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Panova N, Allan NP, Rubas NC, Lee RH, Kunihiro BP, Umeda L, Peres R, Juarez R, Maunakea AK. Sequencing the SARS-CoV-2 Genome from Stool Samples of Post-acute Cases Implicates a Novel Mutation Associated with Reduced Antibody Neutralization. EUROPEAN JOURNAL OF BIOMEDICAL RESEARCH 2023; 2:17-23. [PMID: 37525697 PMCID: PMC10389300 DOI: 10.24018/ejbiomed.2023.2.3.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Whole-genome SARS-CoV-2 sequencing tools are crucial for tracking the COVID-19 pandemic. However, current techniques require sampling of actively infectious patients following COVID-19 testing to recover enough SARS-CoV-2 RNA from the nasopharyngeal passage, which rapidly clears during the first few weeks of infection. A prospective assessment of the viral genome sourced from recovered non-infectious patients would greatly facilitate epidemiological tracking. Thus, we developed a protocol to isolate and sequence the genome of SARS-CoV-2 from stool samples of post-acute SARS-CoV-2 patients, at timepoints ranging from 10-120 days after onset of symptoms. Stool samples were collected from patients at varying timepoints post-convalescence, and viral DNA was isolated and sequenced using the QIAamp Viral RNA Mini Kit (Qiagen Inc.) and Ion Ampliseq™ Library Kit Plus (Life Technologies Corporation). Capacity of neutralizing antibodies in patient plasma was tested using a Luminex panel (Coronavirus Ig Total Human 11-Plex ProcartaPlex™ Panel, ThermoFisher). Of 64 samples obtained from post-acute patients, 21 (32.8%) yielded sufficient material for whole-genome sequencing. This allowed us to identify widely divergent phylogenetic relativity of the SARS-CoV-2 genome from post-acute patients living in the same households and infected around the same time. Additionally, we observed that individuals who recovered from infection expressed varying degrees of antibodies against SARS-CoV-2 structural proteins that corresponded to distinct variants. Interestingly, we identified a novel point mutation in the viral genome where infected patients expressed antibodies with a significantly reduced capacity to neutralize the virus in vitro relative to that of those infected with the wild-type strain. Altogether, we demonstrate a protocol to successfully sequence the SARS-CoV-2 genome from stool samples from patients up to 4 months post-infection, which can be applied to studies that assess the relationship between variants and immune response post-hoc and safe monitoring of the SARS-CoV-2 genome during the pandemic.
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Gh Jeelani P, Muzammil Munawar S, Khaleel Basha S, Krishna P G, Joshua Sinclair B, Dharshini Jenifer A, Ojha N, Mossa AT, Chidambaram R. Exploring possible strategies for treating SARS-CoV-2 in sewage wastewater: A review of current research and future directions. HYGIENE AND ENVIRONMENTAL HEALTH ADVANCES 2023; 6:100056. [PMID: 37131485 PMCID: PMC10088352 DOI: 10.1016/j.heha.2023.100056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 05/04/2023]
Abstract
The advent of acute respiratory coronavirus disease (COVID-19) is convoyed by the shedding of the virus in stool. Although inhalation from person-to-person and aerosol/droplet transmission are the main modes of SARS-Coronavirus-2 (SARS-CoV-2) transmission, currently available evidence indicates the presence of viral RNA in the sewerage wastewater, which highlights the need for more effective corona virus treatment options. In the existing COVID-19 pandemic, a substantial percentage of cases shed SARS-CoV-2 viral RNA in their faeces. Hence the treating this sewerage wastewater with proper surveillance is essential to contain this deadly pathogen from further transmission. Since, the viral disinfectants will not be very effective on sewerage waste as organic matter, and suspended solids in water can protect viruses that adsorb to these particles. More effective methods and measures are needed to prevent this virus from spreading. This review will explore some potential methods to treat the SARS-CoV-2 infected sewerage wastewater, current research and future directions.
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Affiliation(s)
- Peerzada Gh Jeelani
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore, Tamil Nadu, India
| | - Syed Muzammil Munawar
- C. Abdul Hakeem College, (Automous) Melvisharam - 632 509, Ranipet District, Tamilnadu, India
| | - S Khaleel Basha
- C. Abdul Hakeem College, (Automous) Melvisharam - 632 509, Ranipet District, Tamilnadu, India
| | - Gopi Krishna P
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore, Tamil Nadu, India
| | - Bruce Joshua Sinclair
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore, Tamil Nadu, India
| | - A Dharshini Jenifer
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore, Tamil Nadu, India
| | - Nupur Ojha
- Department of Biotechnology, Indian Institute of Technology, Madras, Chennai 600036 Tamil Nadu, India
| | - Abdel-Tawab Mossa
- National Research Centre, Egypt | Cairo, Egypt | NRC 33 El Buhouth St 'Ad Doqi, Dokki, Cairo Governorate 12622, Egypt
| | - Ramalingam Chidambaram
- Nano-Food Research Group, Instrumental and Food Analysis Laboratory, Division of Industrial Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014 Tamil Nadu, India
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Ito A, Okada T, Minato N, Hattori F. Possible internal viral shedding and interferon production after clinical recovery from COVID-19: Case report. Front Med (Lausanne) 2022; 9:959196. [PMID: 35983089 PMCID: PMC9379344 DOI: 10.3389/fmed.2022.959196] [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: 06/01/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
A 70-year-old man underwent off-pump coronary artery bypass grafting 28 days after his recovery from coronavirus disease 2019 (COVID-19), which was confirmed by a negative polymerase chain reaction (PCR) test result for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a nasopharyngeal swab. The PCR test result was also negative for nasopharyngeal sampling 5 days prior to the surgery. However, his redundant saphenous vein and sputum through the endotracheal tube that was taken on the operative day showed the presence of SARS-CoV-2 by PCR. Immunohistochemical analysis of Spike and Nucleoprotein of the saphenous vein showed small clusters of each antigen-positive speckle. Ultrastructural imaging of the saphenous vein showed virus-like particles. The cell-based assay suggested that the patient’s serum contained a higher concentration of type-I interferons than that of healthy control sera. These observations suggest that internal viral shedding and, to some extent, innate immune responses continue after COVID-19 recovery.
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Affiliation(s)
- Asuka Ito
- Department of Anesthesiology, School of Medicine, Kansai Medical University, Osaka, Japan
| | - Takayuki Okada
- Department of Cardiovascular Surgery, School of Medicine, Kansai Medical University, Osaka, Japan
| | - Naoki Minato
- Department of Cardiovascular Surgery, School of Medicine, Kansai Medical University, Osaka, Japan
| | - Fumiyuki Hattori
- Innovative Regenerative Medicine, Graduate School of Medicine, Kansai Medical University, Osaka, Japan
- *Correspondence: Fumiyuki Hattori,
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