1
|
Alcantara DMC, Dos Santos CM, Torres JM, Stutz C, Vieira CA, Moreira RMDS, Rodrigues R, Marcon GEB, Ferreira EDC, Mendes FML, Sarti ECFB, de Oliveira TF, Lemos EF, Andrade UV, Lichs GGDC, Demarchi LHF, Zardin MCSU, Gonçalves CCM, Guilhermino JDF, Fernandez ZDC. Long-term surveillance of SARS-CoV-2 in the school community from Campo Grande, Brazil. BMC Public Health 2024; 24:2057. [PMID: 39085807 PMCID: PMC11290088 DOI: 10.1186/s12889-024-19555-x] [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: 02/27/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic has significantly impacted education systems worldwide, with Brazil being one of the countries with the longest school closures. Over a million children and teenagers have been affected, leading to increased hunger and nutritional deficiencies. This study aimed to implement long-term surveillance of SARS-CoV-2 infections in public and private schools in Campo Grande, Brazil, after returning to in-person classes. METHODS The study involved testing and genomic surveillance at 23 public and private schools in Campo Grande, Mato Grosso do Sul, Brazil, from October 18, 2021 to November 21, 2022. The participants eligible for enrollment were students aged 6-17 years and staff members from school institutions. At the time of collection, participants were asked if they had symptoms in the last two weeks. Whole-genome sequencing of SARS-CoV-2 was conducted to identify circulating variants and to compare them with those detected in the municipality. The demographic data and clinical history of the participants were described, and a logistic regression model was used to understand how the RT-qPCR results could be related to different characteristics. RESULTS The study included 999 participants, most of whom were women. A total of 85 tests were positive, with an overall positivity rate of 3.2%. The dynamics of case frequency were consistent with those observed in the municipality during the study period. The most common symptoms reported were cough, rhinorrhea, headache, and sore throat. Symptoms were significantly associated with SARS-CoV-2 infection. Eleven lineages were identified in school community samples, with a frequency of occurrence per period similar to that found in the sequences available for the municipality. The most prevalent lineages within the sampling period were BA.2 (59.3%) and BA.5 (29.6%). CONCLUSIONS Our findings demonstrate that schools can play a crucial role in epidemiological surveillance, helping trigger rapid responses to pathogens such as SARS-CoV-2. Long-term surveillance can be used to track outbreaks and assess the role of children and adults in transmission. It can also contribute to pandemic preparedness, enabling a rapid response to emergencies, such as COVID-19.
Collapse
Affiliation(s)
| | - Camila Maria Dos Santos
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
| | - Jaire Marinho Torres
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
| | - Claudia Stutz
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição (FACFAN), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Camila Aoyama Vieira
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
| | - Raissa Mariele Dos Santos Moreira
- Instituto Integrado de Saúde (INISA), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Rudielle Rodrigues
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Eduardo de Castro Ferreira
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
- Programa de Pós-graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina (FAMED), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Flavia Maria Lins Mendes
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
| | | | | | - Everton Ferreira Lemos
- Universidade Estadual de Mato Grosso do Sul (UEMS), Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Gislene Garcia de Castro Lichs
- Laboratório Central de Saúde Pública do Estado de Mato Grosso do Sul (LACEN/MS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Luiz Henrique Ferraz Demarchi
- Programa de Pós-graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina (FAMED), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
- Laboratório Central de Saúde Pública do Estado de Mato Grosso do Sul (LACEN/MS), Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Crhistinne Cavalheiro Maymone Gonçalves
- Programa de Pós-graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina (FAMED), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | | |
Collapse
|
2
|
Machado LC, Dezordi FZ, de Lima GB, de Lima RE, Silva LCA, Pereira LDM, da Silva AF, da Silva Neto AM, de Oliveira ALS, Armstrong ADC, Pessoa-e-Silva R, Loyo RM, Silva BDO, de Almeida AR, da Rocha Pitta MG, Santos FDADS, Mendonça Siqueira M, Resende PC, Delatorre E, Naveca FG, Miyajima F, Gräf T, do Carmo RF, Pereira MC, Campos TDL, Bezerra MF, Paiva MHS, Wallau GDL. Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco-Brazil. Microbiol Spectr 2024; 12:e0421823. [PMID: 38651879 PMCID: PMC11237429 DOI: 10.1128/spectrum.04218-23] [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: 12/20/2023] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
SARS-CoV-2 virus emerged as a new threat to humans and spread around the world, leaving a large death toll. As of January 2023, Brazil is among the countries with the highest number of registered deaths. Nonpharmacological and pharmacological interventions have been heterogeneously implemented in the country, which, associated with large socioeconomic differences between the country regions, has led to distinct virus spread dynamics. Here, we investigate the spatiotemporal dispersion of SARS-CoV-2 lineages in the Pernambuco state (Northeast Brazil) throughout the distinct epidemiological scenarios that unfolded in the first 2 years of the pandemic. We generated a total of 1,389 new SARS-CoV-2 genomes from June 2020 to August 2021. This sampling captured the arrival, communitary transmission, and the circulation of the B1.1, B.1.1.28, and B.1.1.33 lineages; the emergence of the former variant of interest P.2; and the emergence and fast replacement of all previous variants by the more transmissible variant of concern P.1 (Gamma). Based on the incidence and lineage spread pattern, we observed an East-to-West to inner state pattern of transmission, which is in agreement with the transmission of more populous metropolitan areas to medium- and small-size country-side cities in the state. Such transmission patterns may be partially explained by the main routes of traffic across municipalities in the state. Our results highlight that the fine-grained intrastate analysis of lineages and incidence spread can provide actionable insights for planning future nonpharmacological intervention for air-borne transmissible human pathogens.IMPORTANCEDuring the COVID-19 pandemic, Brazil was one of the most affected countries, mainly due its continental-size, socioeconomic differences among regions, and heterogeneous implementation of intervention methods. In order to investigate SARS-CoV-2 dynamics in the state of Pernambuco, we conducted a spatiotemporal dispersion study, covering the period from June 2020 to August 2021, to comprehend the dynamics of viral transmission during the first 2 years of the pandemic. Throughout this study, we were able to track three significant epidemiological waves of transmission caused by B1.1, B.1.1.28, B.1.1.33, P.2, and P.1 lineages. These analyses provided valuable insights into the evolution of the epidemiological landscape, contributing to a deeper understanding of the dynamics of virus transmission during the early years of the pandemic in the state of Pernambuco.
Collapse
Affiliation(s)
- Lais Ceschini Machado
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
| | - Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Gustavo Barbosa de Lima
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Raul Emídio de Lima
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Lilian Caroliny Amorim Silva
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Leandro de Mattos Pereira
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Alexandre Freitas da Silva
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | | | - André Luiz Sá de Oliveira
- Núcleo de Estatística e Geoprocessamento, Instituto Aggeu Magalhães (IAM)- Fundação Oswaldo Cruz Pernambuco- FIOCRUZ-PE, Recife, Brazil
| | | | - Rômulo Pessoa-e-Silva
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Rodrigo Moraes Loyo
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Barbara de Oliveira Silva
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Anderson Rodrigues de Almeida
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Maira Galdino da Rocha Pitta
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | | | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ-Amazonas, Manaus, Amazonas, Brazil
| | - Fabio Miyajima
- Analytical Competence Molecular Epidemiology Laboratory (ACME), FIOCRUZ-Ceará, Fortaleza, Ceará, Brazil
| | - Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
| | | | - Michelly Cristiny Pereira
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Tulio de Lima Campos
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Matheus Filgueira Bezerra
- Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Marcelo Henrique Santos Paiva
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Ciências da Vida, Universidade Federal de Pernambuco (UFPE), Centro Acadêmico do Agreste, Caruaru, Brazil
| | - Gabriel da Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
| | - On behalf of Fiocruz COVID-19 Genomic Network
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Núcleo de Estatística e Geoprocessamento, Instituto Aggeu Magalhães (IAM)- Fundação Oswaldo Cruz Pernambuco- FIOCRUZ-PE, Recife, Brazil
- Colegiado de Medicina, Universidade Federal do Vale do São Francisco, Petrolina, Brazil
- Suely-Galdino Therapeutic Innovation Research Center (NUPIT-SG), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Núcleo de Ciências da Vida, Universidade Federal de Pernambuco (UFPE), Centro Acadêmico do Agreste, Caruaru, Brazil
- Laboratory of Respiratory Viruses and Measles (LVRS), Instituto Oswaldo Cruz, FIOCRUZ-Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ-Amazonas, Manaus, Amazonas, Brazil
- Analytical Competence Molecular Epidemiology Laboratory (ACME), FIOCRUZ-Ceará, Fortaleza, Ceará, Brazil
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Paraná, Brazil
- Colegiado de Ciências Farmacêuticas, Universidade Federal do Vale do São Francisco, Petrolina, Brazil
- Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
| |
Collapse
|
3
|
Pourriyahi H, Hajizadeh N, Khosravi M, Pourriahi H, Soleimani S, Hosseini NS, Mohammad AP, Goodarzi A. New variants of COVID-19 (XBB.1.5 and XBB.1.16, the "Arcturus"): A review of highly questioned concerns, a brief comparison between different peaks in the COVID-19 pandemic, with a focused systematic review on expert recommendations for prevention, vaccination, and treatment measures in the general population and at-risk groups. Immun Inflamm Dis 2024; 12:e1323. [PMID: 38938013 PMCID: PMC11211615 DOI: 10.1002/iid3.1323] [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: 01/01/2024] [Revised: 04/11/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024] Open
Abstract
INTRODUCTION The COVID-19 pandemic has taken many forms and continues to evolve, now around the Omicron wave, raising concerns over the globe. With COVID-19 being declared no longer a "public health emergency of international concern (PHEIC)," the COVID pandemic is still far from over, as new Omicron subvariants of interest and concern have risen since January of 2023. Mainly with the XBB.1.5 and XBB.1.16 subvariants, the pandemic is still very much "alive" and "breathing." METHODS This review consists of five highly concerning questions about the current state of the COVID Omicron peak. We searched four main online databases to answer the first four questions. For the last one, we performed a systematic review of the literature, with keywords "Omicron," "Guidelines," and "Recommendations." RESULTS A total of 31 articles were included. The main symptoms of the current Omicron wave include a characteristically high fever, coughing, conjunctivitis (with itching eyes), sore throat, runny nose, congestion, fatigue, body ache, and headache. The median incubation period of the symptoms is shorter than the previous peaks. Vaccination against COVID can still be considered effective for the new subvariants. CONCLUSION Guidelines recommend continuation of personal protective measures, third and fourth dose boosters, along with administration of bivalent messenger RNA vaccine boosters. The consensus antiviral treatment is combination therapy using Nirmatrelvir and Ritonavir, and the consensus for pre-exposure prophylaxis is Tixagevimab and Cilgavimab combination. We hope the present paper raises awareness for the continuing presence of COVID and ways to lower the risks, especially for at-risk groups.
Collapse
Affiliation(s)
- Homa Pourriyahi
- Student Research Committee, School of MedicineIran University of Medical SciencesTehranIran
| | - Nima Hajizadeh
- School of MedicineIran University of Medical SciencesTehranIran
| | - Mina Khosravi
- School of MedicineIran University of Medical SciencesTehranIran
| | - Homayoun Pourriahi
- Student Research Committee, School of MedicineIran University of Medical SciencesTehranIran
| | - Sanaz Soleimani
- Student Research Committee, School of MedicineIran University of Medical SciencesTehranIran
- Rasool Akram Medical Complex Clinical Research Development Center (RCRDC), School of MedicineIran University of Medical SciencesTehranIran
| | | | | | - Azadeh Goodarzi
- Department of Dermatology, Rasool Akram Medical Complex Clinical Research Development Center (RCRDC), School of MedicineIran University of Medical SciencesTehranIran
| |
Collapse
|
4
|
Contreras M, Gomes Naveca F, Carvajal-Cortes JJ, Faviero GF, Saavedra J, Ruback dos Santos E, Alves do Nascimento V, Costa de Souza V, Oliveira do Nascimento F, Silva e Silva D, Luz SLB, Romero Vesga KN, Grisales Nieto JC, Avelino-Silva VI, Benzaken AS. Implementing a provisional overarching intervention for COVID-19 monitoring and control in the Brazil-Colombia-Peru frontier. Front Public Health 2024; 11:1330347. [PMID: 38259793 PMCID: PMC10801231 DOI: 10.3389/fpubh.2023.1330347] [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: 10/30/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction he challenge was to provide comprehensive health resources to a remote and underserved population living in the Brazil-Colombia-Peru border, amid the most disruptive global crisis of the century. Methods In August 2021, Fundação Oswaldo Cruz Amazonia (FIOCRUZ Amazônia) and partner collaborators implemented an overarching provisional program for SARS-CoV-2 detection and lineages characterization, training of laboratory personnel and healthcare providers, donation of diagnostic supplies and personal protective equipment, and COVID-19 vaccination. The expedition was conducted at the Port of Tabatinga, a busy terminal with an intense flux of people arriving and departing in boats of all sizes, located in the Amazon River basin. Local government, non-profit organizations, private companies, and other stakeholders supported the intervention. Results The expedition was accomplished in a convergence point, where migrant workers, traders, army personnel, people living in urban areas, and people from small villages living in riversides and indigenous territories are in close and frequent contact, with widespread cross-border movement. Using a boat as a provisional lab and storage facility, the intervention provided clinical and laboratory monitoring for 891 participants; vaccination for 536 individuals; personal protective equipment for 200 healthcare providers; diagnostic supplies for 1,000 COVID-19 rapid tests; training for 42 community health agents on personal protection, rapid test execution, and pulse oximeter management; and hands-on training for four lab technicians on molecular diagnosis. Discussion Our experience demonstrates that multilateral initiatives can counterweigh the scarcity of health resources in underserved regions. Moreover, provisional programs can have a long-lasting effect if investments are also provided for local capacity building.
Collapse
Affiliation(s)
- Matilde Contreras
- Instituto Leônidas and Maria Deane, Fundação Oswaldo Cruz, Manaus, Brazil
| | | | | | - Guilherme F. Faviero
- AHF Global Public Health Institute at the University of Miami, Miami, FL, United States
| | - Jorge Saavedra
- AHF Global Public Health Institute, Fort Lauderdale, FL, United States
| | | | | | | | | | | | | | | | | | - Vivian I. Avelino-Silva
- Department of Infectious and Parasitic Diseases, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- AIDS Healthcare Foundation, Los Angeles, CA, United States
| | - Adele Schwartz Benzaken
- Instituto Leônidas and Maria Deane, Fundação Oswaldo Cruz, Manaus, Brazil
- AIDS Healthcare Foundation, Los Angeles, CA, United States
| |
Collapse
|
5
|
Barbosa G, Alberto-Lei F, Chaves APC, Carvalho JMA, Conte DD, Moreira LVL, de Souza Luna LK, Perosa AH, Bellei N. Respiratory virus detection among healthcare professionals in Brazil: work-related contact and episode recurrence during the COVID-19 pandemic. Public Health 2024; 226:159-164. [PMID: 38071948 DOI: 10.1016/j.puhe.2023.11.021] [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: 07/26/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 01/15/2024]
Abstract
OBJECTIVES Since the beginning of the COVID-19 pandemic, changes in the circulation of respiratory viruses have been observed after measures to control the spread of SARS-CoV-2 were implemented. In this sense, we aimed to understand the circulation of the respiratory virus and its impact in a controlled healthy population of healthcare professional (HCP) volunteers in phase III of the clinical trial of the ChadOx nCoV1 conducted in São Paulo, Brazil. STUDY DESIGN This was a nested observational cohort study within a clinical trial. METHODS We performed RT-qPCR to detect SARS-CoV-2, influenza virus A and B (IVA and IVB), respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (hMPV), human coronaviruses (hCoVs: HKU-1, NL63, OC43, and 229-E), parainfluenza virus (PiV) I-IV, and q-PCR for adenovirus in nasopharyngeal and oropharyngeal samples obtained from HCP enrolled in the clinical trial to assess respiratory viruses infection among vaccinated and non-vaccinated. RESULTS From July 2020 to January 2022, 876 samples were included from 737 volunteers (median age: 33 years, 62.9% female). New episodes were registered for 119 individuals. We observed an overall positivity of 37.7% for SARS-CoV-2 and 16.4% for other respiratory viruses; HRV was the second most detected virus (8%), followed by RSV (2.4%). Fully vaccinated individuals accounted for 53.3% of collected samples, and 52.9% presented at least one respiratory virus infection, with SARS-CoV-2 being the most predominant etiologic agent (62.3%). Influenza and hMPV were not detected among the tested samples. Among the subjects that presented more than one episode, SARS-CoV-2 and HRV infections were related to direct contact with patients (P < 0.002). CONCLUSIONS Data show high infection rates among HCPs even under mask policies and contact precautions, highlighting the need for improvement in infection control measures in this population regardless of the vaccination program.
Collapse
Affiliation(s)
- G Barbosa
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil.
| | - F Alberto-Lei
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - A P C Chaves
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - J M A Carvalho
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - D D Conte
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - L V L Moreira
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - L K de Souza Luna
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - A H Perosa
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| | - N Bellei
- Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina, Laboratório de Virologia Clínica, São Paulo, SP, Brazil
| |
Collapse
|
6
|
Treeza M M, Augustine S, Mathew AA, Kanthlal S, Panonummal R. Targeting Viral ORF3a Protein: A New Approach to Mitigate COVID-19 Induced Immune Cell Apoptosis and Associated Respiratory Complications. Adv Pharm Bull 2023; 13:678-687. [PMID: 38022818 PMCID: PMC10676557 DOI: 10.34172/apb.2023.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/15/2022] [Accepted: 01/20/2023] [Indexed: 12/01/2023] Open
Abstract
Infection with SARS-CoV-2 is a growing concern to the global well-being of the public at present. Different amino acid mutations alter the biological and epidemiological characteristics, as well as immune resistance of SARS-CoV-2. The virus-induced pulmonary impairment and inflammatory cytokine storm are directly related to its clinical manifestations. But, the fundamental mechanisms of inflammatory responses are found to be the reason for the death of immune cells which render the host immune system failure. Apoptosis of immune cells is one of the most common forms of programmed cell death induced by the virus for its survival and virulence property. ORF3a, a SARS-CoV-2 accessory viral protein, induces apoptosis in host cells and suppress the defense mechanism. This suggests, inhibiting SARS-CoV-2 ORF3a protein is a good therapeutic strategy for the treatment in COVID-19 infection by promoting the host immune defense mechanism.
Collapse
Affiliation(s)
- Minu Treeza M
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| | - Sanu Augustine
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| | | | - S.K. Kanthlal
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| | - Rajitha Panonummal
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| |
Collapse
|
7
|
Sgorlon G, Roca TP, Passos-Silva AM, Queiroz JAS, Teixeira KS, Araújo A, Batista FS, Souza VR, Oliveira FM, Morello LG, Marchini FK, Salcedo JM, Rampazzo RDCP, Naveca FG, Vieira D. The emergence of Omicron VOC and its rapid spread and persistence in the Western Amazon. PLoS One 2023; 18:e0285742. [PMID: 37590264 PMCID: PMC10434903 DOI: 10.1371/journal.pone.0285742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 04/30/2023] [Indexed: 08/19/2023] Open
Abstract
Genomic surveillance represents a strategy to understanding the evolutionary mechanisms, transmission, and infectivity of different SARS-CoV-2 variants. We evaluated 603 individuals positive for SARS-CoV-2 from 34 municipalities of Rondônia between December 2021 to December 2022. Nasopharyngeal samples were collected, RNA was extracted and screened using RT-qPCR for VOCs. RNA of the samples were sequenced and further analyzed for phylogeny, mutations, and lineages, totaling 96.19% of samples positive for Omicron VOC in this cohort. We observed that most individuals had at least two doses, however 18.97% were not vaccinated with any dose. 554 sequences were amenable to analysis for alignment and phylogenetic characterization; this group corresponded to the 27 subvariants of the Omicron VOC; a total of 100 mutations were identified, 48% of which were found in the S gene. In conclusion, the data demonstrated the rapid spread and persistence of Omicron VOC in Rondônia during the 12-month study period. Although high frequency of mutations was found in the analyzed samples, there were no individuals with a severe clinical profile, demonstrating that vaccination had a positive effect in those cases.
Collapse
Affiliation(s)
- Gabriella Sgorlon
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia ‐ FIOCRUZ/RO, Porto Velho, RO, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia ‐ UNIR, Porto Velho, RO, Brazil
- Centro de Pesquisa em Medicina Tropical, CEPEM, Porto Velho, RO, Brazil
| | - Tárcio P. Roca
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia ‐ FIOCRUZ/RO, Porto Velho, RO, Brazil
- Centro de Pesquisa em Medicina Tropical, CEPEM, Porto Velho, RO, Brazil
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz/IOC, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Ana Maisa Passos-Silva
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia ‐ FIOCRUZ/RO, Porto Velho, RO, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia ‐ UNIR, Porto Velho, RO, Brazil
- Centro de Pesquisa em Medicina Tropical, CEPEM, Porto Velho, RO, Brazil
| | - Jackson A. S. Queiroz
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia ‐ FIOCRUZ/RO, Porto Velho, RO, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia ‐ UNIR, Porto Velho, RO, Brazil
- Centro de Pesquisa em Medicina Tropical, CEPEM, Porto Velho, RO, Brazil
| | - Karolaine S. Teixeira
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia ‐ FIOCRUZ/RO, Porto Velho, RO, Brazil
- Centro de Pesquisa em Medicina Tropical, CEPEM, Porto Velho, RO, Brazil
| | - Adrhyan Araújo
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia ‐ FIOCRUZ/RO, Porto Velho, RO, Brazil
- Centro de Pesquisa em Medicina Tropical, CEPEM, Porto Velho, RO, Brazil
| | - Flávia S. Batista
- Coordenação Estadual do COVID-19, AGEVISA/RO, Porto Velho, RO, Brazil
| | - Valquiria R. Souza
- Instituto de Medicina Tropical da Faculdade de Medicina da USP, São Paulo, SP, Brazil
| | - Franciane M. Oliveira
- Instituto de Medicina Tropical da Faculdade de Medicina da USP, São Paulo, SP, Brazil
| | - Luis G. Morello
- Instituto de Biologia Molecular do Paraná ‐ IBMP, Curitiba, PR, Brazil
- Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Curitiba, Paraná, Brazil
| | - Fabricio K. Marchini
- Instituto de Biologia Molecular do Paraná ‐ IBMP, Curitiba, PR, Brazil
- Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Curitiba, Paraná, Brazil
| | - Juan M.V. Salcedo
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia ‐ FIOCRUZ/RO, Porto Velho, RO, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia ‐ UNIR, Porto Velho, RO, Brazil
- Centro de Pesquisa em Medicina Tropical, CEPEM, Porto Velho, RO, Brazil
| | | | - Felipe G. Naveca
- Laboratório de Virologia do Instituto Leônidas e Maria Deane, FIOCRUZ/AM, Manaus, AM, Brazil
| | - Deusilene Vieira
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia ‐ FIOCRUZ/RO, Porto Velho, RO, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia ‐ UNIR, Porto Velho, RO, Brazil
- Centro de Pesquisa em Medicina Tropical, CEPEM, Porto Velho, RO, Brazil
| |
Collapse
|
8
|
Nunes SLP, de França CA, Rocha GD, Oliveira SADS, Freitas MR, da Silva EO, Coutinho KS, Jerônimo AS, de Lima GB, de Lima RE, Bezerra MF, Dezordi FZ, Paiva MHS, Wallau GDL, de Souza CDF, Armstrong ADC, do Carmo RF. Assessment of clinical characteristics and viral load in individuals infected by Delta and Omicron variants of SARS-CoV-2. Heliyon 2023; 9:e18994. [PMID: 37600420 PMCID: PMC10432967 DOI: 10.1016/j.heliyon.2023.e18994] [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: 02/09/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023] Open
Abstract
In late 2021, a new variant of SARS-CoV-2 called Omicron emerged, replacing Delta worldwide. Although it has been associated with a lower risk of hospitalization and severe forms of COVID-19, there is little evidence of its relationship with specific symptoms and viral load. The aim of this study was to verify the relationship between Delta and Omicron variants of concern, viral load, and the occurrence of symptoms in individuals with COVID-19. Nasopharyngeal swab samples were collected and sequenced from patients with COVID-19 from the Northeast Region of Brazil between August 2021 and March 2022. The results showed a gradual replacement of the Delta variant by the Omicron variant during the study period. A total of 316 samples (157 Delta and 159 Omicron) were included. There was a higher prevalence of symptoms in Delta-infected individuals, such as coryza, olfactory and taste disturbances, headache, and myalgia. There was no association between viral load and the variants analyzed. The results reported here contribute to the understanding of the symptoms associated with the Delta and Omicron variants in individuals affected by COVID-19.
Collapse
Affiliation(s)
- Sávio Luiz Pereira Nunes
- Postgraduate Program in Applied Cellular and Molecular Biology, University of Pernambuco (UPE), Recife, Pernambuco, Brazil
| | - Chirles Araújo de França
- Multi-User Research Laboratory (LAMUPE), Dr. Washington Antônio de Barros Hospital – EBSERH/UNIVASF, Petrolina, Pernambuco, Brazil
| | - Gabriela Dias Rocha
- Postgraduate Program in Applied Cellular and Molecular Biology, University of Pernambuco (UPE), Recife, Pernambuco, Brazil
- Multi-User Research Laboratory (LAMUPE), Dr. Washington Antônio de Barros Hospital – EBSERH/UNIVASF, Petrolina, Pernambuco, Brazil
| | - Samily Aquino de Sá Oliveira
- Multi-User Research Laboratory (LAMUPE), Dr. Washington Antônio de Barros Hospital – EBSERH/UNIVASF, Petrolina, Pernambuco, Brazil
| | - Mariana Ramos Freitas
- Multi-User Research Laboratory (LAMUPE), Dr. Washington Antônio de Barros Hospital – EBSERH/UNIVASF, Petrolina, Pernambuco, Brazil
| | - Eliane Oliveira da Silva
- VIII Regional Health Management, State Health Secretariat of Pernambuco, Petrolina, Pernambuco, Brazil
| | - Katia Sampaio Coutinho
- VIII Regional Health Management, State Health Secretariat of Pernambuco, Petrolina, Pernambuco, Brazil
| | - Aline Silva Jerônimo
- VIII Regional Health Management, State Health Secretariat of Pernambuco, Petrolina, Pernambuco, Brazil
| | - Gustavo Barbosa de Lima
- Technology Platforms Center (NPT), Aggeu Magalhães Institute (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Raul Emídio de Lima
- Technology Platforms Center (NPT), Aggeu Magalhães Institute (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Matheus Filgueira Bezerra
- Departament of Microbiology, Aggeu Magalhães Institute (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Filipe Zimmer Dezordi
- Departament of Entomology, Aggeu Magalhães Institute (IAM)- FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Bioinformatics Center (NBI), Aggeu Magalhães Institute (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
| | - Marcelo Henrique Santos Paiva
- Departament of Entomology, Aggeu Magalhães Institute (IAM)- FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Life Sciences Center, Federal University of Pernambuco (UFPE), Caruaru, Pernambuco, Brazil
| | - Gabriel da Luz Wallau
- Departament of Entomology, Aggeu Magalhães Institute (IAM)- FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Bioinformatics Center (NBI), Aggeu Magalhães Institute (IAM), FIOCRUZ-Pernambuco, Recife, Pernambuco, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
| | | | - Anderson da Costa Armstrong
- Collegiate of Medicine, Federal University of the São Francisco Valley – UNIVASF, Petrolina, Pernambuco, Brazil
| | - Rodrigo Feliciano do Carmo
- Postgraduate Program in Applied Cellular and Molecular Biology, University of Pernambuco (UPE), Recife, Pernambuco, Brazil
- Collegiate of Pharmaceutical Sciences, Federal University of the São Francisco Valley – UNIVASF, Petrolina, Pernambuco, Brazil
| |
Collapse
|
9
|
Sgorlon G, Roca TP, Passos-Silva AM, Custódio MGF, Queiroz JADS, da Silva ALF, Teixeira KS, Batista FS, Salcedo JMV, Rampazzo RDCP, Naveca FG, Vieira D. SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia. Bioinform Biol Insights 2023; 17:11779322231186477. [PMID: 37461740 PMCID: PMC10350575 DOI: 10.1177/11779322231186477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/18/2023] [Indexed: 07/20/2023] Open
Abstract
The increased transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has generated variants of concern (VOCs) throughout the pandemic, responsible for waves of cases worldwide. To monitor mutations in the S gene of SARS-CoV-2 in different variants, we evaluated 1497 individuals with COVID-19 in western Amazonia in the period April 2021 to July 2022. The epidemiological and clinical data of the individuals were collected; subsequently, the samples were extracted using a commercial kit, the viral load was assessed, and viral genomes were sequenced. We analyzed the quality and mutations of the genomes and maximum likelihood phylogenetic inference. However, 3 main clusters were observed, referring to Gamma (52.91%), Delta (24.38%), and Omicron (20.38%) VOCs with wide distribution in all health regions of the Rondônia state. Regarding the vaccination profile, there was a higher percentage of unvaccinated and partially vaccinated individuals, with more representatives by the Gamma variant. A total of 1412 sequences were suitable for mutation analysis in the S gene region. The Omicron VOC showed 38 mutations, with the Delta and Gamma variants with 16 and 17, respectively. The VOC Omicron and Gamma shared 4 mutations E484K, H655Y, N501Y, and N679K with high frequency, and Delta and Omicron 2 mutations (T478K and T95I). Regarding the comparison between the frequency of mutations for each variant concerning the vaccination groups, there were no changes in mutations for each group. In conclusion, the study showed a temporal increase in mutations and subvariants for characterized strains. Furthermore, the vaccination profile did not impact significant changes in the mutational profile yet remains a determining factor for severe disease.
Collapse
Affiliation(s)
- Gabriella Sgorlon
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | - Tárcio Peixoto Roca
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz (IOC), FIOCRUZ, Rio de Janeiro, Brazil
| | - Ana Maisa Passos-Silva
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | | | - Jackson Alves da Silva Queiroz
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | - André Luiz Ferreira da Silva
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | - Karolaine Santos Teixeira
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | | | - Juan Miguel Villalobos Salcedo
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| | | | - Felipe Gomes Naveca
- Laboratório de Virologia do Instituto Leônidas e Maria Deane, FIOCRUZ/AM, Manaus, Brazil
| | - Deusilene Vieira
- Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, Brazil
- Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, Brazil
- Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, Brazil
| |
Collapse
|
10
|
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: 4] [Impact Index Per Article: 4.0] [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.
Collapse
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.
| |
Collapse
|
11
|
Amado LA, Coelho WLDCNP, Alves ADR, Carneiro VCDS, Moreira ODC, de Paula VS, Lemos AS, Duarte LA, Gutman EG, Fontes-Dantas FL, Gonçalves JPDC, Ramos CHF, Ramos Filho CHF, Cavalcanti MG, Amaro MP, Kader RL, Medronho RDA, Sarmento DJDS, Alves-Leon SV. Clinical Profile and Risk Factors for Severe COVID-19 in Hospitalized Patients from Rio de Janeiro, Brazil: Comparison between the First and Second Pandemic Waves. J Clin Med 2023; 12:2568. [PMID: 37048652 PMCID: PMC10094970 DOI: 10.3390/jcm12072568] [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: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 03/30/2023] Open
Abstract
Since COVID-19 was declared a pandemic, Brazil has become one of the countries most affected by this disease. A year into the pandemic, a second wave of COVID-19 emerged, with a rapid spread of a new SARS-CoV-2 lineage of concern. Several vaccines have been granted emergency-use authorization, leading to a decrease in mortality and severe cases in many countries. However, the emergence of SARS-CoV-2 variants raises the alert for potential new waves of transmission and an increase in pathogenicity. We compared the demographic and clinical data of critically ill patients infected with COVID-19 hospitalized in Rio de Janeiro during the first and second waves between July 2020 and October 2021. In total, 106 participants were included in this study; among them, 88% had at least one comorbidity, and 37% developed severe disease. Disease severity was associated with older age, pre-existing neurological comorbidities, higher viral load, and dyspnea. Laboratory biomarkers related to white blood cells, coagulation, cellular injury, inflammation, renal, and liver injuries were significantly associated with severe COVID-19. During the second wave of the pandemic, the necessity of invasive respiratory support was higher, and more individuals with COVID-19 developed acute hepatitis, suggesting that the progression of the second wave resulted in an increase in severe cases. These results can contribute to understanding the behavior of the COVID-19 pandemic in Brazil and may be helpful in predicting disease severity, which is a pivotal for guiding clinical care, improving patient outcomes, and defining public policies.
Collapse
Affiliation(s)
- Luciane Almeida Amado
- Laboratory of Technological Development in Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
| | | | - Arthur Daniel Rocha Alves
- Laboratory of Technological Development in Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Vanessa Cristine de Souza Carneiro
- Laboratory of Technological Development in Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
- Laboratory of Molecular Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Otacilio da Cruz Moreira
- Laboratory of Molecular Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
- Real Time PCR Platform RPT09A, Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Vanessa Salete de Paula
- Laboratory of Molecular Virology, Oswaldo Cruz Institute/Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Andreza Salvio Lemos
- Laboratory of Translacional Neurosciences, Biomedical Institute, Federal University of the State of Rio de Janeiro-UNIRIO, Rio de Janeiro 22290-240, Brazil
| | - Larissa Araujo Duarte
- Laboratory of Translacional Neurosciences, Biomedical Institute, Federal University of the State of Rio de Janeiro-UNIRIO, Rio de Janeiro 22290-240, Brazil
- School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Elisa Gouvea Gutman
- Laboratory of Translacional Neurosciences, Biomedical Institute, Federal University of the State of Rio de Janeiro-UNIRIO, Rio de Janeiro 22290-240, Brazil
- School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Fabricia Lima Fontes-Dantas
- Laboratory of Translacional Neurosciences, Biomedical Institute, Federal University of the State of Rio de Janeiro-UNIRIO, Rio de Janeiro 22290-240, Brazil
- Department of Pharmacology and Psychobiology, Roberto Alcântara Gomes Institute Biology (IBRAG), Rio de Janeiro State University (UERJ), Rio de Janeiro 20551-030, Brazil
| | - João Paulo da Costa Gonçalves
- Laboratory of Translacional Neurosciences, Biomedical Institute, Federal University of the State of Rio de Janeiro-UNIRIO, Rio de Janeiro 22290-240, Brazil
| | - Carlos Henrique Ferreira Ramos
- Unit of Intensive Treatment, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | - Marta Guimarães Cavalcanti
- Epidemiology and Evaluation Service, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Marisa Pimentel Amaro
- Post-Graduate Program in Infectious and Parasitic Diseases, School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Rafael Lopes Kader
- Post-Graduate Program in Infectious and Parasitic Diseases, School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | | | - Soniza Vieira Alves-Leon
- Laboratory of Translacional Neurosciences, Biomedical Institute, Federal University of the State of Rio de Janeiro-UNIRIO, Rio de Janeiro 22290-240, Brazil
- School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
- Department of Neurology, Reference and Research Center for Multiple Sclerosis and Other Central Nervous System Idiopathic Demyelinating Inflammatory Diseases, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| |
Collapse
|
12
|
Filippi M, Ribeiro Amorim M, Soares da Silva M, Schons Gularte J, Demoliner M, Girardi V, de Abreu Goes Pereira VM, Witt Hansen A, Fleck JD, Frohlich J, de-Paris F, Motta Rodrigues G, Aparecida Risczik Arruda Correa J, Machado Arlindo De Mattos E, Minuto Paiva R, Deutschendorf C, Soares Falcetta F, Proença Modena JL, Rosado Spilki F. Prolonged SARS-CoV-2 Infection and Intra-Patient Viral Evolution in an Immunodeficient Child. Pediatr Infect Dis J 2023; 42:212-217. [PMID: 36728777 PMCID: PMC9935232 DOI: 10.1097/inf.0000000000003782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/30/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND With the progression of the Coronavirus disease pandemic, the number of mutations in the viral genome has increased, showing the adaptive evolution of severe acute respiratory syndrome coronavirus 2 in humans and intensification in transmissibility. Long-term infections also allow the development of viral diversity. In this study, we report the case of a child with severe combined immu presenting a prolonged severe acute respiratory syndrome coronavirus 2 infection. We aimed to analyze 3 naso-oropharyngeal swab samples collected between August and December 2021 to describe the amino acid changes present in the sequence reads that may have a role in the emergence of new viral variants. METHODS The whole genome from clinical samples was sequenced through high throughput sequencing and analyzed using a workflow to map reads and then find variations/single-nucleotide polymorphisms. In addition, the samples were isolated in cell culture, and a plaque forming units assay was performed, which indicates the presence of viable viral particles. RESULTS The results obtained showed that the virus present in all samples is infectious. Also, there were 20 common mutations among the 3 sequence reads, found in the ORF1ab and ORF10 proteins. As well, a considerable number of uncommon mutations were found. CONCLUSIONS In conclusion, we emphasize that genomic surveillance can be a useful tool to assess possible evolution signals in long-term patients.
Collapse
Affiliation(s)
- Micheli Filippi
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Mariene Ribeiro Amorim
- Laboratório de Vírus Emergentes, Departamento de Genética, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Mariana Soares da Silva
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliana Schons Gularte
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Meriane Demoliner
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Viviane Girardi
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | | | - Alana Witt Hansen
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliane Deise. Fleck
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Júlia Frohlich
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Fernanda de-Paris
- Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | | | | | | | | | - José Luiz Proença Modena
- Laboratório de Vírus Emergentes, Departamento de Genética, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Fernando Rosado Spilki
- From the Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| |
Collapse
|
13
|
SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis. Viruses 2022; 14:v14122715. [PMID: 36560720 PMCID: PMC9784312 DOI: 10.3390/v14122715] [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: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/09/2022] Open
Abstract
Several studies have monitored the SARS-CoV-2 variants in Brazil throughout the pandemic. Here, we systematically reviewed and conducted a scientometric analysis of the SARS-CoV-2 genomic surveillance studies using Brazilian samples. A Pubmed database search on October 2022 returned 492 articles, of which 106 were included. Ninety-six different strains were reported, with variant of concern (VOC) gamma (n = 35,398), VOC delta (n = 15,780), and the variant of interest zeta (n = 1983) being the most common. The top three states with the most samples in the published articles were São Paulo, Rio de Janeiro, and Minas Gerais. Whereas the first year of the pandemic presented primary circulation of B.1.1.28 and B.1.1.33 variants, consecutive replacements were observed between them and VOI zeta, VOC gamma, VOC delta, and VOC omicron. VOI mu, VOI lambda, VOC alpha, and VOC beta were also detected but failed to reach significant circulation. Co-infection, re-infection, and vaccine breakthrough reports were found. Article co-citation differed from the co-authorship structure. Despite the limitations, we expect to give an overview of Brazil's genomic surveillance studies and contribute to future research execution.
Collapse
|
14
|
Lai A, Bergna A, Della Ventura C, Menzo S, Bruzzone B, Sagradi F, Ceccherini-Silberstein F, Weisz A, Clementi N, Brindicci G, Vicenti I, Sasset L, Caucci S, Corvaro B, Ippoliti S, Acciarri C, De Pace V, Lanfranchi L, Bellocchi MC, Giurato G, Ferrarese R, Lagioia A, Francisci D, Colombo ML, Lazzarin S, Ogliastro M, Cappelletti MR, Iannetta M, Rizzo F, Torti C, Fumi M, d’Avenia M, Brusa S, Greco F, Menchise A, Letizia V, Vaccaro E, Santoro CR, Fraccalvieri C, Testa S, Carioti L, Rocco T, Saracino A, Cattelan A, Clementi M, Sarmati L, Riva A, Galli M, Antinori S, Zehender G. Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April-December 2021 in Italy. Viruses 2022; 14:v14112508. [PMID: 36423117 PMCID: PMC9699621 DOI: 10.3390/v14112508] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 is constantly evolving, leading to new variants. We analysed data from 4400 SARS-CoV-2-positive samples in order to pursue epidemiological variant surveillance and to evaluate their impact on public health in Italy in the period of April-December 2021. The main circulating strain (76.2%) was the Delta variant, followed by the Alpha (13.3%), the Omicron (5.3%), and the Gamma variants (2.9%). The B.1.1 lineages, Eta, Beta, Iota, Mu, and Kappa variants, represented around 1% of cases. There were 48.2% of subjects who had not been vaccinated, and they had a lower median age compared to the vaccinated subjects (47 vs. 61 years). An increasing number of infections in the vaccinated subjects were observed over time, with the highest proportion in November (85.2%). The variants correlated with clinical status; the largest proportion of symptomatic patients (59.6%) was observed with the Delta variant, while subjects harbouring the Gamma variant showed the highest proportion of asymptomatic infection (21.6%), albeit also deaths (5.4%). The Omicron variant was only found in the vaccinated subjects, of which 47% had been hospitalised. The diffusivity and pathogenicity associated with the different SARS-CoV-2 variants are likely to have relevant public health implications, both at the national and international levels. Our study provides data on the rapid changes in the epidemiological landscape of the SARS-CoV-2 variants in Italy.
Collapse
Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
- Correspondence: ; Tel.: +39-0250319775
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Carla Della Ventura
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Stefano Menzo
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | | | - Fabio Sagradi
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | | | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | - Nicola Clementi
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20158 Milan, Italy
| | | | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Lolita Sasset
- Infectious Diseases Unit, Azienda Ospedale Università di Padova, 35128 Padova, Italy
| | - Sara Caucci
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Benedetta Corvaro
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Silvia Ippoliti
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Carla Acciarri
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | | | - Leonardo Lanfranchi
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | - Maria C. Bellocchi
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | - Roberto Ferrarese
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20158 Milan, Italy
| | | | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, Santa Maria della Misericordia Hospital, University of Perugia, 06123 Perugia, Italy
| | - Martina L. Colombo
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Samuel Lazzarin
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Matilde Ogliastro
- Department of Health Sciences (DISSAL), University of Genoa, 16126 Genoa, Italy
| | - Maria R. Cappelletti
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | - Marco Iannetta
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | - Carlo Torti
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Maurizio Fumi
- UOC Patologia Clinica, AO San Pio Benevento, 82100 Benevento, Italy
| | - Morena d’Avenia
- UOSVD di Citopatologia e Screening, Department of Laboratory Medicines, 70131 Bari, Italy
| | - Stefano Brusa
- Department of Translational Medical Sciences, Università Federico II, 80138 Naples, Italy
| | - Francesca Greco
- UOC Microbiologia e Virologia, PO Cosenza, 87100 Cosenza, Italy
| | - Angela Menchise
- Microbiology and Virology Laboratory, A.O.R. San Carlo Potenza, 85100 Potenza, Italy
| | - Vittoria Letizia
- UOSD Genetics and Molecular Biology, AORN Sant’Anna e San Sebastiano di Caserta, 81100 Caserta, Italy
| | - Emilia Vaccaro
- Molecular Biology Units, AOU ‘S. Giovanni di Dio e Ruggi d’Aragona’ Università di Salerno, 84131 Salerno, Italy
| | | | | | - Sophie Testa
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Teresa Rocco
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | | | - Annamaria Cattelan
- Infectious Diseases Unit, Azienda Ospedale Università di Padova, 35128 Padova, Italy
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20158 Milan, Italy
| | - Loredana Sarmati
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Agostino Riva
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Spinello Antinori
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | | |
Collapse
|
15
|
Tang SGH, Hadi MHH, Arsad SR, Ker PJ, Ramanathan S, Afandi NAM, Afzal MM, Yaw MW, Krishnan PS, Chen CP, Tiong SK. Prerequisite for COVID-19 Prediction: A Review on Factors Affecting the Infection Rate. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12997. [PMID: 36293576 PMCID: PMC9602751 DOI: 10.3390/ijerph192012997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/24/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Since the year 2020, coronavirus disease 2019 (COVID-19) has emerged as the dominant topic of discussion in the public and research domains. Intensive research has been carried out on several aspects of COVID-19, including vaccines, its transmission mechanism, detection of COVID-19 infection, and its infection rate and factors. The awareness of the public related to the COVID-19 infection factors enables the public to adhere to the standard operating procedures, while a full elucidation on the correlation of different factors to the infection rate facilitates effective measures to minimize the risk of COVID-19 infection by policy makers and enforcers. Hence, this paper aims to provide a comprehensive and analytical review of different factors affecting the COVID-19 infection rate. Furthermore, this review analyses factors which directly and indirectly affect the COVID-19 infection risk, such as physical distance, ventilation, face masks, meteorological factor, socioeconomic factor, vaccination, host factor, SARS-CoV-2 variants, and the availability of COVID-19 testing. Critical analysis was performed for the different factors by providing quantitative and qualitative studies. Lastly, the challenges of correlating each infection risk factor to the predicted risk of COVID-19 infection are discussed, and recommendations for further research works and interventions are outlined.
Collapse
Affiliation(s)
- Shirley Gee Hoon Tang
- Center for Toxicology and Health Risk Studies (CORE), Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Malaysia
| | - Muhamad Haziq Hasnul Hadi
- Institute of Sustainable Energy, Department of Electrical & Electronics, Universiti Tenaga Nasional, Kajang 43000, Malaysia
| | - Siti Rosilah Arsad
- Institute of Sustainable Energy, Department of Electrical & Electronics, Universiti Tenaga Nasional, Kajang 43000, Malaysia
| | - Pin Jern Ker
- Institute of Sustainable Energy, Department of Electrical & Electronics, Universiti Tenaga Nasional, Kajang 43000, Malaysia
| | - Santhi Ramanathan
- Faculty of Business, Multimedia University, Jalan Ayer Keroh Lama, Malacca 75450, Malaysia
| | - Nayli Aliah Mohd Afandi
- Institute of Sustainable Energy, Department of Electrical & Electronics, Universiti Tenaga Nasional, Kajang 43000, Malaysia
| | - Madihah Mohd Afzal
- Center for Toxicology and Health Risk Studies (CORE), Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Malaysia
| | - Mei Wyin Yaw
- Institute of Sustainable Energy, Department of Electrical & Electronics, Universiti Tenaga Nasional, Kajang 43000, Malaysia
| | - Prajindra Sankar Krishnan
- Institute of Sustainable Energy, Department of Electrical & Electronics, Universiti Tenaga Nasional, Kajang 43000, Malaysia
| | - Chai Phing Chen
- Institute of Sustainable Energy, Department of Electrical & Electronics, Universiti Tenaga Nasional, Kajang 43000, Malaysia
| | - Sieh Kiong Tiong
- Institute of Sustainable Energy, Department of Electrical & Electronics, Universiti Tenaga Nasional, Kajang 43000, Malaysia
| |
Collapse
|
16
|
Hill V, Du Plessis L, Peacock TP, Aggarwal D, Colquhoun R, Carabelli AM, Ellaby N, Gallagher E, Groves N, Jackson B, McCrone JT, O’Toole Á, Price A, Sanderson T, Scher E, Southgate J, Volz E, Barclay WS, Barrett JC, Chand M, Connor T, Goodfellow I, Gupta RK, Harrison EM, Loman N, Myers R, Robertson DL, Pybus OG, Rambaut A. The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evol 2022; 8:veac080. [PMID: 36533153 PMCID: PMC9752794 DOI: 10.1093/ve/veac080] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/28/2022] [Accepted: 08/25/2022] [Indexed: 01/06/2023] Open
Abstract
The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha. Originating in early autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK and the imposition of new restrictions, in particular, the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages that preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically infected individual. We conclude that the latter provides the best explanation of the observed behaviour and dynamics of the variant, although the individual need not be immunocompromised, as persistently infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs and find that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations and a lack of the rapid evolutionary rate on its ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms), it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.
Collapse
Affiliation(s)
- Verity Hill
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Louis Du Plessis
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, UK
- Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | - Dinesh Aggarwal
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Rachel Colquhoun
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | | | - Nicholas Ellaby
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Eileen Gallagher
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Natalie Groves
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Ben Jackson
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - J T McCrone
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Áine O’Toole
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Anna Price
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 AX, UK
| | - Theo Sanderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Emily Scher
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Joel Southgate
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 AX, UK
| | - Erik Volz
- MRC Unit for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | - Jeffrey C Barrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Meera Chand
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
- Guy’s and St Thomas’ Hospital NHS Trust, St Thomas’ Hospital, Westminster Bridge Rd, London SE1 7EH, UK
| | - Thomas Connor
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 AX, UK
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff CF14 4XW, UK
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK
- Africa Health Research Institute, Durban, South Africa
| | - Ewan M Harrison
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Nicholas Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Richard Myers
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Oliver G Pybus
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, UK
- Department of Pathobiology and Population Science, The Royal Veterinary College, London, UK
| | - Andrew Rambaut
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| |
Collapse
|
17
|
Long-term SARS-CoV-2 Asymptomatic Carriage in an Immunocompromised Host: Clinical, Immunological, and Virological Implications. J Clin Immunol 2022; 42:1371-1378. [PMID: 35779200 DOI: 10.1007/s10875-022-01313-6] [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: 02/09/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022]
Abstract
PURPOSE SARS-CoV-2 infection in immunocompromised hosts is challenging, and prolonged viral shedding can be a common complication in these patients. We describe the clinical, immunological, and virological course of a patient with eosinophilic granulomatosis with polyangiitis, who developed the status of long-term asymptomatic SARS-CoV-2 carrier for more than 7 months. METHODS Over the study period, the patient underwent 20 RT-PCR tests for SARS-CoV-2 detection on nasopharyngeal swabs. In addition, viral cultures and genetic investigation of SARS-CoV-2 were performed. As for immunological assessment, serological and specific T-cell testing was provided at different time points. RESULTS Despite the patient showing a deep drug-induced B and T adaptive immunity impairment, he did not experience COVID-19 progression to severe complications, and the infection remained asymptomatic during the follow-up period, but he was not able to achieve viral clearance for more than 7 months. The infection was finally cleared by SARS-CoV-2-specific monoclonal antibody treatment, after that remdesivir and convalescent plasma failed in this scope. The genetic investigations evidenced that the infection was sustained by multiple viral subpopulations that had apparently evolved intra-host during the infection. CONCLUSION Our case suggests that people with highly impaired B- and T-cell adaptive immunity can prevent COVID-19 progression to severe complications, but they may not be able to clear SARS-CoV-2 infection. Immunocompromised hosts with a long-term infection may play a role in the emergence of viral variants.
Collapse
|
18
|
Su W, Choy KT, Gu H, Sia SF, Cheng KM, Nizami SIN, Krishnan P, Ng YM, Chang LDJ, Liu Y, Cheng SM, Peiris M, Poon LL, Nicholls JM, Yen HL. Omicron BA.1 and BA.2 sub-lineages show reduced pathogenicity and transmission potential than the early SARS-CoV-2 D614G variant in Syrian hamsters. J Infect Dis 2022; 227:1143-1152. [PMID: 35776136 PMCID: PMC9278237 DOI: 10.1093/infdis/jiac276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background The epidemiological advantage of Omicron variant is evidenced by its rapid spread and the ability to outcompete prior variants. Among Omicron sub-lineages, early outbreaks were dominated by BA.1 while BA.2 has gained dominance since February 2022. The relative pathogenicity and transmissibility of BA.1 and BA.2 have not been fully defined. Methods We compared viral loads and clinical signs in Syrian hamsters after infection with BA.1, BA.2, or D614G variant. A competitive transmission model and next generation sequencing were used to compare the relative transmission potential of BA.1 and BA.2. Results BA.1 and BA.2 caused no apparent clinical signs while D614G caused more than 10% weight loss. Higher viral loads were detected from the nasal washes, nasal turbinate and lungs of BA.1 than BA.2 inoculated hamsters. No aerosol transmission was observed for BA.1 or BA.2 under the experimental condition that D614G transmitted efficiently. BA.1 and BA.2 were able to transmit among hamsters via direct contact; however, BA.1 transmitted more efficiently than BA.2 under the competitive transmission model. No recombination was detected from direct contacts exposed simultaneously to BA.1 and BA.2. Conclusions Omicron BA.1 and BA.2 demonstrated attenuated pathogenicity and reduced transmission potential in hamsters when compared to early SARS-CoV-2 strains.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - John M Nicholls
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | |
Collapse
|
19
|
Grenfell RFQ, Almeida NBF, Filgueiras PS, Corsini CA, Gomes SVC, de Miranda DAP, Lourenço AJ, Martins-Filho OA, de Oliveira JG, Teixeira-Carvalho A, Campos GRF, Nogueira ML, Alves PA, Fernandes GR, Castilho LR, Lima TM, de Abreu DPB, Alvim RGF, Silva TBDS, Jeremias WDJ, Otta DA, Campi-Azevedo AC. Immunogenicity, Effectiveness, and Safety of Inactivated Virus (CoronaVac) Vaccine in a Two-Dose Primary Protocol and BNT162b2 Heterologous Booster in Brazil (Immunita-001): A One Year Period Follow Up Phase 4 Study. Front Immunol 2022; 13:918896. [PMID: 35757764 PMCID: PMC9218743 DOI: 10.3389/fimmu.2022.918896] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/09/2022] [Indexed: 12/30/2022] Open
Abstract
Background Effective and safe vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are critical to controlling the COVID-19 pandemic and will remain the most important tool in limiting the spread of the virus long after the pandemic is over. Methods We bring pioneering contributions on the maintenance of the immune response over a year on a real-life basis study in 1,587 individuals (18-90 yrs, median 39 yrs; 1,208 female/379 male) who underwent vaccination with two doses of CoronaVac and BNT162b2 booster after 6-months of primary protocol. Findings Elevated levels of anti-spike IgG antibodies were detected after CoronaVac vaccination, which significantly decreased after 80 days and remained stable until the introduction of the booster dose. Heterologous booster restored antibody titers up to-1·7-fold, changing overall seropositivity to 96%. Titers of neutralising antibodies to the Omicron variant were lower in all timepoints than those against Delta variant. Individuals presenting neutralising antibodies against Omicron also presented the highest titers against Delta and anti-Spike IgG. Cellular immune response measurement pointed out a mixed immune profile with a robust release of chemokines, cytokines, and growth factors on the first month after CoronaVac vaccination followed by a gradual reduction over time and no increase after the booster dose. A stronger interaction between those mediators was noted over time. Prior exposure to the virus leaded to a more robust cellular immune response and a rise in antibody levels 60 days post CoronaVac than in individuals with no previous COVID-19. Both vaccines were safe and well tolerated among individuals. Interpretation Our data approach the effectiveness of CoronaVac association with BNT162b2 from the clinical and biological perspectives, aspects that have important implications for informing decisions about vaccine boosters. Funding Fiocruz, Brazil.
Collapse
Affiliation(s)
- Rafaella F Q Grenfell
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Nathalie B F Almeida
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Priscilla S Filgueiras
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Camila A Corsini
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Sarah V C Gomes
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Daniel A P de Miranda
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Adelina J Lourenço
- Hospital da Baleia, Benjamin Guimarães Foundation, Belo Horizonte, Brazil
| | - Olindo A Martins-Filho
- Grupo Integrado de Pesquisa em Biomarcadores, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Jaquelline G de Oliveira
- Laboratório de Imunologia Celular e Molecular, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Andrea Teixeira-Carvalho
- Grupo Integrado de Pesquisa em Biomarcadores, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Guilherme R F Campos
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP)São José do Rio Preto, São José do Rio Preto, Brazil
| | - Mauricio L Nogueira
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP)São José do Rio Preto, São José do Rio Preto, Brazil.,Hospital de Base, São José do Rio Preto, Brazil.,Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Pedro Augusto Alves
- Imunologia de Doenças Virais, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Gabriel R Fernandes
- Diagnosis and Therapy of Infectious Diseases and Cancer, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil.,Biosystems Informatics, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | - Leda R Castilho
- Cell Culture Engineering Laboratory (COPPE), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tulio M Lima
- Cell Culture Engineering Laboratory (COPPE), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daniel P B de Abreu
- Cell Culture Engineering Laboratory (COPPE), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renata G F Alvim
- Cell Culture Engineering Laboratory (COPPE), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Wander de J Jeremias
- Laboratório de farmacologia experimental, College of Pharmacy, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Dayane A Otta
- Grupo Integrado de Pesquisa em Biomarcadores, Oswaldo Cruz Foundation (Fiocruz), Belo Horizonte, Brazil
| | | | | |
Collapse
|
20
|
Ortega MA, García-Montero C, Fraile-Martinez O, Colet P, Baizhaxynova A, Mukhtarova K, Alvarez-Mon M, Kanatova K, Asúnsolo A, Sarría-Santamera A. Recapping the Features of SARS-CoV-2 and Its Main Variants: Status and Future Paths. J Pers Med 2022; 12:995. [PMID: 35743779 PMCID: PMC9225183 DOI: 10.3390/jpm12060995] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/06/2022] [Accepted: 06/16/2022] [Indexed: 12/14/2022] Open
Abstract
Over the two years that we have been experiencing the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic, our challenges have been the race to develop vaccines and the difficulties in fighting against new variants due to the rapid ability of the virus to evolve. In this sense, different organizations have identified and classified the different variants that have been emerging, distinguishing between variants of concern (VOC), variants of interest (VOI), or variants under monitoring (VUM). The following review aims to describe the latest updates focusing on VOC and already de-escalated variants, as well as to describe the impact these have had on the global situation. Understanding the intrinsic properties of SARS-CoV-2 and its interaction with the immune system and vaccination is essential to make out the underlying mechanisms that have led to the appearance of these variants, helping to determine the next steps for better public management of this pandemic.
Collapse
Affiliation(s)
- Miguel A. Ortega
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (M.A.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Cielo García-Montero
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (M.A.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Oscar Fraile-Martinez
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (M.A.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Paolo Colet
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan; (P.C.); (A.B.); (K.M.); (K.K.)
| | - Ardak Baizhaxynova
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan; (P.C.); (A.B.); (K.M.); (K.K.)
| | - Kymbat Mukhtarova
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan; (P.C.); (A.B.); (K.M.); (K.K.)
| | - Melchor Alvarez-Mon
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (M.A.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Immune System Diseases-Rheumatology, Oncology Service an Internal Medicine (CIBEREHD), University Hospital Príncipe de Asturias, 28806 Alcala de Henares, Spain
| | - Kaznagul Kanatova
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan; (P.C.); (A.B.); (K.M.); (K.K.)
| | - Angel Asúnsolo
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
| | - Antonio Sarría-Santamera
- Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan 010000, Kazakhstan; (P.C.); (A.B.); (K.M.); (K.K.)
| |
Collapse
|
21
|
Akaishi T. Comparison of Insertion, Deletion, and Point Mutations in the Genomes of Human Adenovirus HAdvC-2 and SARS-CoV-2. TOHOKU J EXP MED 2022; 258:23-27. [PMID: 35705320 DOI: 10.1620/tjem.2022.j049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Tetsuya Akaishi
- Division of General Internal Medicine, Tohoku University Hospital.,Department of Education and Support for Regional Medicine, Tohoku University Hospital.,COVID-19 Screening Test Center, Tohoku University
| |
Collapse
|
22
|
Nguyen H, Lan PD, Nissley DA, O’Brien EP, Li MS. Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, but the Omicron Variant Reduces Its Neutralizing Ability. J Phys Chem B 2022; 126:2812-2823. [PMID: 35403431 PMCID: PMC9016775 DOI: 10.1021/acs.jpcb.2c00708] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A promising approach to combat Covid-19 infections is the development of effective antiviral antibodies that target the SARS-CoV-2 spike protein. Understanding the structures and molecular mechanisms underlying the binding of antibodies to SARS-CoV-2 can contribute to quickly achieving this goal. Recently, a cocktail of REGN10987 and REGN10933 antibodies was shown to be an excellent candidate for the treatment of Covid-19. Here, using all-atom steered molecular dynamics and coarse-grained umbrella sampling, we examine the interactions of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with REGN10987 and REGN10933 separately as well as together. Both computational methods show that REGN10933 binds to RBD more strongly than REGN10987. Importantly, the cocktail binds to RBD (simultaneous binding) more strongly than its components. The dissociation constants of REGN10987-RBD and REGN10933-RBD complexes calculated from the coarse-grained simulations are in good agreement with the experimental data. Thus, REGN10933 is probably a better candidate for treating Covid-19 than REGN10987, although the cocktail appears to neutralize the virus more efficiently than REGN10933 or REGN10987 alone. The association of REGN10987 with RBD is driven by van der Waals interactions, while electrostatic interactions dominate in the case of REGN10933 and the cocktail. We also studied the effectiveness of these antibodies on the two most dangerous variants Delta and Omicron. Consistent with recent experimental reports, our results confirmed that the Omicron variant reduces the neutralizing activity of REGN10933, REGN10987, and REGN10933+REGN10987 with the K417N, N440K, L484A, and Q498R mutations playing a decisive role, while the Delta variant slightly changes their activity.
Collapse
Affiliation(s)
- Hung Nguyen
- Institute
of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Pham Dang Lan
- Life
Science Lab, Institute for Computational
Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam,Faculty
of Physics and Engineering Physics, VNUHCM-University
of Science, 227, Nguyen
Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Daniel A. Nissley
- Department
of Statistics, University of Oxford, Oxford
Protein Bioinformatics Group, OX1 2JD Oxford, United Kingdom
| | - Edward P. O’Brien
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States,Bioinformatics
and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, United States,Institute
for Computational and Data Sciences, Penn
State University, University Park, Pennsylvania 16802, United States
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland,
| |
Collapse
|
23
|
Gräf T, Bello G, Naveca FG, Gomes M, Cardoso VLO, da Silva AF, Dezordi FZ, dos Santos MC, Santos KCDO, Batista ÉLR, Magalhães ALÁ, Vinhal F, Miyajima F, Faoro H, Khouri R, Wallau GL, Delatorre E, Siqueira MM, Resende PC. Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil. iScience 2022; 25:104156. [PMID: 35368908 PMCID: PMC8957357 DOI: 10.1016/j.isci.2022.104156] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/23/2022] [Accepted: 03/21/2022] [Indexed: 11/03/2022] Open
Abstract
The COVID-19 epidemic in Brazil experienced two major lineage replacements until mid-2021. The first was driven by lineage P.2, in late 2020, and the second by lineage Gamma, in early 2021. To understand how these SARS-CoV-2 lineages spread in Brazil, we analyzed 11,724 genomes collected throughout the country between September 2020 and April 2021. Our findings indicate that lineage P.2 probably emerged in July 2020 in the Rio de Janeiro state and Gamma in November 2020 in the Amazonas state. Both states were the main hubs of viral disseminations to other Brazilian locations. We estimate that Gamma was 1.56-3.06 times more transmissible than P.2 in Rio de Janeiro and that the median effective reproductive number (Re) of Gamma varied according to the geographic context (Re = 1.59-3.55). In summary, our findings support that lineage Gamma was more transmissible and spread faster than P.2 in Brazil.
Collapse
Affiliation(s)
- Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Leônidas e Maria Deane Institute, Fiocruz, Manaus, Brazil
| | - Marcelo Gomes
- Grupo de Métodos Analíticos em Vigilância Epidemiológica, Programa de Computação Científica (PROCC), Fiocruz, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | | | | - Fábio Miyajima
- Fundação Oswaldo Cruz - Fiocruz Ceará, Fortaleza, Brazil
| | - Helisson Faoro
- Instituto Carlos Chagas (ICC), Fiocruz-PR, Curitiba, Parana, Brazil
| | - Ricardo Khouri
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Gabriel Luz Wallau
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Edson Delatorre
- Departamento de Biologia. Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, Alegre, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| |
Collapse
|