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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. Res Sq 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] [What about the content of this article? (0)] [Affiliation(s)] [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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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 J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Garcia-Valtanen P, Hope CM, Masavuli MG, Yeow AEL, Balachandran H, Mekonnen ZA, Al-Delfi Z, Abayasingam A, Agapiou D, Stella AO, Aggarwal A, Bouras G, Gummow J, Ferguson C, O'Connor S, McCartney EM, Lynn DJ, Maddern G, Gowans EJ, Reddi BAJ, Shaw D, Kok-Lim C, Beard MR, Weiskopf D, Sette A, Turville SG, Bull RA, Barry SC, Grubor-Bauk B. SARS-CoV-2 Omicron variant escapes neutralizing antibodies and T cell responses more efficiently than other variants in mild COVID-19 convalescents. Cell Rep Med 2022; 3:100651. [PMID: 35654046 PMCID: PMC9110310 DOI: 10.1016/j.xcrm.2022.100651] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/24/2022] [Accepted: 05/11/2022] [Indexed: 12/12/2022]
Abstract
Coronavirus disease 2019 (COVID-19) convalescents living in regions with low vaccination rates rely on post-infection immunity for protection against re-infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We evaluate humoral and T cell immunity against five variants of concern (VOCs) in mild-COVID-19 convalescents at 12 months after infection with ancestral virus. In this cohort, ancestral, receptor-binding domain (RBD)-specific antibody and circulating memory B cell levels are conserved in most individuals, and yet serum neutralization against live B.1.1.529 (Omicron) is completely abrogated and significantly reduced for other VOCs. Likewise, ancestral SARS-CoV-2-specific memory T cell frequencies are maintained in >50% of convalescents, but the cytokine response in these cells to mutated spike epitopes corresponding to B.1.1.529 and B.1.351 (Beta) VOCs were impaired. These results indicate that increased antigen variability in VOCs impairs humoral and spike-specific T cell immunity post-infection, strongly suggesting that COVID-19 convalescents are vulnerable and at risk of re-infection with VOCs, thus stressing the importance of vaccination programs. Most mild COVID-19 convalescents maintain immunity at 12 months after disease onset B.1.1.529 escapes antibodies in convalescents infected with ancestral SARS-CoV-2 SARS-CoV-2 VOCs can partially avoid recognition by antigen-specific T cells Antigenic drift in SARS-CoV-2 VOCs significantly challenges convalescent immunity
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Affiliation(s)
- Pablo Garcia-Valtanen
- Viral Immunology Group, Adelaide Medical School, University of Adelaide and Basil Hetzel Institute for Translational Health Research, Adelaide, SA, Australia
| | - Christopher M Hope
- Molecular Immunology, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia; Women's and Children's Health Network, North Adelaide, SA, Australia
| | - Makutiro G Masavuli
- Viral Immunology Group, Adelaide Medical School, University of Adelaide and Basil Hetzel Institute for Translational Health Research, Adelaide, SA, Australia
| | - Arthur Eng Lip Yeow
- Viral Immunology Group, Adelaide Medical School, University of Adelaide and Basil Hetzel Institute for Translational Health Research, Adelaide, SA, Australia
| | | | - Zelalem A Mekonnen
- Viral Immunology Group, Adelaide Medical School, University of Adelaide and Basil Hetzel Institute for Translational Health Research, Adelaide, SA, Australia
| | - Zahraa Al-Delfi
- Viral Immunology Group, Adelaide Medical School, University of Adelaide and Basil Hetzel Institute for Translational Health Research, Adelaide, SA, Australia
| | | | - David Agapiou
- School of Medical Sciences, Faculty of Medicine, UNSW, Australia, Sydney, NSW, Australia
| | | | - Anupriya Aggarwal
- The Kirby Institute, The University of New South Wales, Sydney, NSW, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia; The Department of Surgery - Otolaryngology, Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville South, SA, Australia
| | - Jason Gummow
- Gene Silencing and Expression Core Facility, Adelaide Health and Medical Sciences, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Catherine Ferguson
- Infectious Diseases Department, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, SA, Australia
| | - Stephanie O'Connor
- Intensive Care Unit, Royal Adelaide Hospital, Central Adelaide Local Health Network and Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Erin M McCartney
- Infectious Diseases Department, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, SA, Australia
| | - David J Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia; Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - Guy Maddern
- Discipline of Surgery, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Eric J Gowans
- Viral Immunology Group, Adelaide Medical School, University of Adelaide and Basil Hetzel Institute for Translational Health Research, Adelaide, SA, Australia
| | - Benjamin A J Reddi
- Intensive Care Unit, Royal Adelaide Hospital, Central Adelaide Local Health Network and Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - David Shaw
- Infectious Diseases Department, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, SA, Australia
| | - Chuan Kok-Lim
- Gene Silencing and Expression Core Facility, Adelaide Health and Medical Sciences, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia; Microbiology and Infectious Diseases Department, SA Pathology, Adelaide, SA, Australia; Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Michael R Beard
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Stuart G Turville
- The Kirby Institute, The University of New South Wales, Sydney, NSW, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, UNSW, Australia, Sydney, NSW, Australia
| | - Simon C Barry
- Molecular Immunology, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia; Women's and Children's Health Network, North Adelaide, SA, Australia.
| | - Branka Grubor-Bauk
- Viral Immunology Group, Adelaide Medical School, University of Adelaide and Basil Hetzel Institute for Translational Health Research, Adelaide, SA, Australia.
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Chen LL, Chua GT, Lu L, Chan BPC, Wong JSC, Chow CCK, Yu TC, Leung ASY, Lam SY, Wong TW, Tsang HW, Wong ICK, Chan KH, Yuen KY, Ip P, Kwan MYW, To KKW. Omicron variant susceptibility to neutralizing antibodies induced in children by natural SARS-CoV-2 infection or COVID-19 vaccine. Emerg Microbes Infect 2022; 11:543-547. [PMID: 35084295 PMCID: PMC8843159 DOI: 10.1080/22221751.2022.2035195] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The novel SARS-CoV-2 Omicron variant may increase the risk of re-infection and vaccine breakthrough infections as it possesses key mutations in the spike protein that affect neutralizing antibody response. Most studies on neutralization susceptibility were conducted using specimens from adult COVID-19 patients or vaccine recipients. However, since the paediatric population has an antibody response to SARS-CoV-2 infection that is distinct from the adult population, it is critical to assess the neutralization susceptibility of pediatric serum specimens. This study compared the neutralization susceptibility of serum specimens collected from 49 individuals of <18 years old, including 34 adolescent BNT162b2 (Pfizer-BioNTech) vaccine recipients, and 15 recovered COVID-19 patients aged between 2 and 17. We demonstrated that only 38.2% of BNT162b2 vaccine recipients and 26.7% of recovered COVID-19 patients had their serum neutralization titre at or above the detection threshold in our live virus microneutralization assay. Furthermore, the neutralizing antibody titer against the Omicron variant was substantially lower than those against the ancestral virus or the Beta variant. Our results suggest that vaccine recipients and COVID-19 patients in the pediatric age group will likely be more susceptible to vaccine breakthrough infections or reinfections due to the Omicron variant than previous variants.
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Affiliation(s)
- Lin-Lei Chen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Gilbert T Chua
- Department of Pediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Pediatrics and Adolescent Medicine, The Hong Kong Children's Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Lu Lu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Brian Pui-Chun Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Joshua Sung-Chih Wong
- Department of Pediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Calvin Chit-Kwong Chow
- Department of Pediatrics and Adolescent Medicine, United Christian Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Tak-Ching Yu
- Department of Pediatrics and Adolescent Medicine, Pamela Youde Nethersole Eastern Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Agnes Sze-Yin Leung
- Department of Pediatrics, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Shu-Yan Lam
- Department of Pediatrics and Adolescent Medicine, Tuen Mun Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Tak-Wai Wong
- Department of Pediatrics and Adolescent Medicine, Alice Ho Miu Ling Nethersole Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Hing-Wai Tsang
- Department of Pediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Ian Chi-Kei Wong
- Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong.,Laboratory of Data Discovery for Health (D 4H), Hong Kong Science and Technology Park.,Research Department of Practice and Policy, School of Pharmacy, University College London
| | - Kwok-Hung Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Patrick Ip
- Department of Pediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Pediatrics and Adolescent Medicine, The Hong Kong Children's Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Mike Yat-Wah Kwan
- Department of Pediatrics and Adolescent Medicine, The Hong Kong Children's Hospital, Hong Kong Special Administrative Region, People's Republic of China.,Department of Pediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
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Luczkowiak J, Labiod N, Rivas G, Rolo M, Lasala F, Lora-Tamayo J, Mancheno-Losa M, Rial-Crestelo D, Rez-Rivilla AP, Folgueira MD, Delgado R. Neutralizing response against SARS-CoV-2 variants 8 months after BNT162b2 vaccination in naïve and COVID-19 convalescent individuals. J Infect Dis 2021; 225:1905-1908. [PMID: 34963008 PMCID: PMC8755312 DOI: 10.1093/infdis/jiab634] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
We have investigated the evolution of the neutralizing response against SARS-CoV-2 variants at 8 months after Pfizer-BNT162b2 vaccination in COVID-19 naïve (n=21) and COVID-19 convalescent (n=21) individuals. Neutralizing levels declined for all variants (range 2-3.7-fold). Eight months after vaccination a significant proportion (4/21) of naïve individuals lacked detectable neutralizing activity against the highly transmissible SARS-CoV-2 delta variant. In the "convalescent" group the impressive high initial humoral response resulted in detectable neutralizing antibody levels against all variants throughout this period.
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Affiliation(s)
| | - Nuria Labiod
- Instituto de Investigación Hospital, Madrid, Spain
| | - Gonzalo Rivas
- Department of Microbiology. Hospital Universitario, Madrid, Spain
| | - Marta Rolo
- Department of Microbiology. Hospital Universitario, Madrid, Spain
| | | | - Jaime Lora-Tamayo
- Department of Internal Medicine. Hospital Universitario, Madrid, Spain
| | | | | | - Alfredo Pé Rez-Rivilla
- Department of Microbiology. Hospital Universitario, Madrid, Spain.,School of Medicine. Universidad Complutense. Madrid, Spain
| | - María Dolores Folgueira
- Instituto de Investigación Hospital, Madrid, Spain.,Department of Microbiology. Hospital Universitario, Madrid, Spain.,School of Medicine. Universidad Complutense. Madrid, Spain
| | - Rafael Delgado
- Instituto de Investigación Hospital, Madrid, Spain.,Department of Microbiology. Hospital Universitario, Madrid, Spain.,School of Medicine. Universidad Complutense. Madrid, Spain
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Abstract
The SARS-COV2 Omicron variant has sparked global concern due to the possibility of enhanced transmissibility and escape from vaccines and therapeutics. In this study, we describe the mutational landscape of the Omicron variant using amino acid interaction (AAI) networks. AAI network analysis is particularly well suited for interrogating the impact of constellations of mutations as occur on Omicron that may function in an epistatic manner. Our analyses suggest that as compared to previous variants of concern, the Omicron variant has increased antibody escape breadth due to mutations in class 3 and 4 antibody epitopes as well as increased escape depth due to accumulated mutations in class 1 antibody epitopes. We note certain RBD mutations that might further enhance Omicron's escape, and in particular advise careful surveillance of two subclades bearing R346S/K mutations with relevance for certain therapeutic antibodies. Further, AAI network analysis suggests that the function of certain therapeutic monoclonal antibodies may be disrupted by Omicron mutations as a result of the cumulative indirect perturbations to the epitope surface properties, despite point-mutation analyses suggesting these antibodies are tolerant of the set of Omicron mutations in isolation. Finally, for several Omicron mutations that do not appear to contribute meaningfully to antibody escape, we find evidence for a plausible role in enhanced transmissibility via disruption of RBD-down conformational stability at the RBD-RBD interface.
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Affiliation(s)
- Nathaniel L. Miller
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Thomas Clark
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rahul Raman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ram Sasisekharan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Singapore-MIT Alliance in Research and Technology (SMART), Singapore 138602, Singapore
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Manouana GP, Maloum MN, Bikangui R, Oye Bingono SO, Ondo GN, Honkpehedji JY, Rossatanga EG, Assoumou SZ, Pallerla SR, Rachakonda S, Ndong RM, Lekana-Douki JB, Siawaya JFD, Borrmann S, Kremsner PG, Lell B, Velavan TP, Adegnika AA. Emergence of B.1.1.318 SARS-CoV-2 viral lineage and high incidence of alpha B.1.1.7 variant of concern in Republic of Gabon. Int J Infect Dis 2021; 114:151-154. [PMID: 34742926 PMCID: PMC8563502 DOI: 10.1016/j.ijid.2021.10.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/09/2021] [Accepted: 10/29/2021] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE Variants of concern (VOCs) associated with relatively high transmissibility appear to be spreading rapidly in Gabon. Therefore, it is imperative to understand the distribution of several variants of concern in the population, which could have implications for transmissibility and vaccine efficacy. METHODS Between February and May 2021, SARS-CoV-2 genomes were sequenced using the Oxford nanopore MinION method and the respective genome diversity was elucidated. Phylogenetic analysis was performed and genomes were classified using pangolin lineages. RESULTS The results highlight the increase (46%) of the alpha variant of concern (B.1.1.7) in the Gabonese population over the study period. In addition, an increase (31%) in the B.1.1.318 lineage, which is associated with high transmission and impaired vaccine efficacy (D614G+E484K+Y144del), was detected. CONCLUSION With the second wave ongoing, our findings highlight the need for surveillance of the SARS-CoV-2 genome in the Republic of Gabon and should provide useful guidance to policy makers in selecting an appropriate vaccine for the population.
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Affiliation(s)
- Gédéon Prince Manouana
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | | | - Rodrigue Bikangui
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Ecole doctorale de Franceville, Franceville, Gabon
| | | | | | | | | | - Samira Zoa Assoumou
- Laboratoire Professeur Daniel Gahouma, Libreville, Gabon; Département de Bactériologie-Virologie, Université des Sciences de la Santé, Libreville, Gabon
| | | | | | | | | | | | - Steffen Borrmann
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany; German Center for Infection Research (DZIF), Tübingen, Germany
| | - Peter G Kremsner
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany; German Center for Infection Research (DZIF), Tübingen, Germany
| | - Bertrand Lell
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany; Medical University of Vienna, Vienna, Austria
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany; Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Ayola Akim Adegnika
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany; German Center for Infection Research (DZIF), Tübingen, Germany; Fondation pour la Recherche Scientifique, Cotonou, Bénin.
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Thangaraj JWV, Yadav P, Kumar CG, Shete A, Nyayanit DA, Rani DS, Kumar A, Kumar MS, Sabarinathan R, Saravana Kumar V, Jagadeesan M, Murhekar M. Predominance of delta variant among the COVID-19 vaccinated and unvaccinated individuals, India, May 2021. J Infect 2021; 84:94-118. [PMID: 34364949 PMCID: PMC8343391 DOI: 10.1016/j.jinf.2021.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 07/29/2021] [Accepted: 08/01/2021] [Indexed: 01/17/2023]
Affiliation(s)
| | - Pragya Yadav
- ICMR National Institute of Virology, Pune, Maharashtra
| | - Cp Girish Kumar
- ICMR National Institute of Epidemiology, Chennai, Tamil Nadu
| | - Anita Shete
- ICMR National Institute of Virology, Pune, Maharashtra
| | | | - D Sudha Rani
- ICMR National Institute of Epidemiology, Chennai, Tamil Nadu
| | | | | | - R Sabarinathan
- ICMR National Institute of Epidemiology, Chennai, Tamil Nadu
| | | | | | - Manoj Murhekar
- National Institute of Epidemiology, R127, TNHB, Ayapakkam, Ambattur, Chennai 600077, India.
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Chen LL, Lu L, Choi CYK, Cai JP, Tsoi HW, Chu AWH, Ip JD, Chan WM, Zhang RR, Zhang X, Tam AR, Lau DPL, To WK, Que TL, Yip CCY, Chan KH, Cheng VCC, Yuen KY, Hung IFN, To KKW. Impact of SARS-CoV-2 variant-associated RBD mutations on the susceptibility to serum antibodies elicited by COVID-19 infection or vaccination. Clin Infect Dis 2021; 74:1623-1630. [PMID: 34309648 DOI: 10.1093/cid/ciab656] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Several SARS-CoV-2 lineages with mutations at the spike protein receptor binding domain (RBD) have reduced susceptibility to antibody neutralization, and have been classified as Variants of Concern (VOCs) or Variants of Interest (VOIs). Here, we systematically compared the neutralization susceptibility and RBD binding of different VOCs/VOIs, including B.1.617.1 (kappa variant) and P.3 (theta variant) which were first detected in India and the Philippines, respectively. METHODS The neutralization susceptibility of the VOCs/VOIs (B.1.351, B.1.617.1 and P.3) and a non-VOC/VOI without RBD mutations (B.1.36.27) to convalescent sera from COVID-19 patients or BNT162b2 vaccinees was determined using a live virus microneutralization (MN) assay. Serum IgG binding to wild type and mutant RBDs were determined using an enzyme immunoassay. RESULTS The geometric mean neutralization titers (GMT) of B.1.351, P.3, and B.1.617.1 were significantly lower than that of B.1.36.27 for COVID-19 patients infected with non-VOCs/VOIs (3.4-5.7-fold lower) or individuals who have received 2 doses of BNT162b2 vaccine (4.4-7.3-fold lower). The GMT of B.1.351 or P.3 were lower than that of B.1.671.1. For the 4 patients infected with B.1.351 or B.1.617.1, the MN titer was highest for their respective lineage. RBD with E484K or E484Q mutation, either alone or in combination with other mutations, showed greatest reduction in serum IgG binding. CONCLUSION P.3 and B.1.617.1 escape serum neutralization induced by natural infection or vaccine. Infection with one variant do not confer cross protection for heterologous lineages. Immunogenicity testing for second generation COVID-19 vaccines should include multiple variant and "non-variant" strains.
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Affiliation(s)
- Lin-Lei Chen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Lu Lu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Charlotte Yee-Ki Choi
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Jian-Piao Cai
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Hoi-Wah Tsoi
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Ricky Ruiqi Zhang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Xiaojuan Zhang
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Anthony Raymond Tam
- Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Daphne Pui-Ling Lau
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Wing-Kin To
- Department of Pathology, Princess Margaret Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Tak-Lun Que
- Department of Pathology, Tuen Mun Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Kwok-Hung Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Vincent Chi-Chung Cheng
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.,Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People's Republic of China
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