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Singh UB, Deb S, Rani L, Gupta R, Verma S, Kumari L, Bhardwaj D, Bala K, Ahmed J, Gaurav S, Perumalla S, Nizam M, Mishra A, Stephenraj J, Shukla J, Nayer J, Aggarwal P, Kabra M, Ahuja V, Chaudhry R, Sinha S, Guleria R. Phylogeny and evolution of SARS-CoV-2 during Delta and Omicron variant waves in India. J Biomol Struct Dyn 2024; 42:4769-4781. [PMID: 37318006 DOI: 10.1080/07391102.2023.2222832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/02/2023] [Indexed: 06/16/2023]
Abstract
SARS-CoV-2 evolution has continued to generate variants, responsible for new pandemic waves locally and globally. Varying disease presentation and severity has been ascribed to inherent variant characteristics and vaccine immunity. This study analyzed genomic data from 305 whole genome sequences from SARS-CoV-2 patients before and through the third wave in India. Delta variant was reported in patients without comorbidity (97%), while Omicron BA.2 was reported in patients with comorbidity (77%). Tissue adaptation studies brought forth higher propensity of Omicron variants to bronchial tissue than lung, contrary to observation in Delta variants from Delhi. Study of codon usage pattern distinguished the prevalent variants, clustering them separately, Omicron BA.2 isolated in February grouped away from December strains, and all BA.2 after December acquired a new mutation S959P in ORF1b (44.3% of BA.2 in the study) indicating ongoing evolution. Loss of critical spike mutations in Omicron BA.2 and gain of immune evasion mutations including G142D, reported in Delta but absent in BA.1, and S371F instead of S371L in BA.1 could explain very brief period of BA.1 in December 2021, followed by complete replacement by BA.2. Higher propensity of Omicron variants to bronchial tissue, probably ensured increased transmission while Omicron BA.2 became the prevalent variant possibly due to evolutionary trade-off. Virus evolution continues to shape the epidemic and its culmination.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Urvashi B Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sushanta Deb
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Lata Rani
- Central Core Research Facility, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Sunita Verma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Lata Kumari
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Deepika Bhardwaj
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Kiran Bala
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jawed Ahmed
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sudesh Gaurav
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sowjanya Perumalla
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Md Nizam
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Anwita Mishra
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - J Stephenraj
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jyoti Shukla
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jamshed Nayer
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Praveen Aggarwal
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Department of Paediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Subrata Sinha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary, Critical Care & Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
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Ogger PP, Martín MG, Jang S, Zhou J, Brown J, Sukhova K, Furnon W, Patel AH, Cowton V, Palmarini M, Barclay WS, Johansson C. SARS-CoV-2 strains bearing Omicron BA.1 spike replicate in C57BL/6 mice. Front Immunol 2024; 15:1383612. [PMID: 38742107 PMCID: PMC11089223 DOI: 10.3389/fimmu.2024.1383612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction SARS-CoV-2, the cause of the COVID pandemic, is an RNA virus with a high propensity to mutate. Successive virus variants, including variants of concern (VOC), have emerged with increased transmission or immune escape. The original pandemic virus and early variants replicated poorly, if at all, in mice at least partly due to a mismatch between the receptor binding domain on the viral spike protein and the murine angiotensin converting enzyme 2 (ACE2). Omicron VOC emerged in late 2021 harboring > 50 new mutations, 35 of them in the spike protein. This variant resulted in a very large wave of infections, even in the face of prior immunity, albeit being inherently less severe than earlier variants. Reflecting the lower severity reported in humans, Omicron displayed attenuated infection in hamsters and also in the K18-hACE2 mouse model. K18-hACE2 mice express both the human ACE2 as well as the endogenous mouse ACE2. Methods Here we infected hACE2 knock-in mice that express only human ACE2 and no murine ACE2, or C57BL/6 wildtype mice with SARS-CoV-2 D614G (first-wave isolate), Delta or Omicron BA.1 variants and assessed infectivity and downstream innate immune responses. Results While replication of SARS-CoV-2 Omicron was lower in the lungs of hACE2 knock-in mice compared with SARS-CoV-2 D614G and VOC Delta, it replicated more efficiently than the earlier variants in C57BL/6 wildtype mice. This opens the opportunity to test the effect of host genetics on SARS-CoV-2 infections in wildtype mice. As a proof of principle, we tested Omicron infection in mice lacking expression of the interferon-alpha receptor-1 (IFNAR1). In these mice we found that loss of type I IFN receptor signaling resulted in higher viral loads in the lungs were detected. Finally, using a chimeric virus of first wave SARS-CoV-2 harboring the Omicron spike protein, we show that Omicron spike increase infection of C57BL/6 wildtype mice, but non-spike genes of Omicron confer attenuation of viral replication. Discussion Since this chimeric virus efficiently infected C57BL/6 wildtype mice, and replicated in their lungs, our findings illustrate a pathway for genetic mapping of virushost interactions during SARS-CoV-2 infection.
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Affiliation(s)
- Patricia P. Ogger
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Minerva Garcia Martín
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Soyeon Jang
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jie Zhou
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jonathan Brown
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Cecilia Johansson
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
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Teixeira DG, Rodrigues-Neto JF, da Cunha DCS, Jeronimo SMB. Understanding SARS-CoV-2 spike glycoprotein clusters and their impact on immunity of the population from Rio Grande do Norte, Brazil. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105556. [PMID: 38242186 DOI: 10.1016/j.meegid.2024.105556] [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: 11/15/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
SARS-CoV-2 genome underwent mutations since it started circulating within the human population. The aim of this study was to understand the fluctuation of the spike clusters concomitant to the population immunity either due to natural infection and/or vaccination in a state of Brazil that had both high rate of natural infection and vaccination coverage. A total of 1725 SARS-CoV-2 sequences from the state of Rio Grande do Norte, Brazil, were retrieved from GISAID and subjected to cluster analysis. Immunoinformatics were used to predict T- and B-cell epitopes, followed by simulation to estimate either pro- or anti-inflammatory responses and to correlate with circulating variants. From March 2020 to June 2022, the state of Rio Grande do Norte reported 579,931 COVID-19 cases with a 1.4% fatality rate across the three major waves: May-Sept 2020, Feb-Aug 2021, and Jan-Mar 2022. Cluster 0 variants (wild type strain, Zeta) were prevalent in the first wave and Delta (AY.*), which circulated in Brazil in the latter half of 2021, featuring fewer unique epitopes. Cluster 1 (Gamma (P.1 + P.1.*)) dominated the first half of 2021. Late 2021 had two new clusters, Cluster 2 (Omicron, (B.1.1.529 + BA.*)), and Cluster 3 (BA.*) with the most unique epitopes, in addition to Cluster 4 (Delta sub lineages) which emerged in the second half of 2021 with fewer unique epitopes. Cluster 1 epitopes showed a high pro-inflammatory propensity, while others exhibited a balanced cytokine induction. The clustering method effectively identified Spike groups that may contribute to immune evasion and clinical presentation, and explain in part the clinical outcome.
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Affiliation(s)
- Diego Gomes Teixeira
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - João Firmino Rodrigues-Neto
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Escola Multicampi de Ciências Médicas do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Caicó, Rio Grande do Norte, Brazil
| | - Dayse Caroline Severiano da Cunha
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Selma Maria Bezerra Jeronimo
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Departmento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande Norte, Natal, Rio Grande do Norte, Brazil; Instituto Nacional de Ciência e Tecnologia de Doenças Tropicais, Natal, Rio Grande do Norte, Brazil.
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Yadav PD, Sardana V, Deshpande GR, Shinde PV, Thangaraj JWV, George LS, Sapkal GN, Patil DY, Sahay RR, Shete AM, Joshi M, Murhekar M, Godbole S, Gupta N, Prakash S, Rathore M, Ujjainiya R, Singh AP, Mishra A, Dash D, Chaudhary K, Sengupta S. Neutralizing antibody responses to SARS-CoV-2 Omicron variants: Post six months following two-dose & three-dose vaccination of ChAdOx1 nCoV-19 or BBV152. Indian J Med Res 2024; 159:223-231. [PMID: 38517215 PMCID: PMC11050759 DOI: 10.4103/ijmr.ijmr_948_23] [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: 05/18/2023] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND OBJECTIVES The Omicron sub-lineages are known to have higher infectivity, immune escape and lower virulence. During December 2022 - January 2023 and March - April 2023, India witnessed increased SARS-CoV-2 infections, mostly due to newer Omicron sub-lineages. With this unprecedented rise in cases, we assessed the neutralization potential of individuals vaccinated with ChAdOx1 nCoV (Covishield) and BBV152 (Covaxin) against emerging Omicron sub-lineages. METHODS Neutralizing antibody responses were measured in the sera collected from individuals six months post-two doses (n=88) of Covishield (n=44) or Covaxin (n=44) and post-three doses (n=102) of Covishield (n=46) or Covaxin (n=56) booster dose against prototype B.1 strain, lineages of Omicron; XBB.1, BQ.1, BA.5.2 and BF.7. RESULTS The sera of individuals collected six months after the two-dose and the three-dose demonstrated neutralizing activity against all variants. The neutralizing antibody (NAbs) level was highest against the prototype B.1 strain, followed by BA5.2 (5-6 fold lower), BF.7 (11-12 fold lower), BQ.1 (12 fold lower) and XBB.1 (18-22 fold lower). INTERPRETATION CONCLUSIONS Persistence of NAb responses was comparable in individuals with two- and three-dose groups post six months of vaccination. Among the Omicron sub-variants, XBB.1 showed marked neutralization escape, thus pointing towards an eventual immune escape, which may cause more infections. Further, the correlation of study data with complete clinical profile of the participants along with observations for cell-mediated immunity may provide a clear picture for the sustained protection due to three-dose vaccination as well as hybrid immunity against the newer variants.
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Affiliation(s)
| | - Viren Sardana
- Big Data and Informatics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | | | | | | | - Leyanna S. George
- Division of Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | | | | | - Rima R. Sahay
- Maximum Containment Laboratory, Pune, Maharashtra, India
| | - Anita M. Shete
- Maximum Containment Laboratory, Pune, Maharashtra, India
| | - Madhavi Joshi
- Department of Science & Technology, Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Manoj Murhekar
- Department of Epidemiology & Biostatistics, ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Sheela Godbole
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Nivedita Gupta
- Division of Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Satyartha Prakash
- Big Data and Informatics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Mamta Rathore
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Rajat Ujjainiya
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Ajay Pratap Singh
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Aastha Mishra
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Debasis Dash
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Kumardeep Chaudhary
- Big Data and Informatics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Shantanu Sengupta
- Big Data and Informatics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
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Kim D, Kim M, Kim J, Baek K, Park H, Park S, Kang BM, Kim S, Kim MJ, Mostafa MN, Maharjan S, Shin HE, Lee MH, Il Kim J, Park MS, Kim YS, Choi EK, Lee Y, Kwon HJ. A mouse xenograft long-term replication yields a SARS-CoV-2 Delta mutant with increased lethality. J Med Virol 2024; 96:e29459. [PMID: 38345153 DOI: 10.1002/jmv.29459] [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: 11/17/2023] [Revised: 12/26/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024]
Abstract
We recently established a long-term SARS-CoV-2 infection model using lung-cancer xenograft mice and identified mutations that arose in the SARS-CoV-2 genome during long-term propagation. Here, we applied our model to the SARS-CoV-2 Delta variant, which has increased transmissibility and immune escape compared with ancestral SARS-CoV-2. We observed limited mutations in SARS-CoV-2 Delta during long-term propagation, including two predominant mutations: R682W in the spike protein and L330W in the nucleocapsid protein. We analyzed two representative isolates, Delta-10 and Delta-12, with both predominant mutations and some additional mutations. Delta-10 and Delta-12 showed lower replication capacity compared with SARS-CoV-2 Delta in cultured cells; however, Delta-12 was more lethal in K18-hACE2 mice compared with SARS-CoV-2 Delta and Delta-10. Mice infected with Delta-12 had higher viral titers, more severe histopathology in the lungs, higher chemokine expression, increased astrocyte and microglia activation, and extensive neutrophil infiltration in the brain. Brain tissue hemorrhage and mild vacuolation were also observed, suggesting that the high lethality of Delta-12 was associated with lung and brain pathology. Our long-term infection model can provide mutant viruses derived from SARS-CoV-2 Delta and knowledge about the possible contributions of emergent mutations to the properties of new variants.
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Affiliation(s)
- Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jinsoo Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Vaccine Innovation Center College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Bo Min Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Suyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Mo-Jong Kim
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
| | - Mohd Najib Mostafa
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
- Department of Biomedical Gerontology, Graduate School of Hallym University, Chuncheon, Republic of Korea
| | - Sony Maharjan
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Ha-Eun Shin
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Myeong-Heon Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Jin Il Kim
- Department of Microbiology, Vaccine Innovation Center College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Vaccine Innovation Center College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Yong-Sun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
| | - Eun-Kyoung Choi
- Ilsong Institute of Life Science, Hallym University, Seoul, Republic of Korea
- Department of Biomedical Gerontology, Graduate School of Hallym University, Chuncheon, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyung-Joo Kwon
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
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6
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Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
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Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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7
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Banho CA, de Carvalho Marques B, Sacchetto L, Sepedro Lima AK, Pereira Parra MC, Jeronimo Lima AR, Ribeiro G, Jorge Martins A, dos Santos Barros CR, Carolina Elias M, Coccuzzo Sampaio S, Nanev Slavov S, Strazza Rodrigues E, Vieira Santos E, Tadeu Covas D, Kashima S, Augusto Brassaloti R, Petry B, Gaspar Clemente L, Lehmann Coutinho L, Akemi Assato P, da Silva da Costa FA, Souza-Neto JA, Maria Tommasini Grotto R, Daiana Poleti M, Cristina Chagas Lesbon J, Chicaroni Mattos E, Fukumasu H, Giovanetti M, Carlos Junior Alcantara L, Rahal P, Pessoa Araújo JF, Althouse BM, Vasilakis N, Lacerda Nogueira M. Dynamic clade transitions and the influence of vaccine rollout on the spatiotemporal circulation of SARS-CoV-2 variants in São Paulo, Brazil. RESEARCH SQUARE 2024:rs.3.rs-3788142. [PMID: 38343798 PMCID: PMC10854302 DOI: 10.21203/rs.3.rs-3788142/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2.
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Affiliation(s)
- Cecília Artico Banho
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Beatriz de Carvalho Marques
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Ana Karoline Sepedro Lima
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Maisa Carla Pereira Parra
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
| | - Alex Ranieri Jeronimo Lima
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Gabriela Ribeiro
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Antonio Jorge Martins
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | | | - Maria Carolina Elias
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Sandra Coccuzzo Sampaio
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Elaine Vieira Santos
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Dimas Tadeu Covas
- Center for Viral Surveillance and Serological Assessment (CeVIVAS), Butantan Institute, São Paulo, Brazil
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | - Bruna Petry
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Luan Gaspar Clemente
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Patricia Akemi Assato
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Felipe Allan da Silva da Costa
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Jayme A. Souza-Neto
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil
| | - Rejane Maria Tommasini Grotto
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil
- Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Marta Giovanetti
- Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil, Americas
- Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Italy
| | - Luiz Carlos Junior Alcantara
- Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
- Climate Amplified Diseases And Epidemics (CLIMADE), Brazil, Americas
| | - Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (Unesp), São José do Rio Preto, Brazil
| | - João Fernando Pessoa Araújo
- Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Botucatu, Brazil
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Brazil
| | - Benjamin M. Althouse
- Department of Biology, New Mexico State University, Las Cruces, NM
- Information School, University of Washington, Seattle, WA
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto, São Paulo, Brazil
- Department of Pathology, University of Texas Medical Branch; Galveston, Texas, United States of America
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8
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Liu YD, Noga H, Allaire C, Bedaiwy MA, Lee CE, Williams C, Booth A, Galea LAM, Kaida A, Ogilvie GS, Brotto LA, Yong PJ. Mental Health Outcomes of Endometriosis Patients during the COVID-19 Pandemic: Impact of Pre-pandemic Central Nervous System Sensitization. THE JOURNAL OF PAIN 2024:104481. [PMID: 38246253 DOI: 10.1016/j.jpain.2024.01.346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
Abstract
To correlate pain-related phenotyping for central nervous system sensitization in endometriosis-associated pain with mental health outcomes during the COVID-19 pandemic, the prospective Endometriosis and Pelvic Pain Interdisciplinary Cohort (ClinicalTrials.gov #NCT02911090) was linked to the COVID-19 Rapid Evidence Study of a Provincial Population-Based Cohort for Gender and Sex (RESPPONSE) dataset. The primary outcomes were depression (PHQ-9) and anxiety (GAD-7) scores during the pandemic. The explanatory variables of interest were the Central Sensitization Inventory (CSI) score (0-100) and endometriosis-associated chronic pain comorbidities/psychological variables before the pandemic. The explanatory and response variables were assessed for correlation, followed by multivariable regression analyses adjusting for PHQ-9 and GAD-7 scores pre-pandemic as well as age, body mass index, and parity. A higher CSI score and a greater number of chronic pain comorbidities before the pandemic were both positively correlated with PHQ-9 and GAD-7 scores during the pandemic. These associations remained significant in adjusted analyses. Increasing the CSI score by 10 was associated with an increase in pandemic PHQ-9 by .74 points (P < .0001) and GAD-7 by .73 points (P < .0001) on average. Each additional chronic pain comorbidity/psychological variable was associated with an increase in pandemic PHQ-9 by an average of .63 points (P = .0004) and GAD-7 by .53 points (P = .0002). Endometriosis patients with a history of central sensitization before the pandemic had worse mental health outcomes during the COVID-19 pandemic. As a risk factor for mental health symptoms in the face of major stressors, clinical proxies for central sensitization can be used to identify endometriosis patients who may need additional support. PERSPECTIVE: This article adds to the growing literature of the clinical importance of central sensitization in endometriosis patients, who had more symptoms of depression and anxiety during the COVID-19 pandemic. Clinical features of central sensitization may help clinicians identify endometriosis patients needing additional support when facing major stressors.
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Affiliation(s)
- Yang D Liu
- University of British Columbia Endometriosis and Pelvic Pain Laboratory, Vancouver, BC, Canada
| | - Heather Noga
- University of British Columbia Endometriosis and Pelvic Pain Laboratory, Vancouver, BC, Canada; Women's Health Research Institute, Vancouver, BC, Canada
| | - Catherine Allaire
- Women's Health Research Institute, Vancouver, BC, Canada; Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Mohamed A Bedaiwy
- Women's Health Research Institute, Vancouver, BC, Canada; Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Caroline E Lee
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Christina Williams
- University of British Columbia Endometriosis and Pelvic Pain Laboratory, Vancouver, BC, Canada; Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Amy Booth
- Women's Health Research Institute, Vancouver, BC, Canada
| | - Liisa A M Galea
- Women's Health Research Institute, Vancouver, BC, Canada; Department of Psychology, University of British Columbia, Vancouver, BC, Canada; Centre for Addiction and Mental Health, Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Angela Kaida
- Women's Health Research Institute, Vancouver, BC, Canada; Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Gina S Ogilvie
- Women's Health Research Institute, Vancouver, BC, Canada; School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada; British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Lori A Brotto
- Women's Health Research Institute, Vancouver, BC, Canada; Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Paul J Yong
- University of British Columbia Endometriosis and Pelvic Pain Laboratory, Vancouver, BC, Canada; Women's Health Research Institute, Vancouver, BC, Canada; Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
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9
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Keller MW, Keong LM, Rambo-Martin BL, Hassell N, Lacek KA, Wilson MM, Kirby MK, Liddell J, Owuor DC, Sheth M, Madden J, Lee JS, Kondor RJ, Wentworth DE, Barnes JR. Targeted amplification and genetic sequencing of the severe acute respiratory syndrome coronavirus 2 surface glycoprotein. Microbiol Spectr 2024; 12:e0298223. [PMID: 38084972 PMCID: PMC10783008 DOI: 10.1128/spectrum.02982-23] [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: 09/06/2023] [Accepted: 11/09/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE The COVID-19 pandemic was accompanied by an unprecedented surveillance effort. The resulting data were and will continue to be critical for surveillance and control of SARS-CoV-2. However, some genomic surveillance methods experienced challenges as the virus evolved, resulting in incomplete and poor quality data. Complete and quality coverage, especially of the S-gene, is important for supporting the selection of vaccine candidates. As such, we developed a robust method to target the S-gene for amplification and sequencing. By focusing on the S-gene and imposing strict coverage and quality metrics, we hope to increase the quality of surveillance data for this continually evolving gene. Our technique is currently being deployed globally to partner laboratories, and public health representatives from 79 countries have received hands-on training and support. Expanding access to quality surveillance methods will undoubtedly lead to earlier detection of novel variants and better inform vaccine strain selection.
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Affiliation(s)
- Matthew W. Keller
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Lisa M. Keong
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Benjamin L. Rambo-Martin
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Norman Hassell
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Kristine A. Lacek
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Malania M. Wilson
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Marie K. Kirby
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Jimma Liddell
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - D. Collins Owuor
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Mili Sheth
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joseph Madden
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Justin S. Lee
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rebecca J. Kondor
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - David E. Wentworth
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - John R. Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
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10
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Raya S, Malla B, Thakali O, Angga MS, Haramoto E. Development of highly sensitive one-step reverse transcription-quantitative PCR for SARS-CoV-2 detection in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167844. [PMID: 37852499 DOI: 10.1016/j.scitotenv.2023.167844] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/23/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is a major public health concern that has highlighted the need to monitor circulating strains to better understand the coronavirus disease 2019 (COVID-19) pandemic. This study was carried out to monitor SARS-CoV-2 RNA and its variant-specific mutations in wastewater using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). One-step RT-qPCR using the SARS-CoV-2 Detection RT-qPCR Kit for Wastewater (Takara Bio), which amplified two N-gene regions simultaneously using CDC N1 and N2 assays with a single fluorescence dye, demonstrated better performance in detecting SARS-CoV-2 RNA (positive ratio, 66 %) compared to two-step RT-qPCR using CDC N1 or N2 assay (40 % each, and 52 % when combined), with significantly lower Ct values. The one-step RT-qPCR assay detected SARS-CoV-2 RNA in 59 % (38/64) of influent samples collected from a wastewater treatment plant in Japan between January 2021 and March 2022. The correlation between the concentration of SARS-CoV-2 RNA in the wastewater and the number of COVID-19 cases reported each day for 7 days pre- and post-sampling was significant (p < 0.05, r = 0.76 ± 0.03). Thirty-one influent samples which showed two-well positive for SARS-CoV-2 RNA were further tested by six mutations site-specific one-step RT-qPCR (E484K, L452R, N501Y, T478K, G339D, and E484A mutations). The N501Y mutation was detected between March and June 2021 but was replaced by the L452R and T478K mutations between July and October 2021, reflecting the shift from Alpha to Delta variants in the study region. The G339D and E484A mutations were identified in January 2022 and later when the incidence of the Omicron variant peaked. These findings indicate that wastewater-based epidemiology has the epidemiological potential to complement clinical tests to track the spread of COVID-19 and monitor variants circulating in communities.
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Affiliation(s)
- Sunayana Raya
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Ocean Thakali
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Made Sandhyana Angga
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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11
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Pérez-Massón B, Quintana-Pérez Y, Tundidor Y, Pérez-Martínez D, Castro-Martínez C, Pupo-Meriño M, Orosa I, Relova-Hernández E, Villegas R, Guirola O, Rojas G. Studying SARS-CoV-2 interactions using phage-displayed receptor binding domain as a model protein. Sci Rep 2024; 14:712. [PMID: 38184672 PMCID: PMC10771503 DOI: 10.1038/s41598-023-50450-4] [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: 09/06/2023] [Accepted: 12/20/2023] [Indexed: 01/08/2024] Open
Abstract
SARS-CoV-2 receptor binding domain (RBD) mediates viral entry into human cells through its interaction with angiotensin converting enzyme 2 (ACE2). Most neutralizing antibodies elicited by infection or vaccination target this domain. Such a functional relevance, together with large RBD sequence variability arising during viral spreading, point to the need of exploring the complex landscape of interactions between RBD-derived variants, ACE2 and antibodies. The current work was aimed at developing a simple platform to do so. Biologically active and antigenic Wuhan-Hu-1 RBD, as well as mutated RBD variants found in nature, were successfully displayed on filamentous phages. Mutational scanning confirmed the global plasticity of the receptor binding motif within RBD, highlighted residues playing a critical role in receptor binding, and identified mutations strengthening the interaction. The ability of vaccine-induced antibodies to inhibit ACE2 binding of many mutated RBD variants, albeit at different extents, was shown. Amino acid replacements which could compromise such inhibitory potential were underscored. The expansion of our approach could be the starting point for a large-scale phage-based exploration of diversity within RBD of SARS-CoV-2 and related coronaviruses, useful to understand structure-function relationships, to engineer RBD proteins, and to anticipate changes to watch during viral evolution.
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Affiliation(s)
- Beatriz Pérez-Massón
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Yazmina Quintana-Pérez
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Yaima Tundidor
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Dayana Pérez-Martínez
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Camila Castro-Martínez
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Mario Pupo-Meriño
- Universidad de Ciencias Informáticas, Carretera a San Antonio de los Baños, km 2 1/2, Torrens, Boyeros, CP 19370, Havana, Cuba
| | - Ivette Orosa
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Ernesto Relova-Hernández
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba
| | - Rosmery Villegas
- Universidad de Ciencias Informáticas, Carretera a San Antonio de los Baños, km 2 1/2, Torrens, Boyeros, CP 19370, Havana, Cuba
| | - Osmany Guirola
- Center for Genetic Engineering and Biotechnology, Ave 31 E/158 y 190, Cubanacán, Playa, CP 11300, Havana, Cuba
| | - Gertrudis Rojas
- Center of Molecular Immunology, Calle 216 esq 15, apartado 16040, Atabey, Playa, CP 11300, Havana, Cuba.
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12
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Zaidi AK, Singh RB. SARS-CoV-2 variant biology and immune evasion. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 202:45-66. [PMID: 38237990 DOI: 10.1016/bs.pmbts.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter discusses the SARS-CoV-2 variants and their immune evasion strategies, shedding light on the dynamic nature of the COVID-19 pandemic. The ecological dynamics and viral evolution of SARS-CoV-2 are explored, considering carriers of infection, individual immunity profiles, and human movement as key factors in the emergence and dissemination of variants. The chapter discusses SARS-CoV-2 mutation, including mutation rate, substitution rate, and recombination, influencing genetic diversity and evolution. Transmission bottlenecks are highlighted as determinants of dominant variants during viral spread. The evolution phases of the pandemic are outlined, from limited early evolution to the emergence of notable changes like the D614G substitution and variants with heavy mutations. Variants of Concern (VOCs), including Alpha, Beta, Gamma, and the recent Omicron variant, are examined, with insights into inter-lineage and intra-lineage dynamics. The origin of VOCs and the Omicron variant is explored, alongside the role of the furin cleavage site (FCS) in variant emergence. The impact of structural and non-structural proteins on viral infectivity is assessed, as well as innate immunity evasion strategies employed by SARS-CoV-2 variants. The chapter concludes by considering future possibilities, including ongoing virus evolution, the need for surveillance, vaccine development, and public health measures.
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Affiliation(s)
| | - Rohan Bir Singh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States; Department of Population, Policy and Practice, Greater Ormond Street Institute of Child Health, University College London, United Kingdom; Discipline of Ophthalmology and Visual Sciences, Adelaide Medical School, University of Adelaide, Australia.
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13
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Zaidi AK, Singh RB. Epidemiology of COVID-19. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 202:25-38. [PMID: 38237988 DOI: 10.1016/bs.pmbts.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter provides a detailed exploration of the epidemiology of COVID-19, focusing on several key aspects that offer valuable insights into the disease progression. A comprehensive comparison is made between the three related coronaviruses: SARS-CoV, MERS-CoV, and SARS-CoV-2, elucidating their similarities and differences in terms of transmission dynamics, clinical presentation, laboratory and radiological findings, infection mechanisms, and mortality rates. The concept of herd immunity is then discussed, exploring its relevance and potential implications for controlling the spread of COVID-19. Next, the chapter delves into the changing epidemiology of the disease, examining how various factors such as human behavior, public health interventions, and viral mutations have influenced its transmission patterns and severity over time. Finally, the timelines and evolution of COVID-19 are outlined, tracing the origins of the virus, its rapid global spread, and the emergence of new variants.
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Affiliation(s)
| | - Rohan Bir Singh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United State; Department of Population, Policy and Practice, Greater Ormond Street Institute of Child Health, University College London, United Kingdom; Discipline of Ophthalmology and Visual Sciences, Adelaide Medical School, University of Adelaide, Australia
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14
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Liu S, Anzai A, Nishiura H. Reconstructing the COVID-19 incidence in India using airport screening data in Japan. BMC Infect Dis 2024; 24:12. [PMID: 38166666 PMCID: PMC10763058 DOI: 10.1186/s12879-023-08882-w] [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: 04/27/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND A major epidemic of COVID-19 caused by the Delta variant (B.1.617.2) occurred in India from March to July 2021, resulting in 19 million documented cases. Given the limited healthcare and testing capacities, the actual number of infections is likely to have been greater than reported, and several modelling studies and excess mortality research indicate that this epidemic involved substantial morbidity and mortality. METHODS To estimate the incidence during this epidemic, we used border entry screening data in Japan to estimate the daily incidence and cumulative incidence of COVID-19 infection in India. Analysing the results of mandatory testing among non-Japanese passengers entering Japan from India, we calculated the prevalence and then backcalculated the incidence in India from February 28 to July 3, 2021. RESULTS The estimated number of infections ranged from 448 to 576 million people, indicating that 31.8% (95% confidence interval (CI): 26.1, 37.7) - 40.9% (95% CI: 33.5, 48.4) of the population in India had experienced COVID-19 infection from February 28 to July 3, 2021. In addition to obtaining cumulative incidence that was consistent with published estimates, we showed that the actual incidence of COVID-19 infection during the 2021 epidemic in India was approximately 30 times greater than that based on documented cases, giving a crude infection fatality risk of 0.47%. Adjusting for test-negative certificate before departure, the quality control of which was partly questionable, the cumulative incidence can potentially be up to 2.3-2.6 times greater than abovementioned estimates. CONCLUSIONS Our estimate of approximately 32-41% cumulative infection risk from February 28 to July 3, 2021 is roughly consistent with other published estimates, and they can potentially be greater, given an exit screening before departure. The present study results suggest the potential utility of border entry screening data to backcalculate the incidence in countries with limited surveillance capacity owing to a major surge in infections.
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Affiliation(s)
- Shiqi Liu
- Kyoto University School of Public Health, Yoshidakonoe cho, Sakyo ku, Kyoto City, 6068501, Japan
| | - Asami Anzai
- Kyoto University School of Public Health, Yoshidakonoe cho, Sakyo ku, Kyoto City, 6068501, Japan
| | - Hiroshi Nishiura
- Kyoto University School of Public Health, Yoshidakonoe cho, Sakyo ku, Kyoto City, 6068501, Japan.
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15
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Yao W, Li Y, Ma D, Hou X, Wang H, Tang X, Cheng D, Zhang H, Du C, Pan H, Li C, Lin H, Sun M, Ding Q, Wang Y, Gao J, Zhong G. Evolution of SARS-CoV-2 Spikes shapes their binding affinities to animal ACE2 orthologs. Microbiol Spectr 2023; 11:e0267623. [PMID: 37943512 PMCID: PMC10715038 DOI: 10.1128/spectrum.02676-23] [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: 07/10/2023] [Accepted: 10/08/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Spike-receptor interaction is a critical determinant for the host range of coronaviruses. In this study, we investigated the SARS-CoV-2 WHU01 strain and five WHO-designated SARS-CoV-2 variants of concern (VOCs), including Alpha, Beta, Gamma, Delta, and the early Omicron variant, for their Spike interactions with ACE2 proteins of 18 animal species. First, the receptor-binding domains (RBDs) of Alpha, Beta, Gamma, and Omicron were found to display progressive gain of affinity to mouse ACE2. More interestingly, these RBDs were also found with progressive loss of affinities to multiple ACE2 orthologs. The Omicron RBD showed decreased or complete loss of affinity to eight tested animal ACE2 orthologs, including that of some livestock animals (horse, donkey, and pig), pet animals (dog and cat), and wild animals (pangolin, American pika, and Rhinolophus sinicus bat). These findings shed light on potential host range shift of SARS-CoV-2 VOCs, especially that of the Omicron variant.
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Affiliation(s)
- Weitong Yao
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
- Hubei JiangXia Laboratory, Wuhan, Hubei, China
| | - Yujun Li
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Danting Ma
- Shenzhen Bay Laboratory, Shenzhen, China
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Xudong Hou
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Haimin Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Xiaojuan Tang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Dechun Cheng
- Shenzhen Bay Laboratory, Shenzhen, China
- Heilongjiang Academy of Medical Sciences, Harbin, China
| | - He Zhang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Chengzhi Du
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Hong Pan
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Chao Li
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Hua Lin
- Biomedical Research Center of South China, Fujian Normal University, Fuzhou, China
| | - Mengsi Sun
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Qiang Ding
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | | | - Jiali Gao
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Guocai Zhong
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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16
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Rodriguez-Nuñez M, Cepeda MDV, Bello C, Lopez MA, Sulbaran Y, Loureiro CL, Liprandi F, Jaspe RC, Pujol FH, Rangel HR. Neutralization of Different Variants of SARS-CoV-2 by a F(ab')2 Preparation from Sera of Horses Immunized with the Viral Receptor Binding Domain. Antibodies (Basel) 2023; 12:80. [PMID: 38131802 PMCID: PMC10740526 DOI: 10.3390/antib12040080] [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: 09/02/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
The Receptor Binding Domain (RBD) of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is the functional region of the viral Spike protein (S), which is involved in cell attachment to target cells. The virus has accumulated progressively mutations in its genome, particularly in the RBD region, many of them associated with immune evasion of the host neutralizing antibodies. Some of the viral lineages derived from this evolution have been classified as Variant of Interest (VOI) or Concern (VOC). The neutralizing capacity of a F(ab')2 preparation from sera of horses immunized with viral RBD was evaluated by lytic plaque reduction assay against different SARS-CoV-2 variants. A F(ab')2 preparation of a hyperimmune serum after nine immunizations with RBD exhibited a high titer of neutralizing antibodies against the ancestral-like strain (1/18,528). A reduction in the titer of the F(ab')2 preparation was observed against the different variants tested compared to the neutralizing activity against the ancestral-like strain. The highest reduction in the neutralization titer was observed for the Omicron VOC (4.7-fold), followed by the Mu VOI (2.6), Delta VOC (1.8-fold), and Gamma VOC (1.5). Even if a progressive reduction in the neutralizing antibodies titer against the different variants evaluated was observed, the serum still exhibited a neutralizing titer against the Mu VOI and the Omicron VOC (1/7113 and 1/3918, respectively), the evaluated strains most resistant to neutralization. Therefore, the preparation retained neutralizing activity against all the strains tested.
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Affiliation(s)
- Mariajosé Rodriguez-Nuñez
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Mariana del Valle Cepeda
- Biotecfar S.A., Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1050, Venezuela; (M.d.V.C.); (C.B.); (M.A.L.)
| | - Carlos Bello
- Biotecfar S.A., Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1050, Venezuela; (M.d.V.C.); (C.B.); (M.A.L.)
| | - Miguel Angel Lopez
- Biotecfar S.A., Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1050, Venezuela; (M.d.V.C.); (C.B.); (M.A.L.)
| | - Yoneira Sulbaran
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Carmen Luisa Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela;
| | - Rossana Celeste Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Flor Helene Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Héctor Rafael Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
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17
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Wei D, Xie Y, Liu X, Chen R, Zhou M, Zhang X, Qu J. Pathogen evolution, prevention/control strategy and clinical features of COVID-19: experiences from China. Front Med 2023; 17:1030-1046. [PMID: 38157194 DOI: 10.1007/s11684-023-1043-5] [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: 06/13/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported at the end of 2019 as a worldwide health concern causing a pandemic of unusual viral pneumonia and many other organ damages, which was defined by the World Health Organization as coronavirus disease 2019 (COVID-19). The pandemic is considered a significant threat to global public health till now. In this review, we have summarized the lessons learnt during the emergence and spread of SARS-CoV-2, including its prototype and variants. The overall clinical features of variants of concern (VOC), heterogeneity in the clinical manifestations, radiology and pathology of COVID-19 patients are also discussed, along with advances in therapeutic agents.
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Affiliation(s)
- Dong Wei
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yusang Xie
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Xuefei Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Rong Chen
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Xinxin Zhang
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China.
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18
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Meijers M, Ruchnewitz D, Eberhardt J, Łuksza M, Lässig M. Population immunity predicts evolutionary trajectories of SARS-CoV-2. Cell 2023; 186:5151-5164.e13. [PMID: 37875109 PMCID: PMC10964984 DOI: 10.1016/j.cell.2023.09.022] [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: 12/02/2022] [Revised: 08/26/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023]
Abstract
The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid turnover of genetic clades. New variants show intrinsic changes, notably increased transmissibility, and antigenic changes that reduce cross-immunity induced by previous infections or vaccinations. How this functional variation shapes global evolution has remained unclear. Here, we establish a predictive fitness model for SARS-CoV-2 that integrates antigenic and intrinsic selection. The model is informed by tracking of time-resolved sequence data, epidemiological records, and cross-neutralization data of viral variants. Our inference shows that immune pressure, including contributions of vaccinations and previous infections, has become the dominant force driving the recent evolution of SARS-CoV-2. The fitness model can serve continued surveillance in two ways. First, it successfully predicts the short-term evolution of circulating strains and flags emerging variants likely to displace the previously predominant variant. Second, it predicts likely antigenic profiles of successful escape variants prior to their emergence.
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Affiliation(s)
- Matthijs Meijers
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Jan Eberhardt
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Marta Łuksza
- Tisch Cancer Institute, Departments of Oncological Sciences and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany.
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19
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Viver T, López-Causapé C, Ribot-Fraile P, Pérez-Mazón C, López-Solé D, Jiménez-Guerra G, Taltavull B, López-López A. The molecular epidemiology of SARS-CoV-2 in the Pityusic Islands shows multiple introductions and fast replacements of variants in a touristic worldwide hot spot. Sci Rep 2023; 13:18053. [PMID: 37872265 PMCID: PMC10593736 DOI: 10.1038/s41598-023-44668-5] [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: 03/23/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
The public health emergency caused by the Covid-19 outbreak in March 2020 encouraged worldwide initiatives to monitor the genetic diversity and features of the SARS-CoV-2 circulating variants, mainly based on the genomic surveillance. However, due to the impossibility to carry out extensive sequencing in resource-limited hospitals, other PCR-based strategies could be applied to efficiently monitor the circulating variants without the need to greatly expand the sequencing capacity. In our case, overpassing the technical limitations inherent to a second level hospital, we were able to characterize the weekly distribution of SARS-CoV-2 by the RT-qPCR amplification patterns visualization, single nucleotide polymorphism genotyping, and sequencing of randomly selected samples. All these molecular approaches allowed us to trace the epidemiology of SARS-CoV-2 viruses circulating in Ibiza and Formentera (Balearic Islands, Spain) during the third to the sixth pandemic waves (January 2021-July 2022), in which three major lineages that were considered as VOCs (Alpha, Delta, and Omicron), and many other non-VOC variants were detected and tracked.
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Affiliation(s)
- T Viver
- Marine Microbiology Group, Mediterranean Institute for Advanced Studies (IMEDEA-CSIC-UIB), Esporles, Spain
| | - C López-Causapé
- Servicio de Microbiología, Hospital Universitario Son Espases, Majorca, Illes Balears, Spain
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Majorca, Illes Balears, Spain
| | - P Ribot-Fraile
- Servicio de Microbiología, Hospital Universitario Son Espases, Majorca, Illes Balears, Spain
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Majorca, Illes Balears, Spain
| | - C Pérez-Mazón
- Servicio de Microbiologíaa y Parasitología, Hospital Can Misses, C/ Corona s/n, 07800, Ibiza, Illes Balears, Spain
| | - D López-Solé
- Servicio de Microbiologíaa y Parasitología, Hospital Can Misses, C/ Corona s/n, 07800, Ibiza, Illes Balears, Spain
| | - G Jiménez-Guerra
- Servicio de Microbiologíaa y Parasitología, Hospital Can Misses, C/ Corona s/n, 07800, Ibiza, Illes Balears, Spain
| | - B Taltavull
- Instituto de Investigación Sanitaria Illes Balears (IdISBa), Majorca, Illes Balears, Spain
| | - A López-López
- Servicio de Microbiologíaa y Parasitología, Hospital Can Misses, C/ Corona s/n, 07800, Ibiza, Illes Balears, Spain.
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20
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Roubidoux EK, Brigleb PH, Vegesana K, Souquette A, Whitt K, Freiden P, Green A, Thomas PG, McGargill MA, Wolf J, Schultz-Cherry S. Utility of nasal swabs for assessing mucosal immune responses towards SARS-CoV-2. Sci Rep 2023; 13:17820. [PMID: 37857783 PMCID: PMC10587113 DOI: 10.1038/s41598-023-44989-5] [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: 07/25/2023] [Accepted: 10/14/2023] [Indexed: 10/21/2023] Open
Abstract
SARS-CoV-2 has caused millions of infections worldwide since its emergence in 2019. Understanding how infection and vaccination induce mucosal immune responses and how they fluctuate over time is important, especially since they are key in preventing infection and reducing disease severity. We established a novel methodology for assessing SARS-CoV-2 cytokine and antibody responses at the nasal epithelium by using nasopharyngeal swabs collected longitudinally before and after either SARS-CoV-2 infection or vaccination. We then compared responses between mucosal and systemic compartments. We demonstrate that cytokine and antibody profiles differ between compartments. Nasal cytokines show a wound healing phenotype while plasma cytokines are consistent with pro-inflammatory pathways. We found that nasal IgA and IgG have different kinetics after infection, with IgA peaking first. Although vaccination results in low nasal IgA, IgG induction persists for up to 180 days post-vaccination. This research highlights the importance of studying mucosal responses in addition to systemic responses to respiratory infections. The methods described herein can be used to further mucosal vaccine development by giving us a better understanding of immunity at the nasal epithelium providing a simpler, alternative clinical practice to studying mucosal responses to infection.
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Affiliation(s)
| | - Pamela H Brigleb
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kasi Vegesana
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aisha Souquette
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kendall Whitt
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pamela Freiden
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Amanda Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maureen A McGargill
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Joshua Wolf
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stacey Schultz-Cherry
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA.
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21
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Liu M, Zhao T, Mu Q, Zhang R, Liu C, Xu F, Liang L, Zhao L, Zhao S, Cai X, Wang M, Huang N, Feng T, Lei S, Yang G, Cui F. Immune-Boosting Effect of the COVID-19 Vaccine: Real-World Bidirectional Cohort Study. JMIR Public Health Surveill 2023; 9:e47272. [PMID: 37819703 PMCID: PMC10569382 DOI: 10.2196/47272] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/25/2023] [Accepted: 08/08/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND As the SARS-CoV-2 attenuates and antibodies from the COVID-19 vaccine decline, long-term attention should be paid to the durability of primary booster administration and the preventive effect of the second or multiple booster doses of the COVID-19 vaccine. OBJECTIVE This study aimed to explore the durability of primary booster administration and the preventive effect of second or multiple booster doses of the COVID-19 vaccine. METHODS We established a bidirectional cohort in Guizhou Province, China. Eligible participants who had received the primary booster dose were enrolled for blood sample collection and administration of the second booster dose. A retrospective cohort for the time of administration was constructed to evaluate antibody attenuation 6-12 months after the primary booster dose, while a prospective cohort on the vaccine effect of the second booster dose was constructed for 4 months after the second administration. RESULTS Between September 21, 2022, and January 30, 2023, a total of 327 participants were included in the final statistical analysis plan. The retrospective cohort revealed that approximately 6-12 months after receiving the primary booster, immunoglobulin G (IgG) slowly declined with time, while immunoglobulin A (IgA) remained almost constant. The prospective cohort showed that 28 days after receiving the second booster, the antibody levels were significantly improved. Higher levels of IgG and IgA were associated with better protection against COVID-19 infection for vaccine recipients. Regarding the protection of antibody levels against post-COVID-19 symptoms, the increase of the IgG had a protective effect on brain fog and sleep quality, while IgA had a protective effect on shortness of breath, brain fog, impaired coordination, and physical pain. CONCLUSIONS The IgG and IgA produced by the second booster dose of COVID-19 vaccines can protect against SARS-CoV-2 infection and may alleviate some post-COVID-19 symptoms. Further data and studies on secondary booster administration are required to confirm these conclusions.
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Affiliation(s)
- Ming Liu
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Tianshuo Zhao
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Center for Infectious Diseases and Policy Research & Global Health and Infectious Diseases Group, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing, China
| | - Qiuyue Mu
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Ruizhi Zhang
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Chunting Liu
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Fei Xu
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Luxiang Liang
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Linglu Zhao
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Suye Zhao
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Xianming Cai
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Center for Infectious Diseases and Policy Research & Global Health and Infectious Diseases Group, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing, China
| | - Mingting Wang
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Center for Infectious Diseases and Policy Research & Global Health and Infectious Diseases Group, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing, China
| | - Ninghua Huang
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Center for Infectious Diseases and Policy Research & Global Health and Infectious Diseases Group, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing, China
| | - Tian Feng
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Shiguang Lei
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Guanghong Yang
- Guizhou Center for Disease Control and Prevention, Guiyang, China
| | - Fuqiang Cui
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, China
- Center for Infectious Diseases and Policy Research & Global Health and Infectious Diseases Group, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing, China
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22
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Shikha S, Jogi MK, Jha R, Kumar RA, Sah T, Singh P, Sagar R, Kumar A, Marwal R, Ponnusamy K, Agarwal SM, Kumar RS, Arif N, Bharadwaj M, Singh S, Kumar P. Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein. Front Immunol 2023; 14:1209513. [PMID: 37849762 PMCID: PMC10577267 DOI: 10.3389/fimmu.2023.1209513] [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: 04/20/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
The SARS-CoV-2 omicron variants keep accumulating a large number of mutations in the spike (S) protein, which contributes to greater transmissibility and a rapid rise to dominance within populations. The identification of mutations and their affinity to the cellular angiotensin-converting enzyme-2 (ACE-2) receptor and immune evasion in the Delhi NCR region was under-acknowledged. The study identifies some mutations (Y505 reversion, G339H, and R346T/N) in genomes from Delhi, India, and their probable implications for altering the immune response and binding affinity for ACE-2. The spike mutations have influenced the neutralizing activity of antibodies against the omicron variant, which shows partial immune escape. However, researchers are currently exploring various mitigation strategies to tackle the potential decline in efficacy or effectiveness against existing and future variants of SARS-CoV-2. These strategies include modifying vaccines to target specific variants, such as the omicron variant, developing multivalent vaccine formulations, and exploring alternative delivery methods. To address this, it is also necessary to understand the impact of these mutations from a different perspective, especially in terms of alterations in antigenic determinants. In this study, we have done whole genome sequencing (WGS) of SARS-CoV-2 in COVID-19 samples from Delhi, NCR, and analyzed the spike's mutation with an emphasis on antigenic alterations. The impact of mutation in terms of epitope formation, loss/gain of efficiency, and interaction of epitopes with antibodies has been studied. Some of the mutations or variant genomes seem to be the progenitors of the upcoming variants in India. Our analyses suggested that weakening interactions with antibodies may lead to immune resistance in the circulating genomes.
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Affiliation(s)
- Sristy Shikha
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Mukesh Kumar Jogi
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Ruchika Jha
- Department of Biotechnology, Vinoba Bhave University, Hazaribagh, Jharkhand, India
| | - Rana Amit Kumar
- Department of Biotechnology, Anugrah Narayan College, Patna, Bihar, India
| | - Tathagat Sah
- Department of Chemical Engineering and Biotechnology, Beant College of Engineering and Technology, Gurdaspur, Punjab, India
| | - Pushpendra Singh
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Ritu Sagar
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Anuj Kumar
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Robin Marwal
- Biotechnology Division, National Centre for Disease Control, Delhi, India
| | | | - Subhash Mohan Agarwal
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - R. Suresh Kumar
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Nazneen Arif
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Mausumi Bharadwaj
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Shalini Singh
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
| | - Pramod Kumar
- Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India
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23
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Volz E. Fitness, growth and transmissibility of SARS-CoV-2 genetic variants. Nat Rev Genet 2023; 24:724-734. [PMID: 37328556 DOI: 10.1038/s41576-023-00610-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2023] [Indexed: 06/18/2023]
Abstract
The massive scale of the global SARS-CoV-2 sequencing effort created new opportunities and challenges for understanding SARS-CoV-2 evolution. Rapid detection and assessment of new variants has become one of the principal objectives of genomic surveillance of SARS-CoV-2. Because of the pace and scale of sequencing, new strategies have been developed for characterizing fitness and transmissibility of emerging variants. In this Review, I discuss a wide range of approaches that have been rapidly developed in response to the public health threat posed by emerging variants, ranging from new applications of classic population genetics models to contemporary synthesis of epidemiological models and phylodynamic analysis. Many of these approaches can be adapted to other pathogens and will have increasing relevance as large-scale pathogen sequencing becomes a regular feature of many public health systems.
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Affiliation(s)
- Erik Volz
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
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24
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Rao V, Banerjee U, Sambaturu N, Chunchanur S, Ambica R, Chandra N. Pressured cytotoxic T cell epitope strength among SARS-CoV-2 variants correlates with COVID-19 severity. HLA 2023; 102:464-476. [PMID: 37134008 DOI: 10.1111/tan.15071] [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: 09/15/2022] [Revised: 02/13/2023] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
Heterogeneity in susceptibility among individuals to COVID-19 has been evident through the pandemic worldwide. Cytotoxic T lymphocyte (CTL) responses generated against pathogens in certain individuals are known to impose selection pressure on the pathogen, thus driving emergence of new variants. In this study, we probe the role played by host genetic heterogeneity in terms of HLA-genotypes in determining differential COVID-19 severity in patients. We use bioinformatic tools for CTL epitope prediction to identify epitopes under immune pressure. Using HLA-genotype data of COVID-19 patients from a local cohort, we observe that the recognition of pressured epitopes from the parent strain Wuhan-Hu-1 correlates with COVID-19 severity. We also identify and rank list HLA-alleles and epitopes that offer protectivity against severe disease in infected individuals. Finally, we shortlist a set of 6 pressured and protective epitopes that represent regions in the viral proteome that are under high immune pressure across SARS-CoV-2 variants. Identification of such epitopes, defined by the distribution of HLA-genotypes among members of a population, could potentially aid in prediction of indigenous variants of SARS-CoV-2 and other pathogens.
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Affiliation(s)
- Vishal Rao
- Department of Biochemistry, Indian Institute of Science (IISc), Bangalore, India
| | - Ushashi Banerjee
- Department of Biochemistry, Indian Institute of Science (IISc), Bangalore, India
| | - Narmada Sambaturu
- Department of Biochemistry, Indian Institute of Science (IISc), Bangalore, India
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Sneha Chunchanur
- Department of Microbiology, Bangalore Medical College and Research Institute (BMCRI), Bangalore, India
| | - R Ambica
- Department of Microbiology, Bangalore Medical College and Research Institute (BMCRI), Bangalore, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science (IISc), Bangalore, India
- Center for BioSystems Science and Engineering (BSSE), Indian Institute of Science (IISc), Bangalore, India
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25
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Martín-Sánchez V, Ruiz-Garcia A, Vitelli-Storelli F, Serrano-Cumplido A, Barquilla-Garcia A, Micó-Pérez RM, Olmo-Quintana V, Calderón-Montero A, Segura-Fragoso A. Case-fatality rate of SARS-CoV-2 infection during the third and fifth epidemic waves in Spain: Impact of vaccination. Semergen 2023; 49:102026. [PMID: 37356278 PMCID: PMC10227204 DOI: 10.1016/j.semerg.2023.102026] [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: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/27/2023]
Abstract
INTRODUCTION During the first and second epidemic waves in Spain, the SARS-CoV-2 case-fatality rates (CFRs) showed significant differences between Autonomous Communities (ACs). Comparing CFRs in the third and fifth epidemic waves can provide information on the impact of the different vaccination coverages in the ACs. OBJECTIVE To evaluate the impact of vaccination on COVID-19 CFRs in the third and fifth epidemic waves in Spain, according to sex, age, and AC. METHODS This work is an observational, descriptive study which uses data on COVID-19 infections, deaths, and vaccinees published by the Spanish Ministry of Health and the regional Health Departments of the ACs. The third epidemic wave was defined as the period from 26th December 2020 to 19th April 2021, and the fifth wave, from 19th July to 19th September 2021. The CFRs (deaths per 1000 infected [‰]) were calculated according to sex, age group, and AC. The standardized case-fatality ratio (SCFR) was adjusted for age and sex for each wave. We estimated the correlation between CFRs and their change between the two epidemic waves with the vaccination coverages reached at the beginning of the fifth wave. RESULTS The CFR in the fifth wave (5.7‰) was lower than in the third wave (16.5‰). In addition, the CFR in both waves was significantly higher in men than in women, and in older people than in younger ones. A decrease in the CFR between both waves was only observed in those older than 49. A strong direct and positive correlation (R2a=0.8399) was found between vaccination coverage by age group and decrease in CFR between both epidemic waves. Significant differences were seen between ACs in the two waves, as regards both CFRs and SCFRs. When comparing ACs, a direct correlation was observed between vaccination coverage and CFRs in the fifth wave, and also - although weak - between vaccination coverage and decrease in CFR between both waves. CONCLUSION The CFR significantly decreased in Spain between the third and the fifth epidemic waves in population aged 50 or older, probably due to the high vaccination coverage in that age group. Differences were observed between CFRs and SCFRs between ACs that are not explained by the differences in vaccination coverage, suggesting the need for further research and evaluation.
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Affiliation(s)
- V Martín-Sánchez
- Research Group in Gene-Environment Interactions and Health, Institute of Biomedicine (IBIOMED), University of León, León, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A Ruiz-Garcia
- Madrid Health Service (SERMAS), Department of Health, Spain
| | - F Vitelli-Storelli
- Research Group in Gene-Environment Interactions and Health, Institute of Biomedicine (IBIOMED), University of León, León, Spain.
| | | | | | - R M Micó-Pérez
- Fontanars dels Alforins Health Center, Xàtiva-Ontinyent Department of Health, 46635 Valencia, Spain
| | - V Olmo-Quintana
- Management Pharmacy Service Primary Health Care, Vice President of Ethical Committee Research with Medicine Hospital Dr. Negrín Gran Canaria Las Palmas (CEI/CEIm) Canary Health Service, Las Palmas, Spain
| | - A Calderón-Montero
- Doctor Pedro Laín Entralgo Health Center, Madrid Health Service (SERMAS), Alcorcón, Madrid, Spain
| | - A Segura-Fragoso
- Health Science Department, Castilla La Mancha University, Talavera de la Reina, Toledo, Spain
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26
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Briggs K, Sweeney R, Blehert DS, Spackman E, Suarez DL, Kapczynski DR. SARS-CoV-2 utilization of ACE2 from different bat species allows for virus entry and replication in vitro. Virology 2023; 586:122-129. [PMID: 37542819 DOI: 10.1016/j.virol.2023.07.002] [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: 04/20/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 08/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is believed to have a zoonotic origin with bats suspected as a natural host. In this work, we individually express the ACE2 of seven bat species including, little brown, great roundleaf, Pearson's horseshoe, greater horseshoe, Brazilian free-tailed, Egyptian rousette, and Chinese rufous horseshoe in DF1 cells and determine their ability to support attachment and replication of SARS-CoV-2 viruses. We demonstrate that the ACE2 receptor of all seven species made DF1 cells permissible to SARS-CoV-2. The level of virus replication differed between bat species and variants tested. The Wuhan lineage SARS-CoV-2 virus replicated to higher titers than either variant virus tested. All viruses tested grew to higher titers in cells expressing the human ACE2 gene compared to a bat ACE2. This study provides a practical in vitromethod for further testing of animal species for potential susceptibility to current and emerging SARS-CoV-2 viruses.
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Affiliation(s)
- Kelsey Briggs
- Exotic and Emerging Avian Disease Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - Ryan Sweeney
- Exotic and Emerging Avian Disease Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - David S Blehert
- U.S. Geological Survey, National Wildlife Health Center, 6006 Schroeder Road, Madison, WI, 53711, USA
| | - Erica Spackman
- Exotic and Emerging Avian Disease Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - David L Suarez
- Exotic and Emerging Avian Disease Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - Darrell R Kapczynski
- Exotic and Emerging Avian Disease Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA.
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27
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Ma W, Fu H, Jian F, Cao Y, Li M. Immune evasion and ACE2 binding affinity contribute to SARS-CoV-2 evolution. Nat Ecol Evol 2023; 7:1457-1466. [PMID: 37443189 DOI: 10.1038/s41559-023-02123-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Mutations in the SARS-CoV-2 genome could confer resistance to pre-existing antibodies and/or increased transmissibility. The recently emerged Omicron subvariants exhibit a strong tendency for immune evasion, suggesting adaptive evolution. However, because previous studies have been limited to specific lineages or subsets of mutations, the overall evolutionary trajectory of SARS-CoV-2 and the underlying driving forces are still not fully understood. Here we analysed all open-access SARS-CoV-2 genomes (up to November 2022) and correlated the mutation incidence and fitness changes with the impacts of mutations on immune evasion and ACE2 binding affinity. Our results show that the Omicron lineage had an accelerated mutation rate in the RBD region, while the mutation incidence in other genomic regions did not change dramatically over time. Mutations in the RBD region exhibited a lineage-specific pattern and tended to become more aggregated over time, and the mutation incidence was positively correlated with the strength of antibody pressure. Additionally, mutation incidence was positively correlated with changes in ACE2 binding affinity, but with a lower correlation coefficient than with immune evasion. In contrast, the effect of mutations on fitness was more closely correlated with changes in ACE2 binding affinity than with immune evasion. Our findings suggest that immune evasion and ACE2 binding affinity play significant and diverse roles in the evolution of SARS-CoV-2.
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Affiliation(s)
- Wentai Ma
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haoyi Fu
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China
| | - Yunlong Cao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China.
- Changping Laboratory, Beijing, China.
| | - Mingkun Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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28
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Ferreira IATM, Lee CYC, Foster WS, Abdullahi A, Dratva LM, Tuong ZK, Stewart BJ, Ferdinand JR, Guillaume SM, Potts MOP, Perera M, Krishna BA, Peñalver A, Cabantous M, Kemp SA, Ceron-Gutierrez L, Ebrahimi S, Lyons P, Smith KGC, Bradley J, Collier DA, McCoy LE, van der Klaauw A, Thaventhiran JED, Farooqi IS, Teichmann SA, MacAry PA, Doffinger R, Wills MR, Linterman MA, Clatworthy MR, Gupta RK. Atypical B cells and impaired SARS-CoV-2 neutralization following heterologous vaccination in the elderly. Cell Rep 2023; 42:112991. [PMID: 37590132 DOI: 10.1016/j.celrep.2023.112991] [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: 10/17/2022] [Revised: 05/15/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
Suboptimal responses to a primary vaccination course have been reported in the elderly, but there is little information regarding the impact of age on responses to booster third doses. Here, we show that individuals 70 years or older (median age 73, range 70-75) who received a primary two-dose schedule with AZD1222 and booster third dose with mRNA vaccine achieve significantly lower neutralizing antibody responses against SARS-CoV-2 spike pseudotyped virus compared with those younger than 70 (median age 66, range 54-69) at 1 month post booster. Impaired neutralization potency and breadth post third dose in the elderly is associated with circulating "atypical" spike-specific B cells expressing CD11c and FCRL5. However, when considering individuals who received three doses of mRNA vaccine, we did not observe differences in neutralization or enrichment in atypical B cells. This work highlights the finding that AdV and mRNA COVID-19 vaccine formats differentially instruct the memory B cell response.
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Affiliation(s)
- Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Colin Y C Lee
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - William S Foster
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Adam Abdullahi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lisa M Dratva
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | - Stephane M Guillaume
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Martin O P Potts
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Marianne Perera
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Benjamin A Krishna
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ana Peñalver
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | - Mia Cabantous
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lourdes Ceron-Gutierrez
- Department of Clinical Biochemistry and Immunology, Cambridge University Hospital NHS Trust, Cambridge, UK
| | - Soraya Ebrahimi
- Department of Clinical Biochemistry and Immunology, Cambridge University Hospital NHS Trust, Cambridge, UK
| | - Paul Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - John Bradley
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Dami A Collier
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Agatha van der Klaauw
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, Cambridge, UK
| | | | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, Cambridge, UK
| | | | - Paul A MacAry
- National University of Singapore, Singapore, Singapore
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Cambridge University Hospital NHS Trust, Cambridge, UK
| | - Mark R Wills
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Michelle A Linterman
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, UK.
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK.
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29
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Biswas S, Chowdhury T, Dutta K, Saha S, Das D. Biochemical Resistivity against Free Radicals and Microbes: Cooperative Action of Zn(II)/Imidazole in Phosphoesterase-Mediated Cell Death. ACS APPLIED BIO MATERIALS 2023; 6:3278-3290. [PMID: 37565455 DOI: 10.1021/acsabm.3c00365] [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] [Indexed: 08/12/2023]
Abstract
This work delivers a targeted synthesis of four isostructural O-substituted imidazole-based zinc(II) complexes, namely, [Zn2(L1)2(I)2](DMF) (1), [Zn2(L2)2(I)2](DMF) (2), [Zn2(L1)2(Br)2] (3), and [Zn2(L2)2(Br)2] (4), derived from homologous Schiff-base ligands HL1 and HL2 to explore their impact on free radicals, microbes, and dephosphorylation of phosphoesters. The antioxidant activity of all complexes was checked by various radical scavenging assays (ABTS+•, DPPH•, and H2O2 radical quenching). Among them, complex 2 showed superior radical quenching activity, as indicated by its lowest EC50 value and thus maximum antioxidative capability. Again, antibacterial assays against several Gram-positive and Gram-negative bacteria were conducted to evaluate the zone of inhibition. The minimum bactericidal concentration and minimum inhibitory concentration values from the microdilution method for all complexes revealed complex 3 to have maximum potency against Gram-positive bacteria. The P-O bond hydrolysis in the phospholipid chain caused by the hydrolytic phosphoesterase activity of the Zn(II)-complexes plays a crucial role in cell membrane rupture. A model substrate 4-PNPP was used to explain the potency of monomeric Zn(II) complex (3) for cell penetration over dimeric one (2) with a proper mechanism. Furthermore, a heme model substrate, Fe(TPP)Cl, has been introduced with the most potent complex 3 and has spectrophotometric evidence for covalent interaction with imidazole and Fe(III) that can disrupt the nitric oxide dioxygenase function of flavohemoglobin, leading to bacterial cell death. To our knowledge, this is the first case to report a novel mechanism of antimicrobial action where both the metal and the ligand are cooperatively involved in bacterial cell death. The main goal of this work is to invent multifunctional therapeutics as well as the proper chemical rationalization of biological processes using mechanistic approaches, which includes investigating the roles of halides, imidazoles, and solution-phase structural variations of complexes..
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Affiliation(s)
- Sneha Biswas
- Department of Chemistry, University College of Science, University of Calcutta, 92 A. P. C. Road, Kolkata 700009, India
| | - Tania Chowdhury
- Department of Chemistry, University College of Science, University of Calcutta, 92 A. P. C. Road, Kolkata 700009, India
| | - Koushik Dutta
- Department of Polymer Science & Technology, University of Calcutta, 92, A.P.C. Road, Kolkata- 700009 West Bengal, India
| | - Sayan Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Debasis Das
- Department of Chemistry, University College of Science, University of Calcutta, 92 A. P. C. Road, Kolkata 700009, India
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30
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Deroche L, Bellecave P, David R, Ouattara E, Garcia M, Roblot F, Boinot L, Faucher JF, Rejasse A, Gschwind G, Malvy D, Filleul L, Rogez S, Lévêque N, Lafon ME. One year of SARS-CoV-2 circulation in the Nouvelle-Aquitaine region, February 2021-2022, France. Front Microbiol 2023; 14:1176575. [PMID: 37577437 PMCID: PMC10420073 DOI: 10.3389/fmicb.2023.1176575] [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: 02/28/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
Background Since 2021, 3 variants of concern (VOC) have spread to France, causing successive epidemic waves. Objectives To describe the features of Alpha, Delta and Omicron VOC circulation in the Nouvelle-Aquitaine region, France, between February 2021 and February 2022. Study design Data from the three university hospitals (UH) of Nouvelle-Aquitaine were used to describe regional SARS-CoV-2 circulation (RT-PCR positive rates and identified VOC) as well as its consequences (total number of hospitalizations and admissions in intensive care unit). They were analyzed according to the predominant variant and compared with national data. Results A total of 611,106 SARS-CoV-2 RT-PCR tests were performed in the 3 Nouvelle-Aquitaine UH during the study period. The 37,750 positive samples were analyzed by variant-specific RT-PCR or whole-genome sequencing. In 2021, Alpha VOC was detected from week 5 until week 35. Delta became the most prevalent variant (77.3%) in week 26, reaching 100% in week 35. It was replaced by Omicron, which was initially detected week 48, represented 77% of positive samples in week 52 and was still predominant in February 2022. The RT-PCR positive rates were 4.3, 4.2, and 21.9% during the Alpha, Delta and Omicron waves, respectively. The ratio between intensive care unit admissions and total hospitalizations was lower during the Omicron wave than during the two previous waves due to the Alpha and Delta variants. Conclusion This study highlighted the need for strong regional cooperation to achieve effective SARS-CoV-2 epidemiological surveillance, in close association with the public health authorities.
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Affiliation(s)
- Luc Deroche
- Virology Laboratory, CHU Poitiers, Poitiers, France
| | | | - Romain David
- Virology Laboratory, CHU Bordeaux, Bordeaux, France
| | - Eric Ouattara
- Medical Information Analysis and Coordination Unit (UCAIM-DIM), Medical Information Department, Bordeaux University Hospital, Bordeaux, France
| | - Magali Garcia
- Virology Laboratory, CHU Poitiers, Poitiers, France
- LITEC UR15560, Université de Poitiers, Poitiers, France
| | - France Roblot
- Tropical Infectious Diseases Department, Poitiers University Hospital, Poitiers, France
- INSERM U1070, Université de Poitiers, Poitiers, France
| | - Laurence Boinot
- Service d’Information Médicale, CHU Poitiers, Poitiers, France
| | - Jean-François Faucher
- Tropical Infectious Diseases Department, Limoges University Hospital, Limoges, France
| | - Aurélie Rejasse
- Medical Information Department, Limoges University Hospital, Limoges, France
| | - Guillaume Gschwind
- Medical Information Department, Limoges University Hospital, Limoges, France
| | - Denis Malvy
- Department of Infectious and Tropical Diseases, CHU Bordeaux, Bordeaux, France
- UMR Inserm 1219/IRD, University of Bordeaux, Bordeaux, France
| | - Laurent Filleul
- Regional Office-Nouvelle Aquitaine, Santé publique France, Bordeaux, France
| | - Sylvie Rogez
- Virology Laboratory, CHU Limoges, Limoges, France
| | - Nicolas Lévêque
- Virology Laboratory, CHU Poitiers, Poitiers, France
- LITEC UR15560, Université de Poitiers, Poitiers, France
| | - Marie-Edith Lafon
- Virology Laboratory, CHU Bordeaux, Bordeaux, France
- CNRS UMR 5234, University of Bordeaux, Bordeaux, France
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31
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Gupta A, Basu R, Bashyam MD. Assessing the evolution of SARS-CoV-2 lineages and the dynamic associations between nucleotide variations. Access Microbiol 2023; 5:acmi000513.v3. [PMID: 37601437 PMCID: PMC10436015 DOI: 10.1099/acmi.0.000513.v3] [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: 09/24/2022] [Accepted: 02/20/2023] [Indexed: 08/22/2023] Open
Abstract
Despite seminal advances towards understanding the infection mechanism of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), it continues to cause significant morbidity and mortality worldwide. Though mass immunization programmes have been implemented in several countries, the viral transmission cycle has shown a continuous progression in the form of multiple waves. A constant change in the frequencies of dominant viral lineages, arising from the accumulation of nucleotide variations (NVs) through favourable selection, is understandably expected to be a major determinant of disease severity and possible vaccine escape. Indeed, worldwide efforts have been initiated to identify specific virus lineage(s) and/or NVs that may cause a severe clinical presentation or facilitate vaccination breakthrough. Since host genetics is expected to play a major role in shaping virus evolution, it is imperative to study the role of genome-wide SARS-CoV-2 NVs across various populations. In the current study, we analysed the whole genome sequence of 3543 SARS-CoV-2-infected samples obtained from the state of Telangana, India (including 210 from our previous study), collected over an extended period from April 2020 to October 2021. We present a unique perspective on the evolution of prevalent virus lineages and NVs during this period. We also highlight the presence of specific NVs likely to be associated favourably with samples classified as vaccination breakthroughs. Finally, we report genome-wide intra-host variations at novel genomic positions. The results presented here provide critical insights into virus evolution over an extended period and pave the way to rigorously investigate the role of specific NVs in vaccination breakthroughs.
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Affiliation(s)
- Asmita Gupta
- Laboratory of Molecular Oncology, Centre of DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Reelina Basu
- Laboratory of Molecular Oncology, Centre of DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Murali Dharan Bashyam
- Laboratory of Molecular Oncology, Centre of DNA Fingerprinting and Diagnostics, Hyderabad, India
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32
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Tegally H, Wilkinson E, Tsui JLH, Moir M, Martin D, Brito AF, Giovanetti M, Khan K, Huber C, Bogoch II, San JE, Poongavanan J, Xavier JS, Candido DDS, Romero F, Baxter C, Pybus OG, Lessells RJ, Faria NR, Kraemer MUG, de Oliveira T. Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern. Cell 2023; 186:3277-3290.e16. [PMID: 37413988 PMCID: PMC10247138 DOI: 10.1016/j.cell.2023.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023]
Abstract
The Alpha, Beta, and Gamma SARS-CoV-2 variants of concern (VOCs) co-circulated globally during 2020 and 2021, fueling waves of infections. They were displaced by Delta during a third wave worldwide in 2021, which, in turn, was displaced by Omicron in late 2021. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of VOCs worldwide. We find that source-sink dynamics varied substantially by VOC and identify countries that acted as global and regional hubs of dissemination. We demonstrate the declining role of presumed origin countries of VOCs in their global dispersal, estimating that India contributed <15% of Delta exports and South Africa <1%-2% of Omicron dispersal. We estimate that >80 countries had received introductions of Omicron within 100 days of its emergence, associated with accelerated passenger air travel and higher transmissibility. Our study highlights the rapid dispersal of highly transmissible variants, with implications for genomic surveillance along the hierarchical airline network.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | | | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Darren Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
| | - Kamran Khan
- BlueDot, Toronto, ON, Canada; Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jenicca Poongavanan
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Joicymara S Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
| | - Darlan da S Candido
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Filipe Romero
- MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK; Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R Faria
- Department of Biology, University of Oxford, Oxford, UK; MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Jameel Institute, School of Public Health, Imperial College London, London, UK; Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Moritz U G Kraemer
- Department of Biology, University of Oxford, Oxford, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK.
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Department of Global Health, University of Washington, Seattle, WA, USA.
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Roubidoux EK, Brigleb PH, Vegesana K, Souquette A, Whitt K, Freiden P, Green A, Thomas PG, McGargill MA, Wolf J, Schultz-Cherry S. Utility of nasal swabs for assessing mucosal immune responses towards SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548630. [PMID: 37503213 PMCID: PMC10370023 DOI: 10.1101/2023.07.12.548630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
SARS-CoV-2 has caused millions of infections worldwide since its emergence in 2019. Understanding how infection and vaccination induce mucosal immune responses and how they fluctuate over time is important, especially since they are key in preventing infection and reducing disease severity. We established a novel methodology for assessing SARS-CoV-2 cytokine and antibody responses at the nasal epithelium by using nasopharyngeal swabs collected longitudinally before and after either SARS-CoV-2 infection or vaccination. We then compared responses between mucosal and systemic compartments. We demonstrate that cytokine and antibody profiles differ markedly between compartments. Nasal cytokines show a wound healing phenotype while plasma cytokines are consistent with pro-inflammatory pathways. We found that nasal IgA and IgG have different kinetics after infection, with IgA peaking first. Although vaccination results in low nasal IgA, IgG induction persists for up to 180 days post-vaccination. This research highlights the importance of studying mucosal responses in addition to systemic responses to respiratory infections to understand the correlates of disease severity and immune memory. The methods described herein can be used to further mucosal vaccine development by giving us a better understanding of immunity at the nasal epithelium providing a simpler, alternative clinical practice to studying mucosal responses to infection. Teaser A nasopharyngeal swab can be used to study the intranasal immune response and yields much more information than a simple viral diagnosis.
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Bahlmann NA, Mautner L, Hoyos M, Sallard E, Berger C, Dangel A, Jönsson F, Fischer JC, Kreppel F, Zhang W, Esposito I, Bölke E, Baiker A, Ehrhardt A. In Vitro Analysis of the Effect of SARS-CoV-2 Non-VOC and four Variants of Concern on MHC-Class-I Expression on Calu-3 and Caco-2 Cells. Genes (Basel) 2023; 14:1348. [PMID: 37510253 PMCID: PMC10378856 DOI: 10.3390/genes14071348] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
As the MHC-I-pathway is key to antigen presentation to cytotoxic T-cells and, therefore, recognition by the host adaptive immune system, we hypothesized that SARS-CoV-2 including its Variants of Concern (VOCs), influences MHC-I expression on epithelial cell surfaces as an immune evasion strategy. We conducted an in vitro time course experiment with the human airway epithelial cell line Calu-3 and the human colorectal adenocarcinoma cell line Caco-2. Cells were infected with SARS-CoV-2 strains non-VOC/B.1.1, Alpha/B.1.1.7, Beta/B.1.351, Gamma/P.1, and Delta/B.1.617.2. At 2, 24, 48 and 72 h post-infection we performed RT-qPCR to track viral replication. Simultaneously, we performed intracellular staining with a serum of a double-vaccinated healthy adult containing a high amount of spike protein antibody. In flow cytometry experiments, we differentiated between infected (spike protein positive) and bystander (spike protein negative) cells. To compare their HLA expression levels, cells were stained extracellularly with anti-HLA-A-IgG and anti-HLA-B,C-IgG. While HLA-A expression was stable on infected Calu-3 cells for all variants, it increased to different degrees on bystander cells in samples infected with VOCs Beta, Gamma, Delta, or non-VOC over the time course analyzed. In contrast, HLA-A levels were stable in bystander Calu-3 cells in samples infected with the Alpha variant. The upregulation of MHC-I on spike protein negative bystander cells in Calu-3 cell cultures infected with Beta, Gamma, Delta, and partly non-VOC might suggest that infected cells are still capable of secreting inflammatory cytokines like type-I interferons stimulating the MHC-I expression on bystander cells. In comparison, there was no distinct effect on HLA expression level on Caco-2 cells of any of the VOCs or non-VOC. Further investigations of the full range of immune evasion strategies of SARS-CoV-2 variants are warranted.
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Affiliation(s)
- Nora A Bahlmann
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
| | - Lena Mautner
- Bavarian Health and Food Safety Authority, 85764 Oberschleißheim, Germany
| | - Mona Hoyos
- Bavarian Health and Food Safety Authority, 85764 Oberschleißheim, Germany
| | - Erwan Sallard
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
| | - Carola Berger
- Bavarian Health and Food Safety Authority, 85764 Oberschleißheim, Germany
| | - Alexandra Dangel
- Bavarian Health and Food Safety Authority, 85764 Oberschleißheim, Germany
| | - Franziska Jönsson
- Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
| | - Johannes C Fischer
- Institute for Transplant Diagnostics and Cell Therapeutics, Heinrich-Heine-University, 40204 Duesseldorf, Germany
| | - Florian Kreppel
- Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
| | - Wenli Zhang
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
| | - Irene Esposito
- Institute of Pathology, Heinrich Heine University and University Hospital, 40204 Duesseldorf, Germany
| | - Edwin Bölke
- Department of Radiation Oncology, Heinrich-Heine-University, 40204 Duesseldorf, Germany
| | - Armin Baiker
- Bavarian Health and Food Safety Authority, 85764 Oberschleißheim, Germany
| | - Anja Ehrhardt
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453 Witten, Germany
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Bhanothu V, Munne K, Pande S, Singh P, Jagtap D, Aranha C, Gogoi D, Bhagat S, Gaonkar R, Kerkar S, Shah K, Mukherjee N, Bhor V, Patel V, Mahale SD, Sachdeva G, Begum S. The dynamics of SARS-CoV-2 infection in unvaccinated and vaccinated populations in Mumbai, India, between 28 December 2020 and 30 August 2021. Arch Virol 2023; 168:188. [PMID: 37351663 DOI: 10.1007/s00705-023-05815-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 02/18/2023] [Indexed: 06/24/2023]
Abstract
The emergence and evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants that could compromise vaccine efficacy (VE) with re-infections in immunized individuals have necessitated continuous surveillance of VE. Here, the occurrence and dynamics of SARS-CoV-2 infections in the context of vaccination during the second wave of infection in Mumbai were evaluated. RT-PCR cycle threshold (Ct) values of the open reading frame (ORF)/envelope (E)/nucleocapsid (N) genes obtained from a total of 42415 samples, comprising unvaccinated (96.88%) and vaccinated cases (3.12%) were analyzed between December 28, 2020, and August 30, 2021. A lower incidence of SARS-CoV-2 infection in fully vaccinated cases (5.07%) compared to partially vaccinated cases (6.5%) and unvaccinated cases (13.453%) was recorded. VE was significant after the first dose of vaccination (ORF gene p-value = 0.003429, and E/N gene p-value = 0.000866). Furthermore, VE was observed to be significant when the post-immunization (first dose) period was stratified to within 30 days (ORF gene p-value = 0.0094 and E/N gene p-value = 0.0023) and to 60 days following the second dose of vaccination (ORF gene p-value = 0.0238). Also, significantly higher efficacy was observed within individuals receiving two doses compared to a single dose (ORF gene p-value = 0.0132 and E/N gene p-value = 0.0387). The emergence of breakthrough infections was also evident (odds ratio= 0.34; 95% confidence interval= 0.27-0.43). Interestingly, viral loads trended towards being higher in some groups of partially vaccinated individuals compared to completely vaccinated and unvaccinated populations. Finally, our results delineated a significantly higher incidence of SARS-CoV-2 acquisition in males, asymptomatic individuals, individuals with comorbidities, and those who were unvaccinated.
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Affiliation(s)
- Venkanna Bhanothu
- Genetic Research Centre, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India.
| | - Kiran Munne
- Department of Clinical Research, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Shailesh Pande
- Genetic Research Centre, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India.
| | - Priyanka Singh
- Viral Immunopathogenesis Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Dhanashree Jagtap
- Cellular & Structural Biology Division, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Clara Aranha
- Molecular Immunology and Microbiology, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Dimpu Gogoi
- Viral Immunopathogenesis Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Sharad Bhagat
- Viral Immunopathogenesis Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Reshma Gaonkar
- Department of Neuroendocrinology, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Shilpa Kerkar
- Department of Clinical Research, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Karan Shah
- Molecular Immunology and Microbiology, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Nupur Mukherjee
- Department of Molecular and Cellular Biology, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Vikrant Bhor
- Molecular Immunology and Microbiology, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Vainav Patel
- Viral Immunopathogenesis Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Smita D Mahale
- ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Geetanjali Sachdeva
- ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
| | - Shahina Begum
- Department of Biostatistics, ICMR-National Institute for Research in Reproductive and Child Health, Jehangir Merwanji Street, Parel, Mumbai, 400012, India
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Zhou B, Sun Y, Mao H, Su L, Lou Y, Yan H, Yao W, Chen H, Zhang Y. Molecular epidemiological characteristics of SARS-CoV-2 in imported cases from 2021 to 2022 in Zhejiang Province, China. Front Public Health 2023; 11:1189969. [PMID: 37427288 PMCID: PMC10323361 DOI: 10.3389/fpubh.2023.1189969] [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: 03/22/2023] [Accepted: 05/30/2023] [Indexed: 07/11/2023] Open
Abstract
Backgrounds The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a global threat since 2020. The emergence of the Omicron variant in 2021, which replaced Delta as the dominant variant of concern, has had a significant adverse impact on the global economy and public health. During this period, Zhejiang Province implemented dynamic zeroing and focused on preventing imported cases. This study aimed to gain clear insight into the characteristics of imported COVID-19 cases in Zhejiang Province. Methods We conducted a systematic molecular epidemiological analysis of 146 imported cases between July 2021 and November 2022 in Zhejiang Province. Virus samples with cycle threshold (Ct) value less than 32 were performed next generation sequencing. Basing the whole genome sequence obtained after quality control and assembly of reads, the whole genome variation map and phylogenetic tree were constructed and further analyzed. Results Our study identified critical months and populations for surveillance, profiled the variation of various lineages, determined the evolutionary relationships among various lineages of SARS-CoV-2, and compared the results in Zhejiang with those obtained worldwide during this period. Conclusion The continuous molecular epidemiological surveillance of imported cases of COVID-19 in Zhejiang Province during 2021 to 2022 is consistent with the global epidemic trend.
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37
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Brown PA. Country-level predictors of COVID-19 mortality. Sci Rep 2023; 13:9263. [PMID: 37286632 DOI: 10.1038/s41598-023-36449-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 06/03/2023] [Indexed: 06/09/2023] Open
Abstract
This study aimed to identify country-level predictors of COVID-19 mortality, after controlling for diverse potential factors, and utilizing current worldwide mortality data. COVID-19 deaths, as well as geographic, demographic, socioeconomic, healthcare, population health, and pandemic-related variables, were obtained for 152 countries. Continuous variables were examined with Spearman's correlation, categorical variables with ANOVA or Welch's Heteroscedastic F Test, and country-level independent predictors of COVID-19 mortality identified by weighted generalized additive models. This study identified independent mortality predictors in six limited models, comprising groups of related variables. However, in the full model, only WHO region, percent of population ≥ 65 years, Corruption Perception Index, hospital beds/100,000 population, and COVID-19 cases/100,000 population were predictive of mortality, with model accounting for 80.7% of variance. These findings suggest areas for focused intervention in the event of similar future public health emergencies, including prioritization of the elderly, optimizing healthcare capacity, and improving deficient health sector-related governance.
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Affiliation(s)
- Paul A Brown
- Department of Basic Medical Sciences, Faculty of Medical Sciences Teaching and Research Complex, The University of the West Indies, Mona, Kingston 7, Jamaica.
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38
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Messali S, Rondina A, Giovanetti M, Bonfanti C, Ciccozzi M, Caruso A, Caccuri F. Traceability of SARS-CoV-2 transmission through quasispecies analysis. J Med Virol 2023; 95:e28848. [PMID: 37294038 DOI: 10.1002/jmv.28848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023]
Abstract
During COVID-19 pandemic, consensus genomic sequences were used for rapidly monitor the spread of the virus worldwide. However, less attention was paid to intrahost genetic diversity. In fact, in the infected host, SARS-CoV-2 consists in an ensemble of replicating and closely related viral variants so-called quasispecies. Here we show that intrahost single nucleotide variants (iSNVs) represent a target for contact tracing analysis. Our data indicate that in the acute phase of infection, in highly likely transmission links, the number of viral particles transmitted from one host to another (bottleneck size) is large enough to propagate iSNVs among individuals. Furthermore, we demonstrate that, during SARS-CoV-2 outbreaks when the consensus sequences are identical, it is possible to reconstruct the transmission chains by genomic investigations of iSNVs. Specifically, we found that it is possible to identify transmission chains by limiting the analysis of iSNVs to only three well-conserved genes, namely nsp2, ORF3, and ORF7.
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Affiliation(s)
- Serena Messali
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Alessandro Rondina
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, Rome, Italy
| | - Carlo Bonfanti
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Massimo Ciccozzi
- Clinical Pathology and Microbiology Laboratory, Unit of Medical Statistics and Molecular Epidemiology, University Hospital Campus Biomedico, Rome, Italy
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Francesca Caccuri
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
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Bhardwaj P, Mishra SK, Behera SP, Zaman K, Kant R, Singh R. Genomic evolution of the SARS-CoV-2 Variants of Concern: COVID-19 pandemic waves in India. EXCLI JOURNAL 2023; 22:451-465. [PMID: 37534220 PMCID: PMC10390896 DOI: 10.17179/excli2023-6098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/30/2023] [Indexed: 08/04/2023]
Abstract
SARS-CoV-2 has mutated rapidly since its first case report in Wuhan, China, leading to the emergence of an indefinite number of variants. India has witnessed three waves of the COVID-19 pandemic. The country saw its first wave of SARS-CoV-2 illness from late January 2020 to February 2021. With a peak surge of cases in mid-September 2020, India recorded more than 11 million cases and a death toll of more than 0.165 million at this time. India faced a brutal second wave driven by the emergence of highly infectious SARS-CoV-2 variants B.1.617.2 (Delta variant) and the third wave with the leading cause of BA.2 (Omicron variant), which has led to an unprecedented rise in COVID-19 cases in the country. On September 14, 2022, India recorded a cumulative 44.51 million cases of COVID-19 with more than 0.528 million deaths. The discovery of common circulating mutants is facilitated by genome sequencing. The changes in the Spike surface glycoprotein recombinant binding domains served as the critical alterations, resulting in enhanced infectivity and transmissibility, with severe clinical effects. Further, the predominant mutation in the SARS-CoV-2 spike protein; the D614G strains served as a model for vaccine development. The mutation of the Wuhan strain to the Variant of Concern led to a significant increase in SARS-CoV-2 infections. In addition, there was a shift in the age group affected by SARS-CoV-2 variant infection. The current review summarized the COVID-19 pandemic's Variant of Concern and the advent of SARS-CoV-2 in India.
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Affiliation(s)
- Pooja Bhardwaj
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Shailendra Kumar Mishra
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Sthita Pragnya Behera
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Kamran Zaman
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Rajni Kant
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Rajeev Singh
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
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40
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Pandit R, Matthews QL. A SARS-CoV-2: Companion Animal Transmission and Variants Classification. Pathogens 2023; 12:775. [PMID: 37375465 DOI: 10.3390/pathogens12060775] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The continuous emergence of novel viruses and their diseases are a threat to global public health as there have been three outbreaks of coronaviruses that are highly pathogenic to humans in the span of the last two decades, severe acute respiratory syndrome (SARS)-CoV in 2002, Middle East respiratory syndrome (MERS)-CoV in 2012, and novel SARS-CoV-2 which emerged in 2019. The unprecedented spread of SARS-CoV-2 worldwide has given rise to multiple SARS-CoV-2 variants that have either altered transmissibility, infectivity, or immune escaping ability, causing diseases in a broad range of animals including human and non-human hosts such as companion, farm, zoo, or wild animals. In this review, we have discussed the recent SARS-CoV-2 outbreak, potential animal reservoirs, and natural infections in companion and farm animals, with a particular focus on SARS-CoV-2 variants. The expeditious development of COVID-19 vaccines and the advancements in antiviral therapeutics have contained the COVID-19 pandemic to some extent; however, extensive research and surveillance concerning viral epidemiology, animal transmission, variants, or seroprevalence in diverse hosts are essential for the future eradication of COVID-19.
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Affiliation(s)
- Rachana Pandit
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Qiana L Matthews
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
- Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
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Subramoney K, Mtileni N, Giandhari J, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Maharaj A, Tshiabuila D, Tegally H, Wilkinson E, de Oliveira T, Fielding BC, Treurnicht FK. Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages. Viruses 2023; 15:v15051194. [PMID: 37243279 PMCID: PMC10223853 DOI: 10.3390/v15051194] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
SARS-CoV-2 lineages and variants of concern (VOC) have gained more efficient transmission and immune evasion properties with time. We describe the circulation of VOCs in South Africa and the potential role of low-frequency lineages on the emergence of future lineages. Whole genome sequencing was performed on SARS-CoV-2 samples from South Africa. Sequences were analysed with Nextstrain pangolin tools and Stanford University Coronavirus Antiviral & Resistance Database. In 2020, 24 lineages were detected, with B.1 (3%; 8/278), B.1.1 (16%; 45/278), B.1.1.348 (3%; 8/278), B.1.1.52 (5%; 13/278), C.1 (13%; 37/278) and C.2 (2%; 6/278) circulating during the first wave. Beta emerged late in 2020, dominating the second wave of infection. B.1 and B.1.1 continued to circulate at low frequencies in 2021 and B.1.1 re-emerged in 2022. Beta was outcompeted by Delta in 2021, which was thereafter outcompeted by Omicron sub-lineages during the 4th and 5th waves in 2022. Several significant mutations identified in VOCs were also detected in low-frequency lineages, including S68F (E protein); I82T (M protein); P13L, R203K and G204R/K (N protein); R126S (ORF3a); P323L (RdRp); and N501Y, E484K, D614G, H655Y and N679K (S protein). Low-frequency variants, together with VOCs circulating, may lead to convergence and the emergence of future lineages that may increase transmissibility, infectivity and escape vaccine-induced or natural host immunity.
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Affiliation(s)
- Kathleen Subramoney
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2193, South Africa
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Nkhensani Mtileni
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2193, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Yajna Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Akhil Maharaj
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Derek Tshiabuila
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Burtram C Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical BioSciences, University of the Western Cape, Cape Town 7535, South Africa
| | - Florette K Treurnicht
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2193, South Africa
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Moisan A, Soares A, De Oliveira F, Alessandri-Gradt E, Lecoquierre F, Fourneaux S, Plantier JC, Gueudin M. Evaluation of Analytical and Clinical Performance and Usefulness in a Real-Life Hospital Setting of Two in-House Real-Time RT-PCR Assays to Track SARS-CoV-2 Variants of Concern. Viruses 2023; 15:v15051115. [PMID: 37243201 DOI: 10.3390/v15051115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/20/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023] Open
Abstract
Since the end of 2020, multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have emerged and spread worldwide. Tracking their evolution has been a challenge due to the huge number of positive samples and limited capacities of whole-genome sequencing. Two in-house variant-screening RT-PCR assays were successively designed in our laboratory in order to detect specific known mutations in the spike region and to rapidly detect successively emerging VOCs. The first one (RT-PCR#1) targeted the 69-70 deletion and the N501Y substitution simultaneously, whereas the second one (RT-PCR#2) targeted the E484K, E484Q, and L452R substitutions simultaneously. To evaluate the analytical performance of these two RT-PCRs, 90 negative and 30 positive thawed nasopharyngeal swabs were retrospectively analyzed, and no discordant results were observed. Concerning the sensitivity, for RT-PCR#1, serial dilutions of the WHO international standard SARS-CoV-2 RNA, corresponding to the genome of an Alpha variant, were all detected up to 500 IU/mL. For RT-PCR#2, dilutions of a sample harboring the E484K substitution and of a sample harboring the L452R and E484Q substitutions were all detected up to 1000 IU/mL and 2000 IU/mL, respectively. To evaluate the performance in a real-life hospital setting, 1308 and 915 profiles of mutations, obtained with RT-PCR#1 and RT-PCR#2, respectively, were prospectively compared to next-generation sequencing (NGS) data. The two RT-PCR assays showed an excellent concordance with the NGS data, with 99.8% for RT-PCR#1 and 99.2% for RT-PCR#2. Finally, for each mutation targeted, the clinical sensitivity, the clinical specificity and the positive and negative predictive values showed excellent clinical performance. Since the beginning of the SARS-CoV-2 pandemic, the emergence of variants-impacting the disease's severity and the efficacy of vaccines and therapies-has forced medical analysis laboratories to constantly adapt to the strong demand for screening them. Our data showed that in-house RT-PCRs are useful and adaptable tools for monitoring such rapid evolution and spread of SARS-CoV-2 VOCs.
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Affiliation(s)
- Alice Moisan
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, F-76000 Rouen, France
| | - Anaïs Soares
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, F-76000 Rouen, France
| | - Fabienne De Oliveira
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, F-76000 Rouen, France
| | - Elodie Alessandri-Gradt
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, F-76000 Rouen, France
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France
| | - Steeve Fourneaux
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France
| | - Jean-Christophe Plantier
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, F-76000 Rouen, France
| | - Marie Gueudin
- Univ Rouen Normandie, UNICAEN, INSERM, DYNAMICURE UMR 1311, CHU Rouen, Department of Virology, F-76000 Rouen, France
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Yurkovetskiy L, Egri S, Kurhade C, Diaz-Salinas MA, Jaimes JA, Nyalile T, Xie X, Choudhary MC, Dauphin A, Li JZ, Munro JB, Shi PY, Shen K, Luban J. S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.535005. [PMID: 37034621 PMCID: PMC10081308 DOI: 10.1101/2023.03.30.535005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
SARS-CoV-2 variants bearing complex combinations of mutations that confer increased transmissibility, COVID-19 severity, and immune escape, were first detected after S:D614G had gone to fixation, and likely originated during persistent infection of immunocompromised hosts. To test the hypothesis that S:D614G facilitated emergence of such variants, S:D614G was reverted to the ancestral sequence in the context of sequential Spike sequences from an immunocompromised individual, and within each of the major SARS-CoV-2 variants of concern. In all cases, infectivity of the S:D614G revertants was severely compromised. The infectivity of atypical SARS-CoV-2 lineages that propagated in the absence of S:D614G was found to be dependent upon either S:Q613H or S:H655Y. Notably, Gamma and Omicron variants possess both S:D614G and S:H655Y, each of which contributed to infectivity of these variants. Among sarbecoviruses, S:Q613H, S:D614G, and S:H655Y are only detected in SARS-CoV-2, which is also distinguished by a polybasic S1/S2 cleavage site. Genetic and biochemical experiments here showed that S:Q613H, S:D614G, and S:H655Y each stabilize Spike on virions, and that they are dispensable in the absence of S1/S2 cleavage, consistent with selection of these mutations by the S1/S2 cleavage site. CryoEM revealed that either S:D614G or S:H655Y shift the Spike receptor binding domain (RBD) towards the open conformation required for ACE2-binding and therefore on pathway for infection. Consistent with this, an smFRET reporter for RBD conformation showed that both S:D614G and S:H655Y spontaneously adopt the conformation that ACE2 induces in the parental Spike. Data from these orthogonal experiments demonstrate that S:D614G and S:H655Y are convergent adaptations to the polybasic S1/S2 cleavage site which stabilize S1 on the virion in the open RBD conformation and act epistatically to promote the fitness of variants bearing complex combinations of clinically significant mutations.
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Affiliation(s)
- Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Shawn Egri
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
- These authors contributed equally
| | - Marco A. Diaz-Salinas
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Javier A. Jaimes
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- These authors contributed equally
| | - Thomas Nyalile
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Manish C. Choudhary
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jonathan Z. Li
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
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Arantes I, Bello G, Nascimento V, Souza V, da Silva A, Silva D, Nascimento F, Mejía M, Brandão MJ, Gonçalves L, Silva G, da Costa CF, Abdalla L, Santos JH, Ramos TCA, Piantham C, Ito K, Siqueira MM, Resende PC, Wallau GL, Delatorre E, Gräf T, Naveca FG. Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas. Nat Commun 2023; 14:2048. [PMID: 37041143 PMCID: PMC10089528 DOI: 10.1038/s41467-023-37541-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/21/2023] [Indexed: 04/13/2023] Open
Abstract
The SARS-CoV-2 variants of concern (VOCs) Delta and Omicron spread globally during mid and late 2021, respectively. In this study, we compare the dissemination dynamics of these VOCs in the Amazonas state, one of Brazil's most heavily affected regions. We sequenced the virus genome from 4128 patients collected in Amazonas between July 1st, 2021, and January 31st, 2022, and investigated the viral dynamics using a phylodynamic approach. The VOCs Delta and Omicron BA.1 displayed similar patterns of phylogeographic spread but different epidemic dynamics. The replacement of Gamma by Delta was gradual and occurred without an upsurge of COVID-19 cases, while the rise of Omicron BA.1 was extremely fast and fueled a sharp increase in cases. Thus, the dissemination dynamics and population-level impact of new SARS-CoV-2 variants introduced in the Amazonian population after mid-2021, a setting with high levels of acquired immunity, greatly vary according to their viral phenotype.
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Affiliation(s)
- Ighor Arantes
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Victor Souza
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Arlesson da Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Dejanane Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Matilde Mejía
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Maria Júlia Brandão
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
| | - Luciana Gonçalves
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
- Fundação de Vigilância em Saúde do Amazonas - Dra Rosemary Costa Pinto, Manaus, Brazil
| | - George Silva
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil
- Fundação Centro de Controle de Oncologia do Estado do Amazonas, Manaus, Brazil
| | - Cristiano Fernandes da Costa
- Fundação de Vigilância em Saúde do Amazonas - Dra Rosemary Costa Pinto, Manaus, Brazil
- Conselho de Secretários Municipais de Saúde do Amazonas COSEMS - AM, Manaus, Brazil
| | | | | | | | - Chayada Piantham
- Graduate School of Infectious Diseases, Hokkaido University, Hokkaido, Japan
| | - Kimihito Ito
- International Institute for Zoonosis Control, Hokkaido University, Hokkaido, Japan
| | - Marilda Mendonça Siqueira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gabriel Luz Wallau
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Brazil
| | - Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fiocruz, Curitiba, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Brazil.
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
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Markov PV, Ghafari M, Beer M, Lythgoe K, Simmonds P, Stilianakis NI, Katzourakis A. The evolution of SARS-CoV-2. Nat Rev Microbiol 2023; 21:361-379. [PMID: 37020110 DOI: 10.1038/s41579-023-00878-2] [Citation(s) in RCA: 178] [Impact Index Per Article: 178.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly be inferred indirectly before, such as the emergence of variants with distinct phenotypes, for example transmissibility, severity and immune evasion. This Review explores the mechanisms that generate genetic variation in SARS-CoV-2, underlying the within-host and population-level processes that underpin these events. We examine the selective forces that likely drove the evolution of higher transmissibility and, in some cases, higher severity during the first year of the pandemic and the role of antigenic evolution during the second and third years, together with the implications of immune escape and reinfections, and the increasing evidence for and potential relevance of recombination. In order to understand how major lineages, such as variants of concern (VOCs), are generated, we contrast the evidence for the chronic infection model underlying the emergence of VOCs with the possibility of an animal reservoir playing a role in SARS-CoV-2 evolution, and conclude that the former is more likely. We evaluate uncertainties and outline scenarios for the possible future evolutionary trajectories of SARS-CoV-2.
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Affiliation(s)
- Peter V Markov
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
- London School of Hygiene & Tropical Medicine, University of London, London, UK.
| | - Mahan Ghafari
- Big Data Institute, University of Oxford, Oxford, UK
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nikolaos I Stilianakis
- European Commission, Joint Research Centre (JRC), Ispra, Italy
- Department of Biometry and Epidemiology, University of Erlangen-Nuremberg, Erlangen, Germany
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46
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Rahman MS, Hoque MN, Chowdhury SR, Siddique MM, Islam OK, Galib SM, Islam MT, Hossain MA. Temporal dynamics and fatality of SARS-CoV-2 variants in Bangladesh. Health Sci Rep 2023; 6:e1209. [PMID: 37077184 PMCID: PMC10108430 DOI: 10.1002/hsr2.1209] [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: 01/11/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 04/21/2023] Open
Abstract
Background and Aims Since the beginning of the SARS-CoV-2 pandemic, multiple new variants have emerged posing an increased risk to global public health. This study aimed to investigate SARS-CoV-2 variants, their temporal dynamics, infection rate (IFR) and case fatality rate (CFR) in Bangladesh by analyzing the published genomes. Methods We retrieved 6610 complete whole genome sequences of the SARS-CoV-2 from the GISAID (Global Initiative on Sharing all Influenza Data) platform from March 2020 to October 2022, and performed different in-silico bioinformatics analyses. The clade and Pango lineages were assigned by using Nextclade v2.8.1. SARS-CoV-2 infections and fatality data were collected from the Institute of Epidemiology Disease Control and Research (IEDCR), Bangladesh. The average IFR was calculated from the monthly COVID-19 cases and population size while average CFR was calculated from the number of monthly deaths and number of confirmed COVID-19 cases. Results SARS-CoV-2 first emerged in Bangladesh on March 3, 2020 and created three pandemic waves so far. The phylogenetic analysis revealed multiple introductions of SARS-CoV-2 variant(s) into Bangladesh with at least 22 Nextstrain clades and 107 Pangolin lineages with respect to the SARS-CoV-2 reference genome of Wuhan/Hu-1/2019. The Delta variant was detected as the most predominant (48.06%) variant followed by Omicron (27.88%), Beta (7.65%), Alpha (1.56%), Eta (0.33%) and Gamma (0.03%) variant. The overall IFR and CFR from circulating variants were 13.59% and 1.45%, respectively. A time-dependent monthly analysis showed significant variations in the IFR (p = 0.012, Kruskal-Wallis test) and CFR (p = 0.032, Kruskal-Wallis test) throughout the study period. We found the highest IFR (14.35%) in 2020 while Delta (20A) and Beta (20H) variants were circulating in Bangladesh. Remarkably, the highest CFR (1.91%) from SARS-CoV-2 variants was recorded in 2021. Conclusion Our findings highlight the importance of genomic surveillance for careful monitoring of variants of concern emergence to interpret correctly their relative IFR and CFR, and thus, for implementation of strengthened public health and social measures to control the spread of the virus. Furthermore, the results of the present study may provide important context for sequence-based inference in SARS-CoV-2 variant(s) evolution and clinical epidemiology beyond Bangladesh.
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Affiliation(s)
- M. Shaminur Rahman
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive HealthBangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh
| | - Susmita Roy Chowdhury
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Md. Moradul Siddique
- Department of Computer Science and EngineeringJashore University of Science and TechnologyJashoreBangladesh
| | - Ovinu Kibria Islam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Syed Md. Galib
- Department of Computer Science and EngineeringJashore University of Science and TechnologyJashoreBangladesh
| | - Md. Tanvir Islam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - M. Anwar Hossain
- Department of MicrobiologyUniversity of DhakaDhakaBangladesh
- Jashore University of Science and TechnologyJashoreBangladesh
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47
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Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou X, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S, Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nat Methods 2023; 20:512-522. [PMID: 36823332 PMCID: PMC10399614 DOI: 10.1038/s41592-023-01769-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 01/17/2023] [Indexed: 02/25/2023]
Abstract
In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info , a platform that currently tracks over 40 million combinations of Pango lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials and the general public. We describe the interpretable visualizations available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data and the server infrastructure that enables widespread data dissemination via a high-performance API that can be accessed using an R package. We show how outbreak.info can be used for genomic surveillance and as a hypothesis-generation tool to understand the ongoing pandemic at varying geographic and temporal scales.
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Affiliation(s)
- Karthik Gangavarapu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Alaa Abdel Latif
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Julia L Mullen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Manar Alkuzweny
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ginger Tsueng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Haag
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karina Zaiets
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marco Cano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Xinghua Zhou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Zhongchao Qian
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rachel Sattler
- Skaggs Graduate School of Biological and Chemical Sciences, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Raphael T C Lee
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Lucas Freitas
- GISAID Global Data Science Initiative, Munich, Germany
- Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Ministry of Health, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew I Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, La Jolla, CA, USA
| | - Laura D Hughes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
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48
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Gopalan V, Chandran A, Arumugam K, Sundaram M, Velladurai S, Govindan K, Azhagesan N, Jeyavel P, Dhandapani P, Sivasubramanian S, Kitambi SS. Distribution and Functional Analyses of Mutations in Spike Protein and Phylogenic Diversity of SARS-CoV-2 Variants Emerged during the Year 2021 in India. J Glob Infect Dis 2023; 15:43-51. [PMID: 37469462 PMCID: PMC10353649 DOI: 10.4103/jgid.jgid_178_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] [Received: 09/20/2022] [Revised: 11/27/2022] [Accepted: 01/04/2023] [Indexed: 07/21/2023] Open
Abstract
Introduction Prolonged COVID-19 pandemic accelerates the emergence and transmissibility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants through the accumulation of adaptive mutations. Particularly, adaptive mutations in spike (S) protein of SARS-CoV-2 leads to increased viral infectivity, severe morbidity and mortality, and immune evasion. This study focuses on the phylodynamic distribution of SARS-CoV-2 variants during the year 2021 in India besides analyzing the functional significance of mutations in S-protein of SARS-CoV-2 variants. Methods Whole genome of SARS-CoV-2 sequences (n = 87957) from the various parts of India over the period of January to December 2021 was retrieved from Global Initiative on Sharing All Influenza Data. All the S-protein sequences were subjected to clade analysis, variant calling, protein stability, immune escape potential, structural divergence, Furin cleavage efficiency, and phylogenetic analysis using various in silico tools. Results Delta variant belonging to 21A, 21I, and 21J clades was found to be predominant throughout the year 2021 though many variants were also present. A total of 4639 amino acid mutations were found in S-protein. D614G was the most predominant mutation in the S-protein followed by P681R, L452R, T19R, T478K, and D950N. The highest number of mutations was found in the N-terminal domain of S-protein. Mutations in the crucial sites of S-protein impacting pathogenicity, immunogenicity, and fusogenicity were identified. Intralineage diversity analysis showed that certain variants of SARS-CoV-2 possess high diversification. Conclusions The study has disclosed the distribution of various variants including the Delta, the predominant variant, in India throughout the year 2021. The study has identified mutations in S-protein of each SARS-CoV-2 variant that can significantly impact the virulence, immune evasion, increased transmissibility, high morbidity, and mortality. In addition, it is found that mutations acquired during each viral replication cycle introduce new sub-lineages as studied by intralineage diversity analysis.
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Affiliation(s)
- Vidya Gopalan
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Aswathi Chandran
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Kishore Arumugam
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Monisha Sundaram
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Selvakumar Velladurai
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Karthikeyan Govindan
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Nivetha Azhagesan
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Padmapriya Jeyavel
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Prabu Dhandapani
- Department of Microbiology, Dr. ALM Post Graduate, Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
| | | | - Satish Srinivas Kitambi
- Department of Translational Sciences, Institute for Healthcare Education and Translational Sciences, Hyderabad, Telengana, India
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He D, Chen B, Zhao S, Stone L. The immune evasion ability of Delta variant is comparable to that of Beta variant in South Africa. BMC Public Health 2023; 23:511. [PMID: 36927400 PMCID: PMC10020070 DOI: 10.1186/s12889-023-15431-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND The high immune evasion ability of SARS-COV-2 Omicron variant surprised the world and appears to be far stronger than any previous variant. Previous to Omicron it has been difficult to assess and compare immune evasion ability of different variants, including the Beta and Delta variants, because of the relatively small numbers of reinfections and because of the problems in correctly identifying reinfections in the population. This has led to different claims appearing in the literature. Thus we find claims of both high and low immune evasion for the Beta variant. Some findings have suggested that the Beta variant has a higher immune evasion ability than the Delta variant in South Africa, and others that it has a lower ability. METHOD In this brief report, we re-analyse a unique dataset of variant-specific reinfection data and a simple model to correct for the infection attack rates of different variants. RESULT We find that a model with the Delta variant having an equal or higher immune evasion ability than Beta variant is compatible with the data. CONCLUSION We conclude that the immune evasion ability of Beta variant is not stronger than Delta variant, and indeed, the immune evasion abilities of both variants are weak in South Africa.
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Affiliation(s)
- Daihai He
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China.
- Research Institute for Future Food, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Boqiang Chen
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China
| | - Shi Zhao
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
- CUHK Shenzhen Research Institute, Shenzhen, China
| | - Lewi Stone
- Mathematical Sciences, School of Science, RMIT University, Melbourne, Australia.
- Biomathematics Unit, School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
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He D, Lin L, Artzy-Randrup Y, Demirhan H, Cowling BJ, Stone L. Resolving the enigma of Iquitos and Manaus: A modeling analysis of multiple COVID-19 epidemic waves in two Amazonian cities. Proc Natl Acad Sci U S A 2023; 120:e2211422120. [PMID: 36848558 PMCID: PMC10013854 DOI: 10.1073/pnas.2211422120] [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: 07/06/2022] [Accepted: 01/17/2023] [Indexed: 03/01/2023] Open
Abstract
The two nearby Amazonian cities of Iquitos and Manaus endured explosive COVID-19 epidemics and may well have suffered the world's highest infection and death rates over 2020, the first year of the pandemic. State-of-the-art epidemiological and modeling studies estimated that the populations of both cities came close to attaining herd immunity (>70% infected) at the termination of the first wave and were thus protected. This makes it difficult to explain the more deadly second wave of COVID-19 that struck again in Manaus just months later, simultaneous with the appearance of a new P.1 variant of concern, creating a catastrophe for the unprepared population. It was suggested that the second wave was driven by reinfections, but the episode has become controversial and an enigma in the history of the pandemic. We present a data-driven model of epidemic dynamics in Iquitos, which we also use to explain and model events in Manaus. By reverse engineering the multiple epidemic waves over 2 y in these two cities, the partially observed Markov process model inferred that the first wave left Manaus with a highly susceptible and vulnerable population (≈40% infected) open to invasion by P.1, in contrast to Iquitos (≈72% infected). The model reconstructed the full epidemic outbreak dynamics from mortality data by fitting a flexible time-varying reproductive number [Formula: see text] while estimating reinfection and impulsive immune evasion. The approach is currently highly relevant given the lack of tools available to assess these factors as new SARS-CoV-2 virus variants appear with different degrees of immune evasion.
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Affiliation(s)
- Daihai He
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China
- Research Institute for Future Food, The Hong Kong Polytechnic University, Hong Kong, China
| | - Lixin Lin
- Mathematical Sciences, School of Science, Royal Melbourne Institute of Technology (RMIT) University, Melbourne, Victoria 3000, Australia
| | - Yael Artzy-Randrup
- Department of Theoretical and Computational Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1090 GE, Amsterdam, Netherlands
| | - Haydar Demirhan
- Mathematical Sciences, School of Science, Royal Melbourne Institute of Technology (RMIT) University, Melbourne, Victoria 3000, Australia
| | - Benjamin J. Cowling
- World Health Organization (WHO) Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lewi Stone
- Mathematical Sciences, School of Science, Royal Melbourne Institute of Technology (RMIT) University, Melbourne, Victoria 3000, Australia
- Biomathematics Unit, School of Zoology, Faculty of Life Sciences, Tel Aviv University, Ramat Aviv69978, Israel
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