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Tsai JJ, Chiou SS, Chen PC, Chen CH, Lin PC, Tsai CY, Chuang WL, Hwang SJ, Chong IW, Liu LT. The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan. J Infect Public Health 2024; 17:102556. [PMID: 39388868 DOI: 10.1016/j.jiph.2024.102556] [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: 05/24/2024] [Revised: 09/13/2024] [Accepted: 09/24/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Omicron, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, entered Taiwan at the end of 2021. The Taiwanese government ended its "zero-COVID" policy in March 2022. Multiple coronavirus disease 2019 (COVID-19) outbreaks began in April 2022. We monitored the replacement of Omicron subvariants after BA.1/BA.2 and analyzed their correlation with COVID-19 outbreaks. METHODS We collected SARS-CoV-2 real-time qRTPCR-positive nasopharyngeal swabs from Kaohsiung Medical University Hospital (KMUH), Kaohsiung City, Taiwan, and performed sequencing for specimens exhibiting a cytopathic effect in Vero E6 cells to determine their clades and lineages. We analyzed the medical records of COVID-19 patients and identified hospitalization risk factor(s). We retrieved SARS-CoV-2 sequences identified in Taiwan from GISAID and analyzed their correlation with COVID-19 data from the Taiwan Centers for Disease Control. RESULTS We analyzed the phylogenesis of KMUH-47 to KMUH-104 (SARS-CoV-2 isolates identified herein) and all of the Omicron subvariants from BA.5 to XBB.1 (n = 1930). Age and comorbidities were hospitalization risk factors. Men generally exhibited a greater fatality rate than women. COVID-19-related deaths predominantly occurred in individuals over 70 years old. The COVID-19-related case fatality rate increased as nucleotide (NT) and amino acid (AA) substitutions increased. The number of COVID-19-related cases and deaths progressively decreased with each outbreak between August 2022 and October 2023. CONCLUSION Hospitalization was associated with age and the presence of comorbidities. COVID-19-related fatality was linked to sex, age, and the accumulation of NT and AA substitutions in emerging Omicron subvariants.
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Affiliation(s)
- Jih-Jin Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shyh-Shin Chiou
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Po-Chih Chen
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Hong Chen
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Miaoli County, Taiwan; National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Ping-Chang Lin
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ching-Yi Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Wan-Long Chuang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shang-Jyh Hwang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Inn-Wen Chong
- Department of Internal Medicine and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Pulmonary Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Li-Teh Liu
- Department of Medical Laboratory Science and Biotechnology, College of Medical Technology, Chung Hwa University of Medical Technology, Tainan, Taiwan.
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Chow N, Long T, Lee LK, Wong ITF, Lee AWT, Tam WY, Wong HFT, Leung JSL, Chow FWN, Luk KS, Ho AYM, Lam JYW, Yau MCY, Que TL, Yip KT, Chow VCY, Wong RCW, Mok BWY, Chen HL, Siu GKH. Transmission Patterns of Co-Circulation of Omicron Sub-Lineages in Hong Kong SAR, China, a City with Rigorous Social Distancing Measures, in 2022. Viruses 2024; 16:981. [PMID: 38932272 PMCID: PMC11209396 DOI: 10.3390/v16060981] [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: 04/05/2024] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
OBJECTIVE This study aimed to characterize the changing landscape of circulating SARS-CoV-2 lineages in the local community of Hong Kong throughout 2022. We examined how adjustments to quarantine arrangements influenced the transmission pattern of Omicron variants in a city with relatively rigorous social distancing measures at that time. METHODS In 2022, a total of 4684 local SARS-CoV-2 genomes were sequenced using the Oxford Nanopore GridION sequencer. SARS-CoV-2 consensus genomes were generated by MAFFT, and the maximum likelihood phylogeny of these genomes was determined using IQ-TREE. The dynamic changes in lineages were depicted in a time tree created by Nextstrain. Statistical analysis was conducted to assess the correlation between changes in the number of lineages and adjustments to quarantine arrangements. RESULTS By the end of 2022, a total of 83 SARS-CoV-2 lineages were identified in the community. The increase in the number of new lineages was significantly associated with the relaxation of quarantine arrangements (One-way ANOVA, F(5, 47) = 18.233, p < 0.001)). Over time, Omicron BA.5 sub-lineages replaced BA.2.2 and became the predominant Omicron variants in Hong Kong. The influx of new lineages reshaped the dynamics of Omicron variants in the community without fluctuating the death rate and hospitalization rate (One-way ANOVA, F(5, 47) = 2.037, p = 0.091). CONCLUSION This study revealed that even with an extended mandatory quarantine period for incoming travelers, it may not be feasible to completely prevent the introduction and subsequent community spread of highly contagious Omicron variants. Ongoing molecular surveillance of COVID-19 remains essential to monitor the emergence of new recombinant variants.
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Affiliation(s)
- Ning Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China; (N.C.); (L.-K.L.); (I.T.-F.W.); (A.W.-T.L.); (W.-Y.T.); (H.F.-T.W.); (J.S.-L.L.); (F.W.-N.C.)
| | - Teng Long
- Centre for Virology, Vaccinology and Therapeutics Limited, The University of Hong Kong, Hong Kong Special Administrative Region, China; (T.L.); (B.W.-Y.M.); (H.-l.C.)
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China; (N.C.); (L.-K.L.); (I.T.-F.W.); (A.W.-T.L.); (W.-Y.T.); (H.F.-T.W.); (J.S.-L.L.); (F.W.-N.C.)
| | - Ivan Tak-Fai Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China; (N.C.); (L.-K.L.); (I.T.-F.W.); (A.W.-T.L.); (W.-Y.T.); (H.F.-T.W.); (J.S.-L.L.); (F.W.-N.C.)
| | - Annie Wing-Tung Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China; (N.C.); (L.-K.L.); (I.T.-F.W.); (A.W.-T.L.); (W.-Y.T.); (H.F.-T.W.); (J.S.-L.L.); (F.W.-N.C.)
| | - Wing-Yin Tam
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China; (N.C.); (L.-K.L.); (I.T.-F.W.); (A.W.-T.L.); (W.-Y.T.); (H.F.-T.W.); (J.S.-L.L.); (F.W.-N.C.)
| | - Harmen Fung-Tin Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China; (N.C.); (L.-K.L.); (I.T.-F.W.); (A.W.-T.L.); (W.-Y.T.); (H.F.-T.W.); (J.S.-L.L.); (F.W.-N.C.)
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China; (N.C.); (L.-K.L.); (I.T.-F.W.); (A.W.-T.L.); (W.-Y.T.); (H.F.-T.W.); (J.S.-L.L.); (F.W.-N.C.)
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China; (N.C.); (L.-K.L.); (I.T.-F.W.); (A.W.-T.L.); (W.-Y.T.); (H.F.-T.W.); (J.S.-L.L.); (F.W.-N.C.)
| | - Kristine Shik Luk
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China; (K.S.L.); (A.Y.-M.H.)
| | - Alex Yat-Man Ho
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, China; (K.S.L.); (A.Y.-M.H.)
| | - Jimmy Yiu-Wing Lam
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong Special Administrative Region, China; (J.Y.-W.L.); (M.C.-Y.Y.)
| | - Miranda Chong-Yee Yau
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong Special Administrative Region, China; (J.Y.-W.L.); (M.C.-Y.Y.)
| | - Tak-Lun Que
- Department of Clinical Pathology, Tuen Mun Hospital, Hong Kong Special Administrative Region, China; (T.-L.Q.); (K.-T.Y.)
| | - Kam-Tong Yip
- Department of Clinical Pathology, Tuen Mun Hospital, Hong Kong Special Administrative Region, China; (T.-L.Q.); (K.-T.Y.)
| | - Viola Chi-Ying Chow
- Department of Microbiology, Prince of Wales Hospital, Hong Kong Special Administrative Region, China; (V.C.-Y.C.); (R.C.-W.W.)
| | - River Chun-Wai Wong
- Department of Microbiology, Prince of Wales Hospital, Hong Kong Special Administrative Region, China; (V.C.-Y.C.); (R.C.-W.W.)
| | - Bobo Wing-Yee Mok
- Centre for Virology, Vaccinology and Therapeutics Limited, The University of Hong Kong, Hong Kong Special Administrative Region, China; (T.L.); (B.W.-Y.M.); (H.-l.C.)
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hong-lin Chen
- Centre for Virology, Vaccinology and Therapeutics Limited, The University of Hong Kong, Hong Kong Special Administrative Region, China; (T.L.); (B.W.-Y.M.); (H.-l.C.)
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China; (N.C.); (L.-K.L.); (I.T.-F.W.); (A.W.-T.L.); (W.-Y.T.); (H.F.-T.W.); (J.S.-L.L.); (F.W.-N.C.)
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Zhu C, Pang S, Liu J, Duan Q. Current Progress, Challenges and Prospects in the Development of COVID-19 Vaccines. Drugs 2024; 84:403-423. [PMID: 38652356 DOI: 10.1007/s40265-024-02013-8] [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] [Accepted: 02/25/2024] [Indexed: 04/25/2024]
Abstract
The COVID-19 pandemic has resulted in over 772 million confirmed cases, including nearly 7 million deaths, according to the World Health Organization (WHO). Leveraging rapid development, accelerated vaccine approval processes, and large-scale production of various COVID-19 vaccines using different technical platforms, the WHO declared an end to the global health emergency of COVID-19 on May 5, 2023. Current COVID-19 vaccines encompass inactivated, live attenuated, viral vector, protein subunit, nucleic acid (DNA and RNA), and virus-like particle (VLP) vaccines. However, the efficacy of these vaccines is diminishing due to the constant mutation of SARS-CoV-2 and the heightened immune evasion abilities of emerging variants. This review examines the impact of the COVID-19 pandemic, the biological characteristics of the virus, and its diverse variants. Moreover, the review underscores the effectiveness, advantages, and disadvantages of authorized COVID-19 vaccines. Additionally, it analyzes the challenges, strategies, and future prospects of developing a safe, broad-spectrum vaccine that confers sufficient and sustainable immune protection against new variants of SARS-CoV-2. These discussions not only offer insight for the development of next-generation COVID-19 vaccines but also summarize experiences for combating future emerging viruses.
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Affiliation(s)
- Congrui Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510000, China
| | - Shengmei Pang
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Jiaqi Liu
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Qiangde Duan
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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Balupuri A, Kim JM, Choi KE, No JS, Kim IH, Rhee JE, Kim EJ, Kang NS. Comparative Computational Analysis of Spike Protein Structural Stability in SARS-CoV-2 Omicron Subvariants. Int J Mol Sci 2023; 24:16069. [PMID: 38003257 PMCID: PMC10671153 DOI: 10.3390/ijms242216069] [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: 10/04/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The continuous emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with multiple spike (S) protein mutations pose serious threats to current coronavirus disease 2019 (COVID-19) therapies. A comprehensive understanding of the structural stability of SARS-CoV-2 variants is vital for the development of effective therapeutic strategies as it can offer valuable insights into their potential impact on viral infectivity. S protein mediates a virus' attachment to host cells by binding to angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain (RBD), and mutations in this protein can affect its stability and binding affinity. We analyzed S protein structural stability in various Omicron subvariants computationally. Notably, the S protein sequences analyzed in this work were obtained directly from our own sample collection. We evaluated the binding free energy between S protein and ACE2 in several complex forms. Additionally, we measured distances between the RBD of each chain in S protein to analyze conformational changes. Unlike most of the prior studies, we analyzed full-length S protein-ACE2 complexes instead of only RBD-ACE2 complexes. Omicron subvariants including BA.1, BA.2, BA.2.12.1, BA.4/BA.5, BA.2.75, BA.2.75_K147E, BA.4.6 and BA.4.6_N658S showed enhanced stability compared to wild type, potentially due to distinct S protein mutations. Among them, BA.2.75 and BA.4.6_N658S exhibited the highest and lowest level of stability, respectively.
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Affiliation(s)
- Anand Balupuri
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (A.B.); (K.-E.C.)
| | - Jeong-Min Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Kwang-Eun Choi
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (A.B.); (K.-E.C.)
| | - Jin Sun No
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Il-Hwan Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Jee Eun Rhee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Eun-Jin Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Nam Sook Kang
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (A.B.); (K.-E.C.)
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Chellapandian H, Jeyachandran S. Efficacy of Omicron variant as a natural vaccine for COVID19 & probabilities to produce synthetic vaccines. J Infect Public Health 2023; 16:1460-1461. [PMID: 37531705 DOI: 10.1016/j.jiph.2023.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/30/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023] Open
Affiliation(s)
- Hethesh Chellapandian
- Lab in Biotechnology & Biosignal transduction, Department of Orthodontics, Saveetha Dental College and Hospitals, Chennai, Tamil Nadu, India
| | - Sivakamavalli Jeyachandran
- Lab in Biotechnology & Biosignal transduction, Department of Orthodontics, Saveetha Dental College and Hospitals, Chennai, Tamil Nadu, India.
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Cano AV, Gitschlag BL, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. Mutation bias and the predictability of evolution. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220055. [PMID: 37004719 PMCID: PMC10067271 DOI: 10.1098/rstb.2022.0055] [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: 11/01/2022] [Accepted: 02/16/2023] [Indexed: 04/04/2023] Open
Abstract
Predicting evolutionary outcomes is an important research goal in a diversity of contexts. The focus of evolutionary forecasting is usually on adaptive processes, and efforts to improve prediction typically focus on selection. However, adaptive processes often rely on new mutations, which can be strongly influenced by predictable biases in mutation. Here, we provide an overview of existing theory and evidence for such mutation-biased adaptation and consider the implications of these results for the problem of prediction, in regard to topics such as the evolution of infectious diseases, resistance to biochemical agents, as well as cancer and other kinds of somatic evolution. We argue that empirical knowledge of mutational biases is likely to improve in the near future, and that this knowledge is readily applicable to the challenges of short-term prediction. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
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Affiliation(s)
- Alejandro V. Cano
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bryan L. Gitschlag
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Hana Rozhoňová
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Arlin Stoltzfus
- Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Rockville, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - David M. McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joshua L. Payne
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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T. Campbell J, Bennett-Brown M, S. Marcotte A, M. Kaufman E, Moscovici Z, R. Adams O, Lovins S, R. Garcia J, N. Gesselman A. American Singles' Attitudes Toward Future Romantic/Sexual Partners' COVID-19 Vaccination Status: Evidence for both Vigilance and Indifference in a National Sample. SEXUALITY & CULTURE 2023; 27:1-24. [PMID: 37360016 PMCID: PMC10196300 DOI: 10.1007/s12119-023-10097-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/07/2023] [Indexed: 06/28/2023]
Abstract
Around 142 million American adults are currently single; at least half of these singles want to pursue a romantic partner. Romantic dating can involve exposure to numerous people. Thus, dating can significantly impact pathogen exposure risk. In a demographically-representative cross-sectional survey conducted in 2021 (N = 5,000), we examined U.S. American singles' COVID-19 vaccination status, assessed their preferences around a potential partner's COVID-19 vaccination status, and identified demographic subgroups of singles particularly opposed to or indifferent to a partner being vaccinated against COVID-19. Our results showed 65% of participants were fully vaccinated, 10% were partially vaccinated, and 26% were unvaccinated against COVID-19. With regards to partner preferences, half wanted a vaccinated partner; 18.9% wanted a vaccinated partner but would make exceptions; 6.1% wanted an unvaccinated partner; and 25% reported that they did not care about their dating partner's vaccination status. Partner preferences were largely aligned with participants' own vaccination status, such that vaccinated participants preferred vaccinated partners. However, those preferring unvaccinated partners-or those willing to make exceptions for a partner-were most likely to identify as men, younger in age, a political affiliation outside of the two-party political system, a gender or sexual minority, or as a racial minority (i.e., Black/African-American or South Asian). Additionally, participants who were employed (vs. unemployed) were more likely to make exceptions for or prefer an unvaccinated partner. These results suggest that singles prefer homophily in COVID-19 vaccine status, and that minoritized subgroups of singles are more likely to maintain a social network including unvaccinated close others. Supplementary Information The online version contains supplementary material available at 10.1007/s12119-023-10097-9.
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Affiliation(s)
| | - Magaret Bennett-Brown
- Indiana University Bloomington, Bloomington, USA
- Texas Tech University, Lubbock, Texas USA
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Alshanbari HM, Iftikhar H, Khan F, Rind M, Ahmad Z, El-Bagoury AAAH. On the Implementation of the Artificial Neural Network Approach for Forecasting Different Healthcare Events. Diagnostics (Basel) 2023; 13:diagnostics13071310. [PMID: 37046528 PMCID: PMC10093335 DOI: 10.3390/diagnostics13071310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/22/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
The rising number of confirmed cases and deaths in Pakistan caused by the coronavirus have caused problems in all areas of the country, not just healthcare. For accurate policy making, it is very important to have accurate and efficient predictions of confirmed cases and death counts. In this article, we use a coronavirus dataset that includes the number of deaths, confirmed cases, and recovered cases to test an artificial neural network model and compare it to different univariate time series models. In contrast to the artificial neural network model, we consider five univariate time series models to predict confirmed cases, deaths count, and recovered cases. The considered models are applied to Pakistan’s daily records of confirmed cases, deaths, and recovered cases from 10 March 2020 to 3 July 2020. Two statistical measures are considered to assess the performances of the models. In addition, a statistical test, namely, the Diebold and Mariano test, is implemented to check the accuracy of the mean errors. The results (mean error and statistical test) show that the artificial neural network model is better suited to predict death and recovered coronavirus cases. In addition, the moving average model outperforms all other confirmed case models, while the autoregressive moving average is the second-best model.
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Affiliation(s)
- Huda M. Alshanbari
- Department of Mathematical Sciences, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
- Correspondence:
| | - Hasnain Iftikhar
- Department of Mathematics, City University of Science and Information Technology, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
- Department of Statistics, Quaid-i-Azam University, Islamabad 44000, Pakistan
| | - Faridoon Khan
- Department of Economics, Institute of Development Economics, Islamabad 44000, Pakistan
| | - Moeeba Rind
- Department of Education, Abasyn University, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
- Department of Psychology, University of Peshawar, Peshawar 25120, Khyber Pakhtunkhwa, Pakistan
| | - Zubair Ahmad
- Department of Statistics, Quaid-i-Azam University, Islamabad 44000, Pakistan
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Tallei TE, Alhumaid S, AlMusa Z, Fatimawali, Kusumawaty D, Alynbiawi A, Alshukairi AN, Rabaan AA. Update on the omicron sub-variants BA.4 and BA.5. Rev Med Virol 2023; 33:e2391. [PMID: 36017597 PMCID: PMC9539252 DOI: 10.1002/rmv.2391] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 01/28/2023]
Abstract
Several nations have recently begun to relax their public health protocols, particularly regarding the use of face masks when engaging in outdoor activities. This is because there has been a general trend towards fewer cases of coronavirus disease 2019 (COVID-19). However, new Omicron sub-variants (designated BA.4 and BA.5) have recently emerged. These two subvariants are thought to be the cause of an increase in COVID-19 cases in South Africa, the United States, and Europe. They have also begun to spread throughout Asia. They evolved from the Omicron lineage with characteristics that make them even more contagious and which allow them to circumvent immunity from a previous infection or vaccination. This article reviews a number of scientific considerations about these new variants, including their apparently reduced clinical severity.
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Affiliation(s)
- Trina Ekawati Tallei
- Department of BiologyFaculty of Mathematics and Natural SciencesSam Ratulangi UniversityManadoNorth SulawesiIndonesia
| | - Saad Alhumaid
- Administration of Pharmaceutical CareAl‐Ahsa Health ClusterMinistry of HealthAl‐AhsaSaudi Arabia
| | - Zainab AlMusa
- Infectious Disease SectionInternal Medicine DepartmentKing Fahad Specialist HospitalDammamSaudi Arabia
| | - Fatimawali
- Pharmacy Study ProgramFaculty of Mathematics and Natural SciencesSam Ratulangi UniversityManadoNorth SulawesiIndonesia
| | - Diah Kusumawaty
- Department of BiologyFaculty of Mathematics and Natural Sciences EducationUniversitas Pendidikan IndonesiaBandungIndonesia
| | - Ahlam Alynbiawi
- Infectious Diseases SectionMedical Specialties DepartmentKing Fahad Medical CityRiyadhSaudi Arabia
| | - Abeer N. Alshukairi
- Department of MedicineKing Faisal Specialist Hospital and Research CenterJeddahSaudi Arabia
- College of MedicineAlfaisal UniversityRiyadhSaudi Arabia
| | - Ali A. Rabaan
- College of MedicineAlfaisal UniversityRiyadhSaudi Arabia
- Molecular Diagnostic LaboratoryJohns Hopkins Aramco HealthcareDhahranSaudi Arabia
- Department of Public Health and NutritionThe University of HaripurHaripurPakistan
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Diani S, Leonardi E, Cavezzi A, Ferrari S, Iacono O, Limoli A, Bouslenko Z, Natalini D, Conti S, Mantovani M, Tramonte S, Donzelli A, Serravalle E. SARS-CoV-2-The Role of Natural Immunity: A Narrative Review. J Clin Med 2022; 11:6272. [PMID: 36362500 PMCID: PMC9655392 DOI: 10.3390/jcm11216272] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Both natural immunity and vaccine-induced immunity to COVID-19 may be useful to reduce the mortality/morbidity of this disease, but still a lot of controversy exists. AIMS This narrative review analyzes the literature regarding these two immunitary processes and more specifically: (a) the duration of natural immunity; (b) cellular immunity; (c) cross-reactivity; (d) the duration of post-vaccination immune protection; (e) the probability of reinfection and its clinical manifestations in the recovered patients; (f) the comparisons between vaccinated and unvaccinated as to the possible reinfections; (g) the role of hybrid immunity; (h) the effectiveness of natural and vaccine-induced immunity against Omicron variant; (i) the comparative incidence of adverse effects after vaccination in recovered individuals vs. COVID-19-naïve subjects. MATERIAL AND METHODS through multiple search engines we investigated COVID-19 literature related to the aims of the review, published since April 2020 through July 2022, including also the previous articles pertinent to the investigated topics. RESULTS nearly 900 studies were collected, and 246 pertinent articles were included. It was highlighted that the vast majority of the individuals after suffering from COVID-19 develop a natural immunity both of cell-mediated and humoral type, which is effective over time and provides protection against both reinfection and serious illness. Vaccine-induced immunity was shown to decay faster than natural immunity. In general, the severity of the symptoms of reinfection is significantly lower than in the primary infection, with a lower degree of hospitalizations (0.06%) and an extremely low mortality. CONCLUSIONS this extensive narrative review regarding a vast number of articles highlighted the valuable protection induced by the natural immunity after COVID-19, which seems comparable or superior to the one induced by anti-SARS-CoV-2 vaccination. Consequently, vaccination of the unvaccinated COVID-19-recovered subjects may not be indicated. Further research is needed in order to: (a) measure the durability of immunity over time; (b) evaluate both the impacts of Omicron BA.5 on vaccinated and healed subjects and the role of hybrid immunity.
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Affiliation(s)
- Sara Diani
- School of Musictherapy, Université Européenne Jean Monnet, 35129 Padova, Italy
| | | | | | | | - Oriana Iacono
- Physical Medicine and Rehabilitation Department, Mirandola Hospital, 41037 Mirandola, Italy
| | - Alice Limoli
- ARPAV (Regional Agency for the Environment Protection), 31100 Treviso, Italy
| | - Zoe Bouslenko
- Cardiology Department, Valdese Hospital, 10100 Torino, Italy
| | | | | | | | - Silvano Tramonte
- Environment and Health Commission, National Bioarchitecture Institute, 20121 Milano, Italy
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11
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Shao J, Fan R, Hu J, Zhang T, Lee C, Huang X, Wang F, Liang H, Jin Y, Jiang Y, Gu Y, Huang G. Clinical Progression and Outcome of Hospitalized Patients Infected with SARS-CoV-2 Omicron Variant in Shanghai, China. Vaccines (Basel) 2022; 10:vaccines10091409. [PMID: 36146487 PMCID: PMC9503563 DOI: 10.3390/vaccines10091409] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 01/08/2023] Open
Abstract
Background: Studies on the Omicron variant infection have generally been restricted to descriptions of its initial clinical and epidemiological characteristics. We investigated the timeline-related progression and clinical outcome in hospitalized individuals with the Omicron variant. Methods: We conducted a retrospective, single-centered study including 226 laboratory-confirmed cases with the Omicron variant between 6 April and 11 May 2022 in Shanghai, China. The final date of follow-up was 30 May 2022. Results: Among 226 enrolled patients, the median age was 52 years, and 118 (52.2%) were female. The duration from onset of symptoms to hospitalization was 3 days (interquartile range (IQR): 2–4 days) for symptomatic patients. Cough occurred in 168 patients (74.3%). The median interval to negative reverse-transcriptase PCR tests of nasopharynx swab was 10 days ((IQR): 8–13 days). No radiographic progressions were found in 196 patients on the 7th day after onset of symptoms. The median duration of fever in all participants was 5 days (IQR: 4–6 days). The median PCR conversion time of Paxlovid-treated patients was 8 days (IQR: 7–10 days) compared with that of a traditional Chinese herb medicine lianhuaqingwen (10 days, IQR: 8–13 days) (p = 0.00056). Booster vaccination can significantly decrease the severity of Omicron infection when compared with unvaccinated patients (p = 0.009). In multivariate logistic analysis, erythrocyte sedimentation rate (ESR) (OR = 1.05) was independently related to the severity of the infection. Conclusions: The majority of clinical symptoms of Omicron infection were not severe. Early and aggressive administration of Paxlovid can significantly reduce the PCR conversion time. Booster vaccination should also be highly recommended in the population over 14 years old.
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Affiliation(s)
- Jiasheng Shao
- Department of Infectious Diseases and Immunology, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201899, China
| | - Rong Fan
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität, 01307 Dresden, Germany
| | - Jianrong Hu
- Department of Respiratory Medicine, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201899, China
| | - Tiejun Zhang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai 200032, China
| | - Catherine Lee
- College of Public Health, University of Georgia, Athens, GA 30602, USA
| | - Xuyuan Huang
- Department of Urology, Renji Hospital, Shanghai Jiaotong University, Shanghai 200127, China
| | - Fei Wang
- Department of Intensive Care Unit, Jiading District Central Hospital, Shanghai 201899, China
| | - Haiying Liang
- Department of Respiratory Medicine, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201899, China
| | - Ye Jin
- Department of Respiratory Medicine, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201899, China
| | - Ying Jiang
- Department of Respiratory Medicine, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai 201899, China
| | - Yanhua Gu
- Department of Nursing, Jiading District Central Hospital, Shanghai 201899, China
| | - Gang Huang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
- Correspondence: ; Tel.: +86-021-65881330
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Chakrabartty I, Khan M, Mahanta S, Chopra H, Dhawan M, Choudhary OP, Bibi S, Mohanta YK, Emran TB. Comparative overview of emerging RNA viruses: Epidemiology, pathogenesis, diagnosis and current treatment. Ann Med Surg (Lond) 2022; 79:103985. [PMID: 35721786 PMCID: PMC9188442 DOI: 10.1016/j.amsu.2022.103985] [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: 04/30/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
From many decades, emerging infections have threatened humanity. The pandemics caused by different CoVs have already claimed and will continue to claim millions of lives. The SARS, Ebola, MERS epidemics and the most recent emergence of COVID-19 pandemic have threatened populations across borders. Since a highly pathogenic CoV has been evolved into the human population in the twenty-first century known as SARS, scientific advancements and innovative methods to tackle these viruses have increased in order to improve response preparedness towards the unpredictable threat posed by these rapidly emerging pathogens. Recently published review articles on SARS-CoV-2 have mainly focused on its pathogenesis, epidemiology and available treatments. However, in this review, we have done a systematic comparison of all three CoVs i.e., SARS, MERS and SARS-CoV-2 along with Ebola and Zika in terms of their epidemiology, virology, clinical features and current treatment strategies. This review focuses on important emerging RNA viruses starting from Zika, Ebola and the CoVs which include SARS, MERS and SARS-CoV-2. Each of these viruses has been elaborated on the basis of their epidemiology, virulence, transmission and treatment. However, special attention has been given to SARS-CoV-2 and the disease caused by it i.e., COVID-19 due to current havoc caused worldwide. At the end, insights into the current understanding of the lessons learned from previous epidemics to combat emerging CoVs have been described. The travel-related viral spread, the unprecedented nosocomial outbreaks and the high case-fatality rates associated with these highly transmissible and pathogenic viruses highlight the need for new prophylactic and therapeutic actions which include but are not limited to clinical indicators, contact tracing, and laboratory investigations as important factors that need to be taken into account in order to arrive at the final conclusion. Recently published review articles on SARS-CoV-2 have mainly focused on its pathogenesis, epidemiology and available treatments. The pandemics caused by different CoVs have already claimed and will continue to claim millions of lives. This review focuses on important emerging RNA viruses starting from Zika, Ebola and the CoVs which include SARS, MERS and SARS-CoV-2. Globally, numerous studies and researchers have recently started fighting this virus.
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Affiliation(s)
- Ishani Chakrabartty
- Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), 9th Mile, Techno City, Baridua, Ri-Bhoi 793101, Meghalaya, India
| | - Maryam Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P, India
| | - Saurov Mahanta
- National Institute of Electronics and Information Technology (NIELIT), Guwahati Centre Guwahati, 781008, Assam, India
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.,Trafford College, Altrincham, Manchester, WA14 5PQ, UK
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy and Histology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, India
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan.,Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Yugal Kishore Mohanta
- Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), 9th Mile, Techno City, Baridua, Ri-Bhoi 793101, Meghalaya, India
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
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13
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Understanding the omicron variant (B.1.1.529) of SARS-CoV-2: Mutational impacts, concerns, and the possible solutions. Ann Med Surg (Lond) 2022; 78:103737. [PMID: 35571678 PMCID: PMC9078452 DOI: 10.1016/j.amsu.2022.103737] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 01/18/2023] Open
Abstract
Despite many nations' best efforts to contain the so-called COVID-19 pandemic, the emergence of the SARS-CoV-2 Omicron strain (B.1.1.529) has been identified as a serious concern. After more than two years of COVID-19 pandemic and more than a year of worldwide vaccination efforts, the globe will not be free of COVID-19 variants such as Delta and Omicron variants. According to current statistics, the Omicron variant has more than 30 mutations when contrasted to other VOCs such as Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). High numbers of changes, particularly in the spike protein (S-Protein), raise worries about the virus's capacity to resist pre-existing immunity acquired by vaccination or spontaneous infection and antibody-based therapy. The Omicron variant raised international concerns, resuming travel bans and coming up with many questions about its severity, transmissibility, testing, detection, and vaccines efficiency against it. Additionally, inadequate health care infrastructures and many immunocompromised individuals increase the infection susceptibility. The current status of low vaccination rates will play a significant role in omicron spreading and create a fertile ground for producing new variants. As a result, this article emphasizes the mutational changes and their consequences. In addition, the potential preventing measures have been examined in detail. In South Africa, WHO designated the first cases of the SARS-CoV-2 Omicron variant (B.1.1.529). This variation is notable for having an extremely high number of spike protein mutations. Omicron has about 50 mutations, particularly 32 spike protein mutations. Omicron considers the most common variant in South Africa as an alternative to Delta.
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