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Sila T, Surasombatpattana S, Rajborirug S, Laochareonsuk W, Choochuen P, Kongkamol C, Ingviya T, Prompat N, Mahasirimongkol S, Sangkhathat S, Aiewsakun P. SARS-CoV-2 variant with the spike protein mutation F306L in the southern border provinces of Thailand. Sci Rep 2024; 14:7729. [PMID: 38565881 PMCID: PMC10987673 DOI: 10.1038/s41598-024-56646-6] [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: 05/15/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
The southernmost part of Thailand is a unique and culturally diverse region that has been greatly affected by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak during the coronavirus disease-2019 pandemic. To gain insights into this situation, we analyzed 1942 whole-genome sequences of SARS-CoV-2 obtained from the five southernmost provinces of Thailand between April 2021 and March 2022, together with those publicly available in the Global Initiative on Sharing All Influenza Data database. Our analysis revealed evidence for transboundary transmissions of the virus in and out of the five southernmost provinces during the study period, from both domestic and international sources. The most prevalent viral variant in our sequence dataset was the Delta B.1.617.2.85 variant, also known as the Delta AY.85 variant, with many samples carrying a non-synonymous mutation F306L in their spike protein. Protein-protein docking and binding interface analyses suggested that the mutation may enhance the binding between the spike protein and host cell receptor protein angiotensin-converting enzyme 2, and we found that the mutation was significantly associated with an increased fatality rate. This mutation has also been observed in other SARS-CoV-2 variants, suggesting that it is of particular interest and should be monitored.
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Affiliation(s)
- Thanit Sila
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Smonrapat Surasombatpattana
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Songyos Rajborirug
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Wison Laochareonsuk
- Division of Surgery, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Pongsakorn Choochuen
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Chanon Kongkamol
- Department of Family Medicine and Preventive Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Thammasin Ingviya
- Department of Family Medicine and Preventive Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Napat Prompat
- Faculty of Medical Technology, Medical of Technology Service Center, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Surakameth Mahasirimongkol
- Department of Medical Sciences, Genetics Center, Medical Life Sciences Institute, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Surasak Sangkhathat
- Division of Surgery, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
| | - Pakorn Aiewsakun
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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Kim SH, Wi YM, Moon C, Kang JM, Kim M, Kim J, Kim JM, Seok H, Shi HJ, Lee SJ, Lee JY, Jeong SJ, Choe PG, Huh K, Lee SO, Kim SI. Recommendations for SARS-CoV-2 testing and organ procurement from deceased donors in the Republic of Korea. KOREAN JOURNAL OF TRANSPLANTATION 2023; 37:145-154. [PMID: 37614183 PMCID: PMC10583974 DOI: 10.4285/kjt.23.0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/20/2023] [Accepted: 07/20/2023] [Indexed: 08/25/2023] Open
Abstract
We present a summary of the evidence on testing for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and organ procurement from deceased donors and provide recommendations based on current clinical data and the guidelines from major transplant organizations. Because of the limited historical experience with coronavirus disease 2019 (COVID-19), certain recommendations in this document are based on theoretical rationales rather than clinical data. The recommendations in this manuscript may be subject to revision as subsequent clinical studies provide definitive evidence regarding COVID-19 in organ procurement.
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Affiliation(s)
- Si-Ho Kim
- Division of Infectious Diseases, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
| | - Yu Mi Wi
- Division of Infectious Diseases, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
| | - Chisook Moon
- Division of Infectious Diseases, Department of Internal Medicine, Inje University Busan Paik Hospital, College of Medicine, Inje University, Busan, Korea
| | - Ji-Man Kang
- Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Minhwa Kim
- Korea Organ Donation Agency, Seoul, Korea
| | - Jungok Kim
- Division of Infectious Diseases, Chungnam National University Sejong Hospital, Sejong, Korea
| | - Jong Man Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyeri Seok
- Division of Infectious Diseases, Department of Medicine, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Korea
| | - Hye Jin Shi
- Division of Infectious Diseases, Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
| | - Su Jin Lee
- Division of Infectious Disease, Department of Internal Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Ji Yeon Lee
- Division of Infectious Diseases, Keimyung University Dongsan Hospital, Keimyung University School of Medicine, Daegu, Korea
| | - Su Jin Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kyungmin Huh
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sang-Oh Lee
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Il Kim
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
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High-Throughput COVID-19 Testing of Naso-Oropharyngeal Swabs Using a Sensitive Extraction-Free Sample Preparation Method. Microbiol Spectr 2022; 10:e0135822. [PMID: 35950846 PMCID: PMC9430511 DOI: 10.1128/spectrum.01358-22] [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
High-throughput diagnostic assays are required for large-scale population testing for severe acute respiratory coronavirus 2 (SARS-CoV-2). The gold standard technique for SARS-CoV-2 detection in nasopharyngeal swab specimens is nucleic acid extraction followed by real-time reverse transcription-PCR. Two high-throughput commercial extraction and detection systems are used routinely in our laboratory: the Roche cobas SARS-CoV-2 assay (cobas) and the Roche MagNA Pure 96 system combined with the SpeeDx PlexPCR SARS-CoV-2 assay (Plex). As an alternative to more costly instrumentation, or tedious sample pooling to increase throughput, we developed a high-throughput extraction-free sample preparation method for naso-oropharyngeal swabs using the PlexPCR SARS-CoV-2 assay (Direct). A collection of SARS-CoV-2-positive (n = 185) and -negative (n = 354) naso-oropharyngeal swabs in transport medium were tested in parallel to compare Plex to Direct. The overall agreement comparing the qualitative outcomes was 99.3%. The mean cycle of quantification (Cq) increase and corresponding mean reduction in viral load for Direct ORF1ab and RdRp compared to Plex was 3.11 Cq (-0.91 log10 IU/mL) and 4.78 Cq (-1.35 log10 IU/mL), respectively. We also compared Direct to a four-sample pool by combining each positive sample (n = 185) with three SARS-CoV-2-negative samples extracted with MagNA Pure 96 and tested with the PlexPCR SARS-CoV-2 assay (Pool). Although less sensitive than Plex or Pool, the Direct method is a sufficiently sensitive and viable approach to increase our throughput by 12,032 results per day. Combining cobas, Plex, and Direct, an overall throughput of 19,364 results can be achieved in a 24-h period. IMPORTANCE Laboratories have experienced extraordinary demand globally for reagents, consumables, and instrumentation, while facing unprecedented testing demand needed for the diagnosis of SARS-CoV-2 infection. A major bottleneck in testing throughput is the purification of viral RNA. Extraction-based methods provide the greatest yield and purity of RNA for downstream PCR. However, these techniques are expensive, time-consuming, and depend on commercial availability of consumables. Extraction-free methods offer an accessible and cost-effective alternative for sample preparation. However, extraction-free methods often lack sensitivity compared to extraction-based methods. We describe a sensitive extraction-free protocol based on a simple purification step using a chelating resin, combined with proteinase K and thermal treatment. We compare the sensitivity qualitatively and quantitatively to a well-known commercial extraction-based system, using a PCR assay calibrated to the 1st WHO international standard for SARS-CoV-2 RNA. This method entails high throughput and is suitable for all laboratories, particularly in jurisdictions where access to instrumentation and reagents is problematic.
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