highly accurate sequences by circular consensus reads. This study compares the performance of a target capture SMRT PacBio protocol for whole-genome sequencing (WGS) of SARS-CoV-2 to that of an amplicon PacBio SMRT sequencing protocol. The median genome coverage was higher (p < 0.05) with the target capture protocol (99.3% [interquartile range, IQR: 96.3-99.5]) than with the amplicon protocol (99.3% [IQR: 69.9-99.3]). The clades of 65 samples determined with both protocols were 100% concordant. After adjusting for Ct values, S gene coverage was higher with the target capture protocol than with the amplicon protocol. After stratification on Ct values, higher S gene coverage with the target capture protocol was observed only for samples with Ct > 17 (p < 0.01). PacBio SMRT sequencing protocols appear to be suitable for WGS, genotyping, and detecting mutations of SARS-CoV-2.
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Affiliation(s)
- Florence Nicot
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | | | - Justine Latour
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Nicolas Jeanne
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Noémie Ranger
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Stéphanie Raymond
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
| | - Chloé Dimeglio
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
| | - Gérald Salin
- Genotoul‐Genome & Transcriptome—Plateforme Génomique (GeT‐PlaGe), US INRAe 1426Castanet‐TolosanFrance
| | - Cécile Donnadieu
- Genotoul‐Genome & Transcriptome—Plateforme Génomique (GeT‐PlaGe), US INRAe 1426Castanet‐TolosanFrance
| | - Jacques Izopet
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
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33
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da Silva SJR, do Nascimento JCF, Germano Mendes RP, Guarines KM, Targino Alves da Silva C, da Silva PG, de Magalhães JJF, Vigar JRJ, Silva-Júnior A, Kohl A, Pardee K, Pena L. Two Years into the COVID-19 Pandemic: Lessons Learned. ACS Infect Dis 2022; 8:1758-1814. [PMID: 35940589 PMCID: PMC9380879 DOI: 10.1021/acsinfecdis.2c00204] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Jessica Catarine Frutuoso do Nascimento
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Poliana Gomes da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), 52171-011 Recife, Pernambuco, Brazil.,University of Pernambuco (UPE), Serra Talhada Campus, 56909-335 Serra Talhada, Pernambuco, Brazil.,Public Health Laboratory of the XI Regional Health, 56912-160 Serra Talhada, Pernambuco, Brazil
| | - Justin R J Vigar
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Abelardo Silva-Júnior
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), 57072-900 Maceió, Alagoas, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
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Gesto JSM, Cabanelas A, Farjun B, dos Santos MC, Fidalgo-Neto AA, Kuriyama SN, Souza TML. Implemented occupational health surveillance limits the spread of SARS-CoV-2 Omicron at the workplace. Front Med (Lausanne) 2022; 9:910176. [PMID: 36111122 PMCID: PMC9468326 DOI: 10.3389/fmed.2022.910176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/11/2022] [Indexed: 11/23/2022] Open
Abstract
The global spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has put an enormous pressure on human societies, at both health and economic levels. Early diagnosis of SARS-CoV-2, the causative agent of 2019 coronavirus disease (COVID-19), has proved an efficient method to rapidly isolate positive individuals and reduce transmission rates, thus alleviating its negative impact on society’s well-being and economic growth. In this work, through a coordinated and centralized effort to monitor SARS-CoV-2 circulation in companies from the State of Rio de Janeiro, Brazil, we have detected and linked an early rise of infection rates in January 2022 to the introduction of the Omicron variant of concern (VoC) (BA.1). Interestingly, when the Omicron genomic isolates were compared to correlates from public datasets, it was revealed that introduction events were multiple, with possible migration routes mapping to: Mali; Oman and United States; and Italy, Latin America, and United States. In addition, we have built a haplotype network with our genomic dataset and found no strong evidence of transmission chains, between and within companies. Considering Omicron’s particularly high transmissibility, and that most of our samples (>87%) arose from 3 out of 10 companies, these findings suggest that workers from such environments were exposed to SARS-CoV-2 outside their company boundaries. Thus, using a mixed strategy in which quick molecular diagnosis finds support in comprehensive genomic analysis, we have shown that a successfully implemented occupational health program should contribute to document emerging VoC and to limit the spread of SARS-CoV-2 at the workplace.
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Affiliation(s)
- João Silveira Moledo Gesto
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Adriana Cabanelas
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
| | - Bruna Farjun
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
| | | | | | - Sergio N. Kuriyama
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
- SENAI Innovation Institute for Green Chemistry, Rio de Janeiro, Brazil
- *Correspondence: Sergio N. Kuriyama,
| | - Thiago Moreno L. Souza
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
- National Institute of Science and Technology for Innovation on Diseases of Neglected Populations (INCT/IDN), Rio de Janeiro, Brazil
- Thiago Moreno L. Souza,
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35
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Wang X, Stelzer-Braid S, Scotch M, Rawlinson WD. Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use. Rev Med Virol 2022; 32:e2375. [PMID: 35775736 PMCID: PMC9539958 DOI: 10.1002/rmv.2375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 11/15/2022]
Abstract
Acute respiratory infection is the third most frequent cause of mortality worldwide, causing over 4.25 million deaths annually. Although most diagnosed acute respiratory infections are thought to be of viral origin, the aetiology often remains unclear. The advent of next‐generation sequencing (NGS) has revolutionised the field of virus discovery and identification, particularly in the detection of unknown respiratory viruses. We systematically reviewed the application of NGS technologies for detecting respiratory viruses from clinical samples and outline potential barriers to the routine clinical introduction of NGS. The five databases searched for studies published in English from 01 January 2010 to 01 February 2021, which led to the inclusion of 52 studies. A total of 14 different models of NGS platforms were summarised from included studies. Among these models, second‐generation sequencing platforms (e.g., Illumina sequencers) were used in the majority of studies (41/52, 79%). Moreover, NGS platforms have proven successful in detecting a variety of respiratory viruses, including influenza A/B viruses (9/52, 17%), SARS‐CoV‐2 (21/52, 40%), parainfluenza virus (3/52, 6%), respiratory syncytial virus (1/52, 2%), human metapneumovirus (2/52, 4%), or a viral panel including other respiratory viruses (16/52, 31%). The review of NGS technologies used in previous studies indicates the advantages of NGS technologies in novel virus detection, virus typing, mutation identification, and infection cluster assessment. Although there remain some technical and ethical challenges associated with NGS use in clinical laboratories, NGS is a promising future tool to improve understanding of respiratory viruses and provide a more accurate diagnosis with simultaneous virus characterisation.
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Affiliation(s)
- Xinye Wang
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew Scotch
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.,Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
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36
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Lee CG, Lee D. Comparison of Laboratory Tests Applied for Diagnosing the SARS-CoV-2 Infection. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2022. [DOI: 10.15324/kjcls.2022.54.2.79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Chang-Gun Lee
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Korea
| | - Dongsup Lee
- Department of Clinical Laboratory Science, Hyejeon College, Hongseong, Korea
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37
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Identification of SARS-CoV-2 Variants of Concern Using Amplicon Next-Generation Sequencing. Microbiol Spectr 2022; 10:e0073622. [PMID: 35758686 PMCID: PMC9430688 DOI: 10.1128/spectrum.00736-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
COVID-19 is caused by SARS-CoV-2, several virulent variants of which have emerged since 2019. More than 529 million people have been infected, and at least 6 million have died. Our aim was to develop a fast, accurate, low-cost method for detecting and identifying newly emerging variants of concern (VOCs) that could pose a global threat. The 341-bp DNA sequence of a specific region of the SARS-CoV-2’s spike protein was amplified by a one-step PCR on RNA samples from 46 patients. The product was sequenced using next-generation sequencing (NGS). DNA sequences from seven genomes, the original Wuhan isolate and six different representative variants obtained from the GISAID website, were used as references. Complete whole-genome sequences from local isolates were also obtained from the GISAID website, and their RNA was used for comparison. We used an amplicon-based NGS method (termed VOC-NGS) for genotyping and successfully identified all 46 samples. Fifteen (32.6%) were like the original isolate. Twenty-seven were VOCs: nine (19.5%) Alpha, eight (19%) Delta, six (14%) Beta, and four (8.7%) Omicron. Two were variants of interest (VOI): one (2%) Kappa and one (2%) Zeta. Two samples were mixtures of two variants, one of Alpha and Beta and one of Alpha and Delta. The Spearman correlation between whole-genome sequencing (WGS) and VOC-NGS was significant (P < 0.001) with perfect agreement (Kappa = 0.916) for 36/38 (94.7%) samples with VOC-NGS detecting all the known VOCs. Genotyping by VOC-NGS enables rapid screening of high-throughput clinical samples that includes the identification of VOCs and mixtures of variants, at lower cost than WGS. IMPORTANCE The manuscript described SARS-Cov-2 genotyping by VOC-NGS, which presents an ideal balance of accuracy, rapidity, and cost for detecting and globally tracking VOCs and some VOI of SARS-CoV-2. A large number of clinical samples can be tested together. Rapid introduction of new mutations at a specific site of the spike protein necessitates efficient strain detection and identification to enable choice of treatment and the application of vaccination, as well as planning public health policy.
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38
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Cohen-Aharonov LA, Rebibo-Sabbah A, Yaacov A, Granit RZ, Strauss M, Colodner R, Cheshin O, Rosenberg S, Eavri R. High throughput SARS-CoV-2 variant analysis using molecular barcodes coupled with next generation sequencing. PLoS One 2022; 17:e0253404. [PMID: 35727806 PMCID: PMC9212143 DOI: 10.1371/journal.pone.0253404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 04/24/2022] [Indexed: 11/18/2022] Open
Abstract
The identification of SARS-CoV-2 variants across the globe and their implications on the outspread of the pandemic, infection potential and resistance to vaccination, requires modification of the current diagnostic methods to map out viral mutations rapidly and reliably. Here, we demonstrate that integrating DNA barcoding technology, sample pooling and Next Generation Sequencing (NGS) provide an applicable solution for large-population viral screening combined with specific variant analysis. Our solution allows high throughput testing by barcoding each sample, followed by pooling of test samples using a multi-step procedure. First, patient-specific barcodes are added to the primers used in a one-step RT-PCR reaction, amplifying three different viral genes and one human housekeeping gene (as internal control). Then, samples are pooled, purified and finally, the generated sequences are read using an Illumina NGS system to identify the positive samples with a sensitivity of 82.5% and a specificity of 97.3%. Using this solution, we were able to identify six known and one unknown SARS-CoV-2 variants in a screen of 960 samples out of which 258 (27%) were positive for the virus. Thus, our diagnostic solution integrates the benefits of large population and epidemiological screening together with sensitive and specific identification of positive samples including variant analysis at a single nucleotide resolution.
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Affiliation(s)
| | | | - Adar Yaacov
- Laboratory for Computational Biology of Cancer, Sharett Institute for Oncology, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
- The Wohl Institute for Translational Medicine, Hadassah – Hebrew University Medical Center, Jerusalem, Israel
| | | | - Merav Strauss
- Microbiology Laboratory, Emek Medical Center, Afula, Israel
| | - Raul Colodner
- Microbiology Laboratory, Emek Medical Center, Afula, Israel
| | - Ori Cheshin
- Internal Medicine E, Emek Medical Center, Afula, Israel
| | - Shai Rosenberg
- Laboratory for Computational Biology of Cancer, Sharett Institute for Oncology, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
- The Wohl Institute for Translational Medicine, Hadassah – Hebrew University Medical Center, Jerusalem, Israel
| | - Ronen Eavri
- Barcode Diagnostics Ltd., Nazareth, Israel
- * E-mail:
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Effectiveness of the ChAdOx1 nCoV-19 Coronavirus Vaccine (Covishield TM) in Preventing SARS-CoV2 Infection, Chennai, Tamil Nadu, India, 2021. Vaccines (Basel) 2022; 10:vaccines10060970. [PMID: 35746578 PMCID: PMC9228854 DOI: 10.3390/vaccines10060970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/06/2022] [Accepted: 06/14/2022] [Indexed: 12/20/2022] Open
Abstract
We estimated the effectiveness of two doses of the ChAdOx1 nCoV-19 (Covishield) vaccine against any COVID-19 infection among individuals ≥45 years in Chennai, Tamil Nadu, India. A community-based cohort study was conducted from May to September 2021 in a selected geographic area in Chennai. The estimated sample size was 10,232. We enrolled 69,435 individuals, of which 21,793 were above 45 years. Two-dose coverage of Covishield in the 18+ and 45+ age group was 18% and 31%, respectively. Genomic analysis of 74 out of the 90 aliquots collected from the 303 COVID-19-positive individuals in the 45+ age group showed delta variants and their sub-lineages. The vaccine’s effectiveness against COVID-19 disease in the ≥45 age group was 61.3% (95% CI: 43.6–73.4) at least 2 weeks after receiving the second dose of Covishield. We demonstrated the effectiveness of two doses of the ChAdOx1 vaccine against the delta variant in the general population of Chennai. We recommend similar future studies considering emerging variants and newer vaccines. Two-dose vaccine coverage could be ensured to protect against COVID-19 infection.
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Di Giacomo D, Di Domenico M, Defourny SVP, Malatesta D, Di Teodoro G, Martino M, Viola A, D’Alterio N, Cammà C, Modesto P, Petrini A. Validation of AmpliSeq NGS Panel for BRCA1 and BRCA2 Variant Detection in Canine Formalin-Fixed Paraffin-Embedded Mammary Tumors. Life (Basel) 2022; 12:life12060851. [PMID: 35743882 PMCID: PMC9225004 DOI: 10.3390/life12060851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/01/2022] Open
Abstract
Mammary carcinomas are the most common neoplasms observed in women and in female dogs. Canine mammary tumors show epidemiological, clinical, genetic, and prognostic characteristics comparable to human breast cancers. The recent introduction of next generation sequencing (NGS) technologies has greatly improved research and diagnostics for humans, while these new tools still need to be implemented in animal models. In this study we developed and validated an AmpliSeq Panel assay for the identification of BRCA variants in twenty-two different dogs. The amplicon mean coverage was 5499× and uniformity was higher than 98% in all samples. The results of germline single nucleotide variants (SNVs) and insertions/deletions (INDELs) were fully concordant regardless of the types of samples considered (blood, fresh and FFPE tissues). Moreover, despite the high DNA degradation observed in older FFPE blocks (>5 years), the assay allowed full coverage of all amplicons for downstream analyses. We consider the NGS panel developed in this study as a useful tool for expanding information on BRCA genes in the veterinary field and for human health from a comparative oncology perspective.
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Affiliation(s)
- Daniela Di Giacomo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy
- Correspondence:
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy
| | - Sabrina Vanessa Patrizia Defourny
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
| | - Daniela Malatesta
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
| | - Giovanni Di Teodoro
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
| | - Michele Martino
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
| | - Antonello Viola
- Veterinary Practitioner, Centro Veterinario Nova Julia, Via Galileo Galilei 177, 64021 Giulianova, Italy;
| | - Nicola D’Alterio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy
| | - Paola Modesto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy;
| | - Antonio Petrini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
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SARS-CoV-2 Lineage A.27: New Data from African Countries and Dynamics in the Context of the COVID-19 Pandemic. Viruses 2022; 14:v14051007. [PMID: 35632749 PMCID: PMC9144831 DOI: 10.3390/v14051007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
SARS-CoV-2 is constantly evolving with lineages emerging and others eclipsing. Some lineages have an important epidemiological impact and are known as variants of interest (VOIs), variants under monitoring (VUMs) or variants of concern (VOCs). Lineage A.27 was first defined as a VUM since it holds mutations of concern. Here, we report additional lineage A.27 data and sequences from five African countries and describe the molecular characteristics, and the genetic history of this lineage worldwide. Based on the new sequences investigated, the most recent ancestor (tMRCA) of lineage A.27 was estimated to be from April 2020 from Niger. It then spread to Europe and other parts of the world with a peak observed between February and April 2021. The detection rate of A.27 then decreased with only a few cases reported during summer 2021. The phylogenetic analysis revealed many sub-lineages. Among them, one was defined by the substitution Q677H in the spike (S) gene, one was defined by the substitution D358N in the nucleoprotein (N) gene and one was defined by the substitution A2143V in the ORF1b gene. This work highlights the importance of molecular characterization and the timely submission of sequences to correctly describe the circulation of particular strains in order to be proactive in monitoring the pandemic.
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Dhanalakshmi M, Das K, Pandya M, Shah S, Gadnayak A, Dave S, Das J. Artificial Neural Network-Based Study Predicts GS-441524 as a Potential Inhibitor of SARS-CoV-2 Activator Protein Furin: a Polypharmacology Approach. Appl Biochem Biotechnol 2022; 194:4511-4529. [PMID: 35507249 PMCID: PMC9066385 DOI: 10.1007/s12010-022-03928-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Furin, a pro-protein convertase, plays a significant role as a biological scissor in bacterial, viral, and even mammalian substrates which in turn decides the fate of many viral and bacterial infections along with the numerous ailments caused by cancer, diabetes, inflammations, and neurological disorders. In the wake of the current pandemic caused by the virus SARS-CoV-2, furin has become the center of attraction for researchers as the spike protein contains a polybasic furin cleavage site. In the present work, we have searched for novel inhibitors against this interesting human target from FDA-approved antiviral. To enhance the selection of new inhibitors, we employed Kohonen's artificial neural network-based self-organizing maps for ligand-based virtual screening. Promising results were obtained which can help in drug repurposing and network pharmacology studies can address the errors generated due to promiscuity/polypharmacology. We found 15 existing FDA antiviral drugs having the potential to inhibit furin. Among these, six compounds have targets on important human proteins (LDLR, FCGR1A, PCK1, TLR7, DNA, and PNP). The role of these 15 drugs inhibiting furin can be established by studying further on patients infected with number of viruses including SARS-CoV-2. Here we propose two promising candidate FDA drugs GS-441524 and Grazoprevir (MK-5172) for repurposing as inhibitors of furin. The best results were observed with GS-441524.
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Affiliation(s)
- M Dhanalakshmi
- Research and Development Centre, Bharathiar University, Marudhamalai Rd, Coimbatore, Tamil Nadu, India
| | - Kajari Das
- Department of Biotechnology, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Medha Pandya
- The KPES Science College, Maharaja krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, India
| | - Sejal Shah
- Department of Microbiology, Faculty of Science, Marwadi University, Rajkot, Gujarat, India
| | - Ayushman Gadnayak
- Centre for Genomics & Biomedical Informatics, IMS and SUM Hospital, Siksha "O" Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Sushma Dave
- Department of Applied Sciences, JIET, Jodhpur, Rajasthan, India.
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Donzelli S, Ciuffreda L, Pontone M, Betti M, Massacci A, Mottini C, De Nicola F, Orlandi G, Goeman F, Giuliani E, Sperandio E, Piaggio G. Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking. Comput Struct Biotechnol J 2022; 20:2558-2563. [PMID: 35611117 PMCID: PMC9119164 DOI: 10.1016/j.csbj.2022.05.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/06/2022] [Accepted: 05/16/2022] [Indexed: 02/05/2023] Open
Abstract
The SARS-CoV-2 Variants of Concern tracking via Whole Genome Sequencing represents a pillar of public health measures for the containment of the pandemic. The ability to track down the lineage distribution on a local and global scale leads to a better understanding of immune escape and to adopting interventions to contain novel outbreaks. This scenario poses a challenge for NGS laboratories worldwide that are pressed to have both a faster turnaround time and a high-throughput processing of swabs for sequencing and analysis. In this study, we present an optimization of the Illumina COVID-seq protocol carried out on thousands of SARS-CoV-2 samples at the wet and dry level. We discuss the unique challenges related to processing hundreds of swabs per week such as the tradeoff between ultra-high sensitivity and negative contamination levels, cost efficiency and bioinformatics quality metrics.
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Goswami C, Sheldon M, Bixby C, Keddache M, Bogdanowicz A, Wang Y, Schultz J, McDevitt J, LaPorta J, Kwon E, Buyske S, Garbolino D, Biloholowski G, Pastuszak A, Storella M, Bhalla A, Charlier-Rodriguez F, Hager R, Grimwood R, Nahas SA. Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program. BMC Infect Dis 2022; 22:404. [PMID: 35468749 PMCID: PMC9035976 DOI: 10.1186/s12879-022-07374-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Centers for Disease Control and Prevention contracted with laboratories to sequence the SARS-CoV-2 genome from positive samples across the United States to enable public health officials to investigate the impact of variants on disease severity as well as the effectiveness of vaccines and treatment. Herein we present the initial results correlating RT-PCR quality control metrics with sample collection and sequencing methods from full SARS-CoV-2 viral genomic sequencing of 24,441 positive patient samples between April and June 2021. METHODS RT-PCR confirmed (N Gene Ct value < 30) positive patient samples, with nucleic acid extracted from saliva, nasopharyngeal and oropharyngeal swabs were selected for viral whole genome SARS-CoV-2 sequencing. Sequencing was performed using Illumina COVIDSeq™ protocol on either the NextSeq550 or NovaSeq6000 systems. Informatic variant calling, and lineage analysis were performed using DRAGEN COVID Lineage applications on Illumina's Basespace cloud analytical system. All sequence data and variant calls were uploaded to NCBI and GISAID. RESULTS An association was observed between higher sequencing coverage, quality, and samples with a lower Ct value, with < 27 being optimal, across both sequencing platforms and sample collection methods. Both nasopharyngeal swabs and saliva samples were found to be optimal samples of choice for SARS-CoV-2 surveillance sequencing studies, both in terms of strain identification and sequencing depth of coverage, with NovaSeq 6000 providing higher coverage than the NextSeq 550. The most frequent variants identified were the B.1.617.2 Delta (India) and P.1 Gamma (Brazil) variants in the samples sequenced between April 2021 and June 2021. At the time of submission, the most common variant > 99% of positives sequenced was Omicron. CONCLUSION These initial analyses highlight the importance of sequencing platform, sample collection methods, and RT-PCR Ct values in guiding surveillance efforts. These surveillance studies evaluating genetic changes of SARS-CoV-2 have been identified as critical by the CDC that can affect many aspects of public health including transmission, disease severity, diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Chirayu Goswami
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Michael Sheldon
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Christian Bixby
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | | | - Yihe Wang
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Jonathan Schultz
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Jessica McDevitt
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - James LaPorta
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Elaine Kwon
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Steven Buyske
- Rutgers University, 559 Hill Center, 110 Frelinghuysen Rd, Piscataway, NJ, 08854, USA
| | - Dana Garbolino
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | - Alex Pastuszak
- Vault Health, 115 Broadway Suite 1800, 18th Floor, Dobbs Ferry, NY, 10522, USA
| | - Mary Storella
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Amit Bhalla
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | - Russ Hager
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Robin Grimwood
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Shareef A Nahas
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA.
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Lippi G, Favresse J, Gromiha MM, SoRelle JA, Plebani M, Henry BM. Ad interim recommendations for diagnosing SARS-CoV-2 infection by the IFCC SARS-CoV-2 variants working group. Clin Chem Lab Med 2022; 60:975-981. [PMID: 35452576 DOI: 10.1515/cclm-2022-0345] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 12/28/2022]
Abstract
This document, endorsed by the IFCC Working Group on SARS-CoV-2 Variants, aims to update previous indications for diagnosing acute SARS-CoV-2 infection, taking into consideration the evidence that has emerged after the origin and spread of new lineages and sub-lineages of the virus characterized by mutated genetics and altered biochemical, biological and clinical characteristics. These indications encompass the use of different diagnostic strategies in specific clinical settings, such as high risk of SARS-CoV-2 infection (symptomatic patients), low risk of SARS-CoV-2 infection (asymptomatic subjects) at hospital admission/contact tracing, testing in asymptomatic subjects, in epidemiologic surveys and/or population screening, along with tentative indications for identification of new lineages and/or sub-lineages of SARS-CoV-2.
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Affiliation(s)
- Giuseppe Lippi
- IFCC SARS-CoV-2 Variants Working Group, Verona, Italy
- IFCC Task Force on COVID-19, Verona, Italy
- Section of Clinical Biochemistry and School of Medicine, University of Verona, Verona, Italy
| | - Julien Favresse
- IFCC SARS-CoV-2 Variants Working Group, Verona, Italy
- Department of Laboratory Medicine, Clinique St-Luc Bouge, Namur, Belgium
| | - Michael M Gromiha
- IFCC SARS-CoV-2 Variants Working Group, Verona, Italy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Jeffrey A SoRelle
- IFCC SARS-CoV-2 Variants Working Group, Verona, Italy
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mario Plebani
- IFCC SARS-CoV-2 Variants Working Group, Verona, Italy
- Department of Medicine-DIMED, University of Padova, Padova, Italy
| | - Brandon M Henry
- IFCC SARS-CoV-2 Variants Working Group, Verona, Italy
- Clinical Laboratory, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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Niu M, Han Y, Dong X, Yang L, Li F, Zhang Y, Hu Q, Xia X, Li H, Sun Y. Highly Sensitive Detection Method for HV69-70del in SARS-CoV-2 Alpha and Omicron Variants Based on CRISPR/Cas13a. Front Bioeng Biotechnol 2022; 10:831332. [PMID: 35497364 PMCID: PMC9039052 DOI: 10.3389/fbioe.2022.831332] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
As SARS-CoV-2 variants continue to evolve, identifying variants with adaptive diagnostic tool is critical to containing the ongoing COVID-19 pandemic. Herein, we establish a highly sensitive and portable on-site detection method for the HV69-70del which exist in SARS-CoV-2 Alpha and Omicron variants using a PCR-based CRISPR/Cas13a detection system (PCR-CRISPR). The specific crRNA (CRISPR RNA) targeting the HV69-70del is screened using the fluorescence-based CRISPR assay, and the sensitivity and specificity of this method are evaluated using diluted nucleic acids of SARS-CoV-2 variants and other pathogens. The results show that the PCR-CRISPR detection method can detect 1 copies/μL SARS-CoV-2 HV69-70del mutant RNA and identify 0.1% of mutant RNA in mixed samples, which is more sensitive than the RT-qPCR based commercial SARS-CoV-2 variants detection kits and sanger sequencing. And it has no cross reactivity with ten other pathogens nucleic acids. Additionally, by combined with our previously developed ERASE (Easy-Readout and Sensitive Enhanced) lateral flow strip suitable for CRISPR detection, we provide a novel diagnosis tool to identify SARS-CoV-2 variants in primary and resource-limited medical institutions without professional and expensive fluorescent detector.
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Affiliation(s)
- Mengwei Niu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yao Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xue Dong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lan Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fan Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Youcui Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Qiang Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yansong Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Yermanos A, Hong KL, Agrafiotis A, Han J, Nadeau S, Valenzuela C, Azizoglu A, Ehling R, Gao B, Spahr M, Neumeier D, Chang CH, Dounas A, Petrillo E, Nissen I, Burcklen E, Feldkamp M, Beisel C, Oxenius A, Savic M, Stadler T, Rudolf F, Reddy ST. DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. BMC Genomics 2022; 23:289. [PMID: 35410128 PMCID: PMC8995413 DOI: 10.1186/s12864-022-08403-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e.g., whole genome sequencing) are performed separately, thus limiting the detection and tracing of SARS-CoV-2 and emerging variants. RESULTS Here, we developed DeepSARS, a high-throughput platform for simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 by the integration of molecular barcoding, targeted deep sequencing, and computational phylogenetics. DeepSARS enables highly sensitive viral detection, while also capturing genomic diversity and viral evolution. We show that DeepSARS can be rapidly adapted for identification of emerging variants, such as alpha, beta, gamma, and delta strains, and profile mutational changes at the population level. CONCLUSIONS DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity. DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. Image was created using Biorender.com .
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Affiliation(s)
- Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,Botnar Research Centre for Child Health, Basel, Switzerland. .,Institute of Microbiology, ETH Zurich, Zurich, Switzerland. .,Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland.
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland
| | - Andreas Agrafiotis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland
| | - Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Cecilia Valenzuela
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Asli Azizoglu
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Roy Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Beichen Gao
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Michael Spahr
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ching-Hsiang Chang
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Andreas Dounas
- Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
| | - Ezequiel Petrillo
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, Buenos Aires, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ina Nissen
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Elodie Burcklen
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Mirjam Feldkamp
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Miodrag Savic
- Department of Health, Economics and Health Directorate Canton Basel-Landschaft, Liestal, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,Botnar Research Centre for Child Health, Basel, Switzerland.
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48
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Zhang X, Meng H, Liu H, Ye Q. Advances in laboratory detection methods and technology application of SARS-CoV-2. J Med Virol 2022; 94:1357-1365. [PMID: 34854101 PMCID: PMC9015480 DOI: 10.1002/jmv.27494] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023]
Abstract
At present, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is raging worldwide, and the coronavirus disease 2019 outbreak caused by SARS-CoV-2 seriously threatens the life and health of all humankind. There is no specific medicine for novel coronavirus yet. So, laboratory diagnoses of novel coronavirus as soon as possible and isolation of the source of infection play a vital role in preventing and controlling the epidemic. Therefore, selecting appropriate detection techniques and methods is particularly important to improve the efficiency of disease diagnosis and treatment and to curb the outbreak of infectious diseases. In this paper, virus nucleic acid, protein, and serum immunology were reviewed to provide a reference for further developing virus detection technology to provide better prevention and treatment strategies and research ideas for clinicians and researchers.
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Affiliation(s)
- Xiucai Zhang
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Hanyan Meng
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Huihui Liu
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Qing Ye
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
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Unravelling Vitamin B12 as a potential inhibitor against SARS-CoV-2: A computational approach. INFORMATICS IN MEDICINE UNLOCKED 2022; 30:100951. [PMID: 35475214 PMCID: PMC9020503 DOI: 10.1016/j.imu.2022.100951] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 04/15/2022] [Accepted: 04/15/2022] [Indexed: 01/22/2023] Open
Abstract
The new severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) is the etiological agent of Coronavirus disease 2019 (COVID-19), which becomes an eventual pandemic outbreak. Lack of proper therapeutic management has accelerated the researchers to repurpose existing drugs with known preclinical and toxicity profiles, which can easily enter Phase 3 or 4 or can be used directly in clinical settings. Vitamins are necessary nutrients for cell growth, function, and development. Furthermore, they play an important role in pathogen defence via cell-mediated responses and boost immunity. Using a computational approach, we intend to identify the probable inhibitory effect of all vitamins on the drug targets of COVID-19. The computational analysis demonstrated that vitamin B12 resulted in depicting suitable significant binding with furin, RNA dependent RNA polymerase (RdRp), Main proteases (Mpro), ORF3a and ORF7a and Vitamin D3 with spike protein and vitamin B9 with non structural protein 3 (NSP3). A detailed examination of vitamins suggests that vitamin B12 may be the component that reduces virulence by blocking furin which is responsible for entry of virus in the host cell. Details from the Molecular Dynamics (MD) simulation study aided in determining vitamin B12 as a possible furin inhibitor.
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Thiruvengadam R, Awasthi A, Medigeshi G, Bhattacharya S, Mani S, Sivasubbu S, Shrivastava T, Samal S, Rathna Murugesan D, Koundinya Desiraju B, Kshetrapal P, Pandey R, Scaria V, Kumar Malik P, Taneja J, Binayke A, Vohra T, Zaheer A, Rathore D, Ahmad Khan N, Shaman H, Ahmed S, Kumar R, Deshpande S, Subramani C, Wadhwa N, Gupta N, Pandey AK, Bhattacharya J, Agrawal A, Vrati S, Bhatnagar S, Garg PK. Effectiveness of ChAdOx1 nCoV-19 vaccine against SARS-CoV-2 infection during the delta (B.1.617.2) variant surge in India: a test-negative, case-control study and a mechanistic study of post-vaccination immune responses. THE LANCET INFECTIOUS DISEASES 2022; 22:473-482. [PMID: 34838183 PMCID: PMC8616567 DOI: 10.1016/s1473-3099(21)00680-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022]
Abstract
Background SARS-CoV-2 variants of concern (VOCs) have threatened COVID-19 vaccine effectiveness. We aimed to assess the effectiveness of the ChAdOx1 nCoV-19 vaccine, predominantly against the delta (B.1.617.2) variant, in addition to the cellular immune response to vaccination. Methods We did a test-negative, case-control study at two medical research centres in Faridabad, India. All individuals who had a positive RT-PCR test for SARS-CoV-2 infection between April 1, 2021, and May 31, 2021, were included as cases and individuals who had a negative RT-PCR test were included as controls after matching with cases on calendar week of RT-PCR test. The primary outcome was effectiveness of complete vaccination with the ChAdOx1 nCoV-19 vaccine against laboratory-confirmed SARS-CoV-2 infection. The secondary outcomes were effectiveness of a single dose against SARS-CoV-2 infection and effectiveness of a single dose and complete vaccination against moderate-to-severe disease among infected individuals. Additionally, we tested in-vitro live-virus neutralisation and T-cell immune responses to the spike protein of the wild-type SARS-CoV-2 and VOCs among healthy (anti-nucleocapsid antibody negative) recipients of the ChAdOx1 nCoV-19 vaccine. Findings Of 2379 cases of confirmed SARS-CoV-2 infection, 85 (3·6%) were fully vaccinated compared with 168 (8·5%) of 1981 controls (adjusted OR [aOR] 0·37 [95% CI 0·28–0·48]), giving a vaccine effectiveness against SARS-CoV-2 infection of 63·1% (95% CI 51·5–72·1). 157 (6·4%) of 2451 of cases and 181 (9·1%) of 1994) controls had received a single dose of the ChAdOx1 nCoV-19 vaccine (aOR 0·54 [95% CI 0·42–0·68]), thus vaccine effectiveness of a single dose against SARS-CoV-2 infection was 46·2% (95% CI 31·6–57·7). One of 84 cases with moderate-to-severe COVID-19 was fully vaccinated compared with 84 of 2295 cases with mild COVID-19 (aOR 0·19 [95% CI 0·01–0·90]), giving a vaccine effectiveness of complete vaccination against moderate-to-severe disease of 81·5% (95% CI 9·9–99·0). The effectiveness of a single dose against moderate-to-severe disease was 79·2% (95% CI 46·1–94·0); four of 87 individuals with moderate-to-severe COVID-19 had received a single dose compared with 153 of 2364 participants with mild disease (aOR 0·20 [95% CI 0·06–0·54]). Among 49 healthy, fully vaccinated individuals, neutralising antibody responses were lower against the alpha (B.1.1.7; geometric mean titre 244·7 [95% CI 151·8–394·4]), beta (B.1.351; 97·6 [61·2–155·8]), kappa (B.1.617.1; 112·8 [72·7–175·0]), and delta (88·4 [61·2–127·8]) variants than against wild-type SARS-CoV-2 (599·4 [376·9–953·2]). However, the antigen-specific CD4 and CD8 T-cell responses were conserved against both the delta variant and wild-type SARS-CoV-2. Interpretation The ChAdOx1 nCoV-19 vaccine remained effective against moderate-to-severe COVID-19, even during a surge that was dominated by the highly transmissible delta variant of SARS-CoV-2. Spike-specific T-cell responses were maintained against the delta variant. Such cellular immune protection might compensate for waning humoral immunity. Funding Department of Biotechnology India, Council of Scientific and Industrial Research India, and Fondation Botnar.
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Affiliation(s)
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, India
| | | | | | - Shailendra Mani
- Translational Health Science and Technology Institute, Faridabad, India
| | - Sridhar Sivasubbu
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Sweety Samal
- Translational Health Science and Technology Institute, Faridabad, India
| | | | | | | | - Rajesh Pandey
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vinod Scaria
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Juhi Taneja
- ESIC Medical College and Hospital, Faridabad, India
| | - Akshay Binayke
- Translational Health Science and Technology Institute, Faridabad, India
| | - Tarini Vohra
- Translational Health Science and Technology Institute, Faridabad, India
| | - Aymaan Zaheer
- Translational Health Science and Technology Institute, Faridabad, India
| | - Deepak Rathore
- Translational Health Science and Technology Institute, Faridabad, India
| | - Naseem Ahmad Khan
- Translational Health Science and Technology Institute, Faridabad, India
| | - Heena Shaman
- Translational Health Science and Technology Institute, Faridabad, India
| | - Shubbir Ahmed
- Translational Health Science and Technology Institute, Faridabad, India
| | - Rajesh Kumar
- Translational Health Science and Technology Institute, Faridabad, India
| | - Suprit Deshpande
- Translational Health Science and Technology Institute, Faridabad, India
| | | | - Nitya Wadhwa
- Translational Health Science and Technology Institute, Faridabad, India
| | | | | | - Jayanta Bhattacharya
- Translational Health Science and Technology Institute, Faridabad, India; International AIDS Vaccine Initiative, New Delhi, India
| | - Anurag Agrawal
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
| | | | | | - Pramod Kumar Garg
- Translational Health Science and Technology Institute, Faridabad, India.
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