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Adzdzakiy MM, Sutarno S, Asyifa IZ, Sativa AR, Fiqri AR, Fibriani A, Ristandi RB, Ningrum RA, Iryanto SB, Prasetyoputri A, Dharmayanthi AB, Saputra S. SARS-CoV-2 genetic variation and bacterial communities of naso-oropharyngeal samples in middle-aged and elderly COVID-19 patients in West Java, Indonesia. J Taibah Univ Med Sci 2024; 19:70-81. [PMID: 37868100 PMCID: PMC10589881 DOI: 10.1016/j.jtumed.2023.09.001] [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: 02/24/2023] [Revised: 07/21/2023] [Accepted: 09/01/2023] [Indexed: 10/24/2023] Open
Abstract
Objective The number of COVID-19 cases in Indonesia reflects the disease severity and rapid dissemination. In response to the mounting threat, SARS-CoV-2 genomic surveillance and the investigation of naso-oropharyngeal bacterial communities in West Java were conducted, as dysbiosis of the upper respiratory tract microbiota might adversely affect the clinical condition of patients. Methods We utilized the Oxford Nanopore sequencing platform to analyze genetic variation of 43 samples of SARS-CoV-2 and 11 selected samples for 16S rRNA gene sequencing, using samples collected from May to August 2021. Results The prevalence of AY.23 (>82%) predominated among five virus lineages in the populations (AY.23, AY.24, AY.26, AY.42, B.1.1.7). The region in the SARS-CoV-2 genome found to have the highest number of mutations was the spike (S) protein (>20%). There was no association between SARS-CoV-2 lineages, mutation frequency, patient profile, and COVID-19 rapid spread-categorized cases. There was no association of bacterial relative abundance, alpha-beta diversity, and linear discriminant analysis effect size analysis with patient profile and rapid spread cases. MetagenomeSeq analysis showed eight differential abundance species in individual patient profiles, including Pseudomonas aeruginosa and Haemophilus parainfluenzae. Conclusions The data demonstrated relevant AY.23 dominance (the Delta variant) in West Java during that period supporting the importance of surveillance program in monitoring disease progression. The inconsistent results of the bacterial communities suggest that a complex multifactor process may contribute to the progression of bacterial-induced disease in each patient.
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Affiliation(s)
- Muhammad M. Adzdzakiy
- Graduate School of Bioscience, Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret, Jl. Ir. Sutami 36A Surakarta, Central Java, Indonesia
| | - Sutarno Sutarno
- Graduate School of Bioscience, Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret, Jl. Ir. Sutami 36A Surakarta, Central Java, Indonesia
| | - Isnaini Z. Asyifa
- Master Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya No.6, Jakarta, Indonesia
| | - Alvira R. Sativa
- School of Life Science and Technology, Institut Teknologi Bandung, Jl. Ganesa 10, Bandung, West Java, Indonesia
| | - Ahmad R.A. Fiqri
- Master Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya No.6, Jakarta, Indonesia
| | - Azzania Fibriani
- School of Life Science and Technology, Institut Teknologi Bandung, Jl. Ganesa 10, Bandung, West Java, Indonesia
| | - Ryan B. Ristandi
- West Java Health Laboratory, Jl. Sederhana No. 3-5, Pasteur, Sukajadi, Bandung, West Java, Indonesia
| | - Ratih A. Ningrum
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
| | - Syam B. Iryanto
- Research Center for Computation, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
| | - Anggia Prasetyoputri
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
| | - Anik B. Dharmayanthi
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
| | - Sugiyono Saputra
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
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2
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Acevedo-Sánchez G, Mora-Aguilera G, Coria-Contreras JJ, Álvarez-Maya I. Were metabolic and other chronic diseases the driven onset epidemic forces of COVID-19 in Mexico? Front Public Health 2023; 11:995602. [PMID: 37608984 PMCID: PMC10441236 DOI: 10.3389/fpubh.2023.995602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 07/14/2023] [Indexed: 08/24/2023] Open
Abstract
The underline hypothesis of this study was that SARS-CoV-2 can infect individuals regardless of health condition, sex, and age in opposition to the classical epidemiological assumption of an identifiable susceptible subpopulation for epidemic development. To address this issue, a population cohort with 24.4 million metadata associated with 226,089 official RT-qPCR positive and 283,450 negative cases, including 27,769 deceased, linked putatively to B.1. and B.1.1. SARS-CoV-2 lineages were analyzed. The analysis baseline was to determine the infection and mortality structure of the diseased cohort at the onset-exponential phase of the first epidemic wave in Mexico under the assumption of limited herd immunity. Individuals with nonchronic diseases (NOCDs) were compared with those exhibiting at least one of 10 chronic diseases (CDs) adjusted by age and sex. Risk factors for infection and mortality were estimated with classification and regression tree (CART) and cluster analysis based on Spearman's matrix of rho-values in RStudio®, complemented with two proposed mortality indices. SARS-CoV-2 infection was independent of health condition (52.8% NOCD vs. 47.2% CDs; p = 0.001-0.009) but influenced by age >46 in one risk analysis scenario (p < 0.001). Sex contributed 9.7% to the overall risk. The independent effect was supported by the health structure of negative cases with a similar tendency but a higher proportion of NOCDs (61.4%, p = 0.007). The infection probability in individuals with one CD was determined by the disease type and age, which was higher in those older individuals (≥56 years) exhibiting diabetes (12.3%, cp = 0.0006), hypertension (10.1%, cp < 0.0001), and obesity (7.8%, cp = 0.001). In contrast, the mortality risk was heavily influenced by CD conditioned by sex and age, accounting for 72.3% of total deaths (p = 0.001-0.008). Significant mortality risk (48%) was comprised of women and men (w, m) aged ≥56 years with diabetes (19% w and 27.9% m, cp < 0.0004), hypertension (11.5% w, cp = 0.0001), and CKD (3.5% w and 5.3% m, cp = 0.0009). Older people with diabetes and hypertension comorbidity increased the risk to 60.5% (p = 0.001). Based on a mortality-weighted index, women were more vulnerable to preexisting metabolic or cardiovascular diseases. These findings support our hypothesis and justify the need for surveillance systems at a communitarian level. This is the first study addressing this fundamental epidemiological question.
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Affiliation(s)
- Gerardo Acevedo-Sánchez
- Laboratory of Epidemiological Risk Analysis (LANREF), Postgraduate College, Montecillo Campus, Texcoco, State of Mexico, Mexico
| | - Gustavo Mora-Aguilera
- Laboratory of Epidemiological Risk Analysis (LANREF), Postgraduate College, Montecillo Campus, Texcoco, State of Mexico, Mexico
| | - Juan J. Coria-Contreras
- Laboratory of Epidemiological Risk Analysis (LANREF), Postgraduate College, Montecillo Campus, Texcoco, State of Mexico, Mexico
| | - Ikuri Álvarez-Maya
- Center for Research and Applied Technology in Jalisco (CIATEJ), Guadalajara, Jalisco, Mexico
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3
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Izquierdo-Lara RW, Heijnen L, Oude Munnink BB, Schapendonk CME, Elsinga G, Langeveld J, Post J, Prasad DK, Carrizosa C, Been F, van Beek J, Schilperoort R, Vriend R, Fanoy E, de Schepper EIT, Sikkema RS, Molenkamp R, Aarestrup FM, Medema G, Koopmans MPG, de Graaf M. Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162209. [PMID: 36796689 PMCID: PMC9927792 DOI: 10.1016/j.scitotenv.2023.162209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 06/04/2023]
Abstract
Monitoring of SARS-CoV-2 in wastewater (WW) is a promising tool for epidemiological surveillance, correlating not only viral RNA levels with the infection dynamics within the population, but also to viral diversity. However, the complex mixture of viral lineages in WW samples makes tracking of specific variants or lineages circulating in the population a challenging task. We sequenced sewage samples of 9 WW-catchment areas within the city of Rotterdam, used specific signature mutations from individual SARS-CoV-2 lineages to estimate their relative abundances in WW and compared them against those observed in clinical genomic surveillance of infected individuals between September 2020 and December 2021. We showed that especially for dominant lineages, the median of the frequencies of signature mutations coincides with the occurrence of those lineages in Rotterdam's clinical genomic surveillance. This, along with digital droplet RT-PCR targeting signature mutations of specific variants of concern (VOCs), showed that several VOCs emerged, became dominant and were replaced by the next VOC in Rotterdam at different time points during the study. In addition, single nucleotide variant (SNV) analysis provided evidence that spatio-temporal clusters can also be discerned from WW samples. We were able to detect specific SNVs in sewage, including one resulting in the Q183H amino acid change in the Spike gene, that was not captured by clinical genomic surveillance. Our results highlight the potential use of WW samples for genomic surveillance, increasing the set of epidemiological tools to monitor SARS-CoV-2 diversity.
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Affiliation(s)
- Ray W Izquierdo-Lara
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Goffe Elsinga
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Jeroen Langeveld
- Partners4urbanwater, Nijmegen, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
| | - Johan Post
- Partners4urbanwater, Nijmegen, the Netherlands
| | - Divyae K Prasad
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Christian Carrizosa
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Frederic Been
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Janko van Beek
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Rianne Vriend
- Regional Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Ewout Fanoy
- Regional Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Evelien I T de Schepper
- Department of General Practice, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Reina S Sikkema
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands.
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4
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Harne R, Williams B, Abdelaal HFM, Baldwin SL, Coler RN. SARS-CoV-2 infection and immune responses. AIMS Microbiol 2023; 9:245-276. [PMID: 37091818 PMCID: PMC10113164 DOI: 10.3934/microbiol.2023015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
The recent pandemic caused by the SARS-CoV-2 virus continues to be an enormous global challenge faced by the healthcare sector. Availability of new vaccines and drugs targeting SARS-CoV-2 and sequelae of COVID-19 has given the world hope in ending the pandemic. However, the emergence of mutations in the SARS-CoV-2 viral genome every couple of months in different parts of world is a persistent danger to public health. Currently there is no single treatment to eradicate the risk of COVID-19. The widespread transmission of SARS-CoV-2 due to the Omicron variant necessitates continued work on the development and implementation of effective vaccines. Moreover, there is evidence that mutations in the receptor domain of the SARS-CoV-2 spike glycoprotein led to the decrease in current vaccine efficacy by escaping antibody recognition. Therefore, it is essential to actively identify the mechanisms by which SARS-CoV-2 evades the host immune system, study the long-lasting effects of COVID-19 and develop therapeutics targeting SARS-CoV-2 infections in humans and preclinical models. In this review, we describe the pathogenic mechanisms of SARS-CoV-2 infection as well as the innate and adaptive host immune responses to infection. We address the ongoing need to develop effective vaccines that provide protection against different variants of SARS-CoV-2, as well as validated endpoint assays to evaluate the immunogenicity of vaccines in the pipeline, medications, anti-viral drug therapies and public health measures, that will be required to successfully end the COVID-19 pandemic.
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Affiliation(s)
- Rakhi Harne
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Brittany Williams
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Hazem F. M. Abdelaal
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Susan L. Baldwin
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Rhea N. Coler
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
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5
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SpikeSeq: A rapid, cost efficient and simple method to identify SARS-CoV-2 variants of concern by Sanger sequencing part of the spike protein gene. J Virol Methods 2023; 312:114648. [PMID: 36368344 PMCID: PMC9642040 DOI: 10.1016/j.jviromet.2022.114648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]
Abstract
In 2020, the novel coronavirus, SARS-CoV-2, caused a pandemic, which is still raging at the time of writing this. Here, we present results from SpikeSeq, the first published Sanger sequencing-based method for the detection of Variants of Concern (VOC) and key mutations, using a 1 kb amplicon from the recognized ARTIC Network primers. The proposed setup relies entirely on materials and methods already in use in diagnostic RT-qPCR labs and on existing commercial infrastructure offering sequencing services. For data analysis, we provide an automated, open source, and browser-based mutation calling software (https://github.com/kblin/covid-spike-classification, https://ssi.biolib.com/covid-spike-classification). We validated the setup on 195 SARS-CoV-2 positive samples, and we were able to profile 85% of RT-qPCR positive samples, where the last 15% largely stemmed from samples with low viral count. We compared the SpikeSeq results to WGS results. SpikeSeq has been used as the primary variant identification tool on > 10.000 SARS-CoV-2 positive clinical samples during 2021. At approximately 4€ per sample in material cost, minimal hands-on time, little data handling, and a short turnaround time, the setup is simple enough to be implemented in any SARS-CoV-2 RT-qPCR diagnostic lab. Our protocol provides results that can be used to choose antibodies in a clinical setting and for the tracking and surveillance of all positive samples for new variants and known ones such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1) Delta (B.1.617.2), Omicron BA.1(B.1.1.529), BA.2, BA.4/5, BA.2.75.x, and many more, as of October 2022.
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6
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Kotov I, Saenko V, Borisova N, Kolesnikov A, Kondrasheva L, Tivanova E, Khafizov K, Akimkin V. Effective Approaches to Study the Genetic Variability of SARS-CoV-2. Viruses 2022; 14:v14091855. [PMID: 36146662 PMCID: PMC9504788 DOI: 10.3390/v14091855] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Significant efforts are being made in many countries around the world to respond to the COVID-19 pandemic by developing diagnostic reagent kits, identifying infected people, determining treatment methods, and finally producing effective vaccines. However, novel coronavirus variants may potentially reduce the effectiveness of all these efforts, demonstrating increased transmissibility and abated response to therapy or vaccines, as well as the possibility of false negative results in diagnostic procedures based on nucleic acid amplification methods. Since the end of 2020, several variants of concern have been discovered around the world. When information about a new, potentially more dangerous strain of pathogen appears, it is crucial to determine the moment of its emergence in a region. Eventually, that permits taking timely measures and minimizing new risks associated with the spreading of the virus. Therefore, numerous nations have made tremendous efforts to identify and trace these virus variants, which necessitates serious technological processes to sequence a large number of viral genomes. Here, we report on our experience as one of the primary laboratories involved in monitoring SARS-CoV-2 variants in Russia. We discuss the various approaches used, describe effective protocols, and outline a potential technique combining several methods to increase the ability to trace genetic variants while minimizing financial and labor costs.
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Affiliation(s)
- Ivan Kotov
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 115184 Dolgoprudny, Russia
| | - Valeriia Saenko
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
| | - Nadezhda Borisova
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
| | - Anton Kolesnikov
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
| | - Larisa Kondrasheva
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
| | - Elena Tivanova
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
| | - Kamil Khafizov
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
- Correspondence:
| | - Vasily Akimkin
- FSBI Central Research Institute for Epidemiology of the Federal Service for Surveillance of Consumer Rights Protection and Human Wellbeing, 111123 Moscow, Russia
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7
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Determining the International Spread of B.1.1.523 SARS-CoV-2 Lineage with a Set of Mutations Highly Associated with Reduced Immune Neutralization. Microorganisms 2022; 10:microorganisms10071356. [PMID: 35889075 PMCID: PMC9320768 DOI: 10.3390/microorganisms10071356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 02/05/2023] Open
Abstract
Here, we report the emergence of the variant lineage B.1.1.523 that contains a set of mutations including 156_158del, E484K and S494P in the spike protein. E484K and S494P are known to significantly reduce SARS-CoV-2 neutralization by convalescent and vaccinated sera and are considered as mutations of concern. Lineage B.1.1.523 presumably originated in the Russian Federation and spread across European countries with the peak of transmission in April–May 2021. The B.1.1.523 lineage has now been reported from 31 countries. In this article, we analyze the possible origin of this mutation subset and its immune response using in silico methods.
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Viala VL, Slavov SN, de Lima LPO, Lima ARJ, Ribeiro G, Martins AJ, Petry B, Banho CA, Barros CRDS, Moncau CT, Moretti DB, de La-Roque DGL, Marqueze EC, Mattos EC, da Costa FADS, Fukumasu H, Bernardino JDST, Souza-Neto JA, Lesbon JCC, Kayanoki LP, Bernardo LL, Sacchetto L, Clemente LG, Alcantara LCJ, Coutinho LL, Marques BDC, Giovanetti M, Nogueira ML, Poleti MD, Assato PA, Cattony Neto PDQ, Cassano RDLRC, Neto RM, Grotto RMT, Brassaloti RA, Kashima S, Covas DT, Elias MC, Sampaio SC. The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela. Viruses 2022; 14:v14071481. [PMID: 35891460 PMCID: PMC9323713 DOI: 10.3390/v14071481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/19/2022] [Accepted: 06/30/2022] [Indexed: 02/04/2023] Open
Abstract
Our effort in SARS-CoV-2 genomic surveillance in Brazil has detected the Alpha Variant of Concern with a predominance higher than 75% in the population of Ilhabela island (São Paulo State) at a time when the Gamma VOC was already predominating the mainland raised concerns for closer surveillance on this island. Therefore, we intensified the surveillance for 24 weeks by generating data from 34% of local positive cases. Our data show that the patterns of VOC predominance dynamics and infection rates were in general distinct from the mainland. We report here the first known case of Alpha predominance in a Brazilian population, a delay greater than 3 months for the Gamma to dominate the previous variants compared to the mainland, and a faster dispersion rate of Gamma and Delta VOCs compared to the mainland. Phylogenetic analysis revealed the SARS-CoV-2 transmission dynamics in Ilhabela were characterized by multiple independent introduction events of Gamma and Delta, with a few events of Alpha introduction, two of them followed by community transmission. This study evidenced the peculiar behavior of SARS-CoV-2 variants in an isolated population and brought to light the importance of specific programs for SARS-CoV-2 genomic surveillance in isolated populations.
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Affiliation(s)
- Vincent Louis Viala
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
- Correspondence: (V.L.V.); (M.C.E.); (S.C.S.)
| | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (S.N.S.); (D.G.L.d.L.-R.); (S.K.)
| | - Loyze Paola Oliveira de Lima
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
| | - Alex Ranieri Jeronimo Lima
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
| | - Gabriela Ribeiro
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
| | - Antonio Jorge Martins
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
| | - Bruna Petry
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (B.P.); (C.T.M.); (L.G.C.); (L.L.C.); (R.d.L.R.C.C.); (R.A.B.)
| | - Cecilia Artico Banho
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil; (C.A.B.); (L.S.); (B.d.C.M.); (M.L.N.)
| | - Claudia Renata dos Santos Barros
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
| | - Cristina Tschorny Moncau
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (B.P.); (C.T.M.); (L.G.C.); (L.L.C.); (R.d.L.R.C.C.); (R.A.B.)
| | - Debora Botequio Moretti
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
| | - Debora Glenda Lima de La-Roque
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (S.N.S.); (D.G.L.d.L.-R.); (S.K.)
| | - Elaine Cristina Marqueze
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
| | - Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, SP, Brazil; (E.C.M.); (H.F.); (J.C.C.L.); (M.D.P.)
| | - Felipe Allan da Silva da Costa
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil; (F.A.d.S.d.C.); (P.A.A.)
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, SP, Brazil; (E.C.M.); (H.F.); (J.C.C.L.); (M.D.P.)
| | - Jardelina de Souza Todao Bernardino
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
| | - Jayme A. Souza-Neto
- School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil; (J.A.S.-N.); (R.M.T.G.)
| | - Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, SP, Brazil; (E.C.M.); (H.F.); (J.C.C.L.); (M.D.P.)
| | | | | | - Lívia Sacchetto
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil; (C.A.B.); (L.S.); (B.d.C.M.); (M.L.N.)
| | - Luan Gaspar Clemente
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (B.P.); (C.T.M.); (L.G.C.); (L.L.C.); (R.d.L.R.C.C.); (R.A.B.)
| | - Luiz Carlos Júnior Alcantara
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-360, RJ, Brazil
| | - Luiz Lehmann Coutinho
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (B.P.); (C.T.M.); (L.G.C.); (L.L.C.); (R.d.L.R.C.C.); (R.A.B.)
| | - Beatriz de Carvalho Marques
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil; (C.A.B.); (L.S.); (B.d.C.M.); (M.L.N.)
| | - Marta Giovanetti
- Reference Laboratory of Flavivirus, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, RJ, Brazil;
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Maurício Lacerda Nogueira
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil; (C.A.B.); (L.S.); (B.d.C.M.); (M.L.N.)
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, SP, Brazil; (E.C.M.); (H.F.); (J.C.C.L.); (M.D.P.)
| | - Patricia Akemi Assato
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil; (F.A.d.S.d.C.); (P.A.A.)
| | - Pedro De Queiroz Cattony Neto
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
| | - Raquel de Lello Rocha Campos Cassano
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (B.P.); (C.T.M.); (L.G.C.); (L.L.C.); (R.d.L.R.C.C.); (R.A.B.)
| | - Raul Machado Neto
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
| | - Rejane Maria Tommasini Grotto
- School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil; (J.A.S.-N.); (R.M.T.G.)
- Molecular Biology and Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, Botucatu 18610-034, SP, Brazil
| | - Ricardo Augusto Brassaloti
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (B.P.); (C.T.M.); (L.G.C.); (L.L.C.); (R.d.L.R.C.C.); (R.A.B.)
| | - Simone Kashima
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (S.N.S.); (D.G.L.d.L.-R.); (S.K.)
| | - Dimas Tadeu Covas
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (S.N.S.); (D.G.L.d.L.-R.); (S.K.)
| | - Maria Carolina Elias
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
- Correspondence: (V.L.V.); (M.C.E.); (S.C.S.)
| | - Sandra Coccuzzo Sampaio
- Butantan Institute, São Paulo 05503-900, SP, Brazil; (L.P.O.d.L.); (A.R.J.L.); (G.R.); (A.J.M.); (C.R.d.S.B.); (D.B.M.); (E.C.M.); (J.d.S.T.B.); (P.D.Q.C.N.); (R.M.N.); (D.T.C.)
- Correspondence: (V.L.V.); (M.C.E.); (S.C.S.)
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9
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Asghar R, Rasheed M, ul Hassan J, Rafique M, Khan M, Deng Y. Advancements in Testing Strategies for COVID-19. BIOSENSORS 2022; 12:410. [PMID: 35735558 PMCID: PMC9220779 DOI: 10.3390/bios12060410] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022]
Abstract
The SARS-CoV-2 coronavirus, also known as the disease-causing agent for COVID-19, is a virulent pathogen that may infect people and certain animals. The global spread of COVID-19 and its emerging variation necessitates the development of rapid, reliable, simple, and low-cost diagnostic tools. Many methodologies and devices have been developed for the highly sensitive, selective, cost-effective, and rapid diagnosis of COVID-19. This review organizes the diagnosis platforms into four groups: imaging, molecular-based detection, serological testing, and biosensors. Each platform's principle, advancement, utilization, and challenges for monitoring SARS-CoV-2 are discussed in detail. In addition, an overview of the impact of variants on detection, commercially available kits, and readout signal analysis has been presented. This review will expand our understanding of developing advanced diagnostic approaches to evolve into susceptible, precise, and reproducible technologies to combat any future outbreak.
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Affiliation(s)
- Rabia Asghar
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
| | - Madiha Rasheed
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
| | - Jalees ul Hassan
- Department of Wildlife and Ecology, Faculty of Fisheries and Wildlife, University of Veterinary and Animal Sciences-UVAS, Lahore 54000, Pakistan;
| | - Mohsin Rafique
- Beijing Academy of Quantum Information Sciences, Beijing 100193, China;
| | - Mashooq Khan
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China;
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
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10
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Chadha J, Khullar L, Mittal N. Facing the wrath of enigmatic mutations: a review on the emergence of severe acute respiratory syndrome coronavirus 2 variants amid coronavirus disease-19 pandemic. Environ Microbiol 2022; 24:2615-2629. [PMID: 34320263 PMCID: PMC8441773 DOI: 10.1111/1462-2920.15687] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 12/27/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging respiratory virus responsible for the ongoing coronavirus disease 19 (COVID-19) pandemic. More than a year into this pandemic, the COVID-19 fatigue is still escalating and takes hold of the entire world population. Driven by the ongoing geographical expansion and upcoming mutations, the COVID-19 pandemic has taken a new shape in the form of emerging SARS-CoV-2 variants. These mutations in the viral spike (S) protein enhance the virulence of SARS-CoV-2 variants by improving viral infectivity, transmissibility and immune evasion abilities. Such variants have resulted in cluster outbreaks and fresh infection waves in various parts of the world with increased disease severity and poor clinical outcomes. Hence, the variants of SARS-CoV-2 pose a threat to human health and public safety. This review enlists the most recent updates regarding the presently characterized variants of SARS-CoV-2 recognized by the global regulatory health authorities (WHO, CDC). Based on the slender literature on SARS-CoV-2 variants, we collate information on the biological implications of these mutations on virus pathology. We also shed light on the efficacy of therapeutics and COVID-19 vaccines against the emerging SARS-CoV-2 variants.
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Affiliation(s)
- Jatin Chadha
- Department of MicrobiologyPanjab UniversityChandigarhIndia
| | | | - Nidhi Mittal
- Molecular Biophysics UnitIndian Institute of Science (IISc)BengaluruIndia
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11
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CAVES: A Novel Tool for Comparative Analysis of Variant Epitope Sequences. Viruses 2022; 14:v14061152. [PMID: 35746624 PMCID: PMC9227564 DOI: 10.3390/v14061152] [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: 02/28/2022] [Revised: 05/06/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
In silico methods for immune epitope prediction have become essential for vaccine and therapeutic design, but manual intra-species comparison of putative epitopes remains challenging and subject to human error. Created initially for analyzing SARS-CoV-2 variants of concern, comparative analysis of variant epitope sequences (CAVES) is a novel tool designed to carry out rapid comparative analyses of epitopes amongst closely related pathogens, substantially reducing the required time and user workload. CAVES applies a two-level analysis approach. The Level-one (L1) analysis compares two epitope prediction files, and the Level-two (L2) analysis incorporates search results from the IEDB database of experimentally confirmed epitopes. Both L1 and L2 analyses sort epitopes into categories of exact matches, partial matches, or novel epitopes based on the degree to which they match with peptides from the compared file. Furthermore, CAVES uses positional sequence data to improve its accuracy and speed, taking only a fraction of the time required by manual analyses and minimizing human error. CAVES is widely applicable for evolutionary analyses and antigenic comparisons of any closely related pathogen species. CAVES is open-source software that runs through a graphical user interface on Windows operating systems, making it widely accessible regardless of coding expertise. The CAVES source code and test dataset presented here are publicly available on the CAVES GitHub page.
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12
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Zárate S, Taboada B, Muñoz-Medina JE, Iša P, Sanchez-Flores A, Boukadida C, Herrera-Estrella A, Selem Mojica N, Rosales-Rivera M, Gómez-Gil B, Salas-Lais AG, Santacruz-Tinoco CE, Montoya-Fuentes H, Alvarado-Yaah JE, Molina-Salinas GM, Espinoza-Ayala GE, Enciso-Moreno JA, Gutiérrez-Ríos RM, Loza A, Moreno-Contreras J, García-López R, Rivera-Gutierrez X, Comas-García A, Wong-Chew RM, Jiménez-Corona ME, del Angel RM, Vazquez-Perez JA, Matías-Florentino M, Pérez-García M, Ávila-Ríos S, Castelán-Sánchez HG, Delaye L, Martínez-Castilla LP, Escalera-Zamudio M, López S, Arias CF. The Alpha Variant (B.1.1.7) of SARS-CoV-2 Failed to Become Dominant in Mexico. Microbiol Spectr 2022; 10:e0224021. [PMID: 35389245 PMCID: PMC9045257 DOI: 10.1128/spectrum.02240-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/17/2022] [Indexed: 12/26/2022] Open
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, the emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in the United Kingdom in September 2020, was well documented in different areas of the world and became a global public health concern because of its increased transmissibility. The B.1.1.7 lineage was first detected in Mexico during December 2020, showing a slow progressive increase in its circulation frequency, which reached its maximum in May 2021 but never became predominant. In this work, we analyzed the patterns of diversity and distribution of this lineage in Mexico using phylogenetic and haplotype network analyses. Despite the reported increase in transmissibility of the B.1.1.7 lineage, in most Mexican states, it did not displace cocirculating lineages, such as B.1.1.519, which dominated the country from February to May 2021. Our results show that the states with the highest prevalence of B.1.1.7 were those at the Mexico-U.S. border. An apparent pattern of dispersion of this lineage from the northern states of Mexico toward the center or the southeast was observed in the largest transmission chains, indicating possible independent introduction events from the United States. However, other entry points cannot be excluded, as shown by multiple introduction events. Local transmission led to a few successful haplotypes with a localized distribution and specific mutations indicating sustained community transmission. IMPORTANCE The emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout the world were due to its increased transmissibility. However, it did not displace cocirculating lineages in most of Mexico, particularly B.1.1.519, which dominated the country from February to May 2021. In this work, we analyzed the distribution of B.1.1.7 in Mexico using phylogenetic and haplotype network analyses. Our results show that the states with the highest prevalence of B.1.1.7 (around 30%) were those at the Mexico-U.S. border, which also exhibited the highest lineage diversity, indicating possible introduction events from the United States. Also, several haplotypes were identified with a localized distribution and specific mutations, indicating that sustained community transmission occurred in the country.
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Affiliation(s)
- Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Nelly Selem Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, México
| | - Mauricio Rosales-Rivera
- Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Unidad Mazatlám, Mazatlán, México
| | - Angel Gustavo Salas-Lais
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | - Héctor Montoya-Fuentes
- Centro de Investigación Biomedica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, México
| | - Julio Elias Alvarado-Yaah
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | | | - José Antonio Enciso-Moreno
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas, Zacatecas, México
| | - Rosa María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Antonio Loza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Joaquín Moreno-Contreras
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Xaira Rivera-Gutierrez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Andreu Comas-García
- Facultad de Medicna y Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Rosa María Wong-Chew
- Facultad de Medicina, Laboratorio de Investigación en Enfermedades Infecciosas, División de Investigación, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Rosa María del Angel
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav, Ciudad de México, México
| | - Joel Armando Vazquez-Perez
- Laboratorio de Biología Molecular de Enfermedades Emergentes y EPOC Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Marissa Pérez-García
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Hugo G. Castelán-Sánchez
- Programa de Investigadoras e investigadores por México Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Luis Delaye
- Departamento de Ingeniería Genética, Cinvestav Unidad Irapuato, Guanajuato, México
| | - León P. Martínez-Castilla
- Programa de Investigadoras e investigadores por México Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, México
| | | | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
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13
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Zhao Y, Huang J, Zhang L, Chen S, Gao J, Jiao H. The global transmission of new coronavirus variants. ENVIRONMENTAL RESEARCH 2022; 206:112240. [PMID: 34688639 PMCID: PMC8530777 DOI: 10.1016/j.envres.2021.112240] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 05/27/2023]
Abstract
Coronavirus Disease 2019 (COVID-19) has caused tremendous losses to the world. This study addresses the impact and diffusion of the five major new coronavirus variants namely Alpha, Beta, Gamma, Eta, and Delta lineage. The results of this study indicate that Africa and Europe will be affected by new coronavirus variants the most compared with other continents. The comparative analysis indicates that vaccination can contain the spread of the virus in most of the continent, and non-pharmaceutical interventions (NPIs), such as restriction on gatherings and close public transport, will effectively curb the pandemic, especially in densely populated continents. According to our Global Prediction System of COVID-19 Pandemic, the diffusion of delta lineage in the US shows seasonal oscillation characteristics, and the first wave will occur in October 2021, with the record of 323,360, and followed by a small resurgence in April 2022, with the record of 184,196, while the second wave will reach to 232,622 cases in October 2022. Our study will raise the awareness of new coronavirus variants among the public, and will help the governments make appropriate directives to cope with the new coronavirus variants.
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Affiliation(s)
- Yingjie Zhao
- Collaborative Innovation Centre for West Ecological Safety (CIWES), Lanzhou University, Lanzhou, 730000, China
| | - Jianping Huang
- Collaborative Innovation Centre for West Ecological Safety (CIWES), Lanzhou University, Lanzhou, 730000, China; College of Atmospheric Sciences, Lanzhou University, Lanzhou, China.
| | - Li Zhang
- Collaborative Innovation Centre for West Ecological Safety (CIWES), Lanzhou University, Lanzhou, 730000, China; College of Atmospheric Sciences, Lanzhou University, Lanzhou, China
| | - Siyu Chen
- Collaborative Innovation Centre for West Ecological Safety (CIWES), Lanzhou University, Lanzhou, 730000, China; College of Atmospheric Sciences, Lanzhou University, Lanzhou, China
| | - Jinfeng Gao
- Collaborative Innovation Centre for West Ecological Safety (CIWES), Lanzhou University, Lanzhou, 730000, China
| | - Hui Jiao
- Collaborative Innovation Centre for West Ecological Safety (CIWES), Lanzhou University, Lanzhou, 730000, China
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14
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Oh C, Sashittal P, Zhou A, Wang L, El-Kebir M, Nguyen TH. Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Appl Environ Microbiol 2022; 88:e0228921. [PMID: 35285246 PMCID: PMC9004361 DOI: 10.1128/aem.02289-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Monitoring the prevalence of SARS-CoV-2 variants is necessary to make informed public health decisions during the COVID-19 pandemic. PCR assays have received global attention, facilitating a rapid understanding of variant dynamics because they are more accessible and scalable than genome sequencing. However, as PCR assays target only a few mutations, their accuracy could be reduced when these mutations are not exclusive to the target variants. Here we introduce PRIMES, an algorithm that evaluates the sensitivity and specificity of SARS-CoV-2 variant-specific PCR assays across different geographical regions by incorporating sequences deposited in the GISAID database. Using PRIMES, we determined that the accuracy of several PCR assays decreased when applied beyond the geographic scope of the study in which the assays were developed. Subsequently, we used this tool to design Alpha and Delta variant-specific PCR assays for samples from Illinois, USA. In silico analysis using PRIMES determined the sensitivity/specificity to be 0.99/0.99 for the Alpha variant-specific PCR assay and 0.98/1.00 for the Delta variant-specific PCR assay in Illinois, respectively. We applied these two variant-specific PCR assays to six local sewage samples and determined the dominant SARS-CoV-2 variant of either the wild type, the Alpha variant, or the Delta variant. Using next-generation sequencing (NGS) of the spike (S) gene amplicons of the Delta variant-dominant samples, we found six mutations exclusive to the Delta variant (S:T19R, S:Δ156/157, S:L452R, S:T478K, S:P681R, and S:D950N). The consistency between the variant-specific PCR assays and the NGS results supports the applicability of PRIMES. IMPORTANCE Monitoring the introduction and prevalence of variants of concern (VOCs) and variants of interest (VOIs) in a community can help the local authorities make informed public health decisions. PCR assays can be designed to keep track of SARS-CoV-2 variants by measuring unique mutation markers that are exclusive to the target variants. However, the mutation markers may not be exclusive to the target variants because of regional and temporal differences in variant dynamics. We introduce PRIMES, an algorithm that enables the design of reliable PCR assays for variant detection. Because PCR is more accessible, scalable, and robust for sewage samples than sequencing technology, our findings will contribute to improving global SARS-CoV-2 variant surveillance.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Palash Sashittal
- Department of Computer Science, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Mohammed El-Kebir
- Department of Computer Science, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
- Institute of Genomic Biology, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
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15
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Jiang Y, Wu Q, Song P, You C. The Variation of SARS-CoV-2 and Advanced Research on Current Vaccines. Front Med (Lausanne) 2022; 8:806641. [PMID: 35118097 PMCID: PMC8804231 DOI: 10.3389/fmed.2021.806641] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/16/2021] [Indexed: 12/15/2022] Open
Abstract
Over the past 2 years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) and rapidly spread worldwide. In the process of evolution, new mutations of SARS-CoV-2 began to appear to be more adaptable to the diverse changes of various cellular environments and hosts. Generally, the emerging SARS-CoV-2 variants are characterized by high infectivity, augmented virulence, and fast transmissibility, posing a serious threat to the prevention and control of the global epidemic. At present, there is a paucity of effective measurements to cure COVID-19. It is extremely crucial to develop vaccines against SARS-CoV-2 and emerging variants to enhance individual immunity, but it is not yet known whether they are approved by the authority. Therefore, we systematically reviewed the main characteristics of the emerging various variants of SARS-CoV-2, including their distribution, mutations, transmissibility, severity, and susceptibility to immune responses, especially the Delta variant and the new emerging Omicron variant. Furthermore, we overviewed the suitable crowd, the efficacy, and adverse events (AEs) of current vaccines.
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Affiliation(s)
| | | | | | - Chongge You
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou, China
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16
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López-Causapé C, Fraile-Ribot PA, Jiménez-Serrano S, Cabot G, del Barrio-Tofiño E, Prado MC, Linares JM, López A, Hurtado A, Riera E, Serra A, Roselló E, Carbó L, Fernández-Baca MV, Gallegos C, Saurina J, Arteaga E, Salom MM, Salvá A, Nicolau A, González-Candelas F, Comas I, Oliver A. A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. Front Microbiol 2022; 12:803827. [PMID: 35095814 PMCID: PMC8790175 DOI: 10.3389/fmicb.2021.803827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022] Open
Abstract
Objective: To analyze the SARS-CoV-2 genomic epidemiology in the Balearic Islands, a unique setting in which the course of the pandemic has been influenced by a complex interplay between insularity, severe social restrictions and tourism travels. Methods: Since the onset of the pandemic, more than 2,700 SARS-CoV-2 positive respiratory samples have been randomly selected and sequenced in the Balearic Islands. Genetic diversity of circulating variants was assessed by lineage assignment of consensus whole genome sequences with PANGOLIN and investigation of additional spike mutations. Results: Consensus sequences were assigned to 46 different PANGO lineages and 75% of genomes were classified within a VOC, VUI, or VUM variant according to the WHO definitions. Highest genetic diversity was documented in the island of Majorca (42 different lineages detected). Globally, lineages B.1.1.7 and B.1.617.2/AY.X were identified as the 2 major lineages circulating in the Balearic Islands during the pandemic, distantly followed by lineages B.1.177/B.1.177.X. However, in Ibiza/Formentera lineage distribution was slightly different and lineage B.1.221 was the third most prevalent. Temporal distribution analysis showed that B.1 and B.1.5 lineages dominated the first epidemic wave, lineage B.1.177 dominated the second and third, and lineage B.1.617.2 the fourth. Of note, lineage B.1.1.7 became the most prevalent circulating lineage during first half of 2021; however, it was not associated with an increased in COVID-19 cases likely due to severe social restrictions and limited travels. Additional spike mutations were rarely documented with the exception of mutation S:Q613H which has been detected in several genomes (n = 25) since July 2021. Conclusion: Virus evolution, mainly driven by the acquisition and selection of spike substitutions conferring biological advantages, social restrictions, and size population are apparently key factors for explaining the epidemic patterns registered in the Balearic Islands.
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Affiliation(s)
- Carla López-Causapé
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Pablo A. Fraile-Ribot
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | | | - Gabriel Cabot
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Ester del Barrio-Tofiño
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - M. Carmen Prado
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain
| | - Juana María Linares
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain
| | - Aranzazu López
- Servicio de Microbiología, Hospital Can Misses, Ibiza, Spain
| | | | - Elena Riera
- Servicio de Microbiología, Hospital de Manacor, Manacor, Spain
| | - Antoni Serra
- Servicio de Microbiología, Hospital de Manacor, Manacor, Spain
| | - Eva Roselló
- Servicio de Microbiología, Hospital Mateu Orfila, Mahón, Spain
| | - Lluis Carbó
- Servicio de Microbiología, Hospital Mateu Orfila, Mahón, Spain
| | | | - Carmen Gallegos
- Servicio de Microbiología, Hospital Universitari Son Llàtzer, Palma, Spain
| | - Juan Saurina
- Servicio de Microbiología, Hospital Comarcal de Inca, Inca, Spain
| | - Emilio Arteaga
- Servicio de Microbiología, Hospital Comarcal de Inca, Inca, Spain
| | | | - Antonia Salvá
- Gabinete Técnico-Asistencial, Servicio de Salud de las Islas Baleares, Palma, Spain
| | - Antoni Nicolau
- Servicio de Epidemiología de las Islas Baleares, Palma, Spain
| | - Fernando González-Candelas
- Unidad Mixta de Investigación “Infección y Salud Pública” FISABIO-Universidad de Valencia, Instituto de Biología Integrativa de Sistemas (I2SysBIO, CSIC-UV), Valencia, Spain
- CIBER en Epidemiología y Salud Publica (CIBERESP), Madrid, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia, Valencia, Spain
- CIBER en Epidemiología y Salud Publica (CIBERESP), Madrid, Spain
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de las Islas Baleares, Palma, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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17
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Abstract
The field of molecular epidemiology responded to the SARS-CoV-2 pandemic with an unrivaled amount of whole viral genome sequencing. By the time this sentence is published we will have well surpassed 1.5 million whole genomes, more than 4 times the number of all microbial whole genomes deposited in GenBank and 35 times the total number of viral genomes. This extraordinary dataset that accrued in near real time has also given us an opportunity to chart the global and local evolution of a virus as it moves through the world population. The data itself presents challenges that have never been dealt with in molecular epidemiology, and tracking a virus that is changing so rapidly means that we are often running to catch up. Here we review what is known about the evolution of the virus, and the critical impact that whole genomes have had on our ability to trace back and track forward the spread of lineages of SARS-CoV-2. We then review what whole genomes have told us about basic biological properties of the virus such as transmissibility, virulence, and immune escape with a special emphasis on pediatric disease. We couch this discussion within the framework of systematic biology and phylogenetics, disciplines that have proven their worth again and again for identifying and deciphering the spread of epidemics, though they were largely developed in areas far removed from infectious disease and medicine.
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Affiliation(s)
- Ahmed M Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
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18
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Gupta D, Sharma P, Singh M, Kumar M, Ethayathulla AS, Kaur P. Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants. Cell Mol Life Sci 2021; 78:7967-7989. [PMID: 34731254 PMCID: PMC11073194 DOI: 10.1007/s00018-021-04008-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 02/07/2023]
Abstract
Since the emergence of the first case of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), the viral genome has constantly undergone rapid mutations for better adaptation in the host system. These newer mutations have given rise to several lineages/ variants of the virus that have resulted in high transmission and virulence rates compared to the previously circulating variants. Owing to this, the overall caseload and related mortality have tremendously increased globally to > 233 million infections and > 4.7 million deaths as of Sept. 28th, 2021. SARS-CoV-2, Spike (S) protein binds to host cells by recognizing human angiotensin-converting enzyme 2 (hACE2) receptor. The viral S protein contains S1 and S2 domains that constitute the binding and fusion machinery, respectively. Structural analysis of viral S protein reveals that the virus undergoes conformational flexibility and dynamicity to interact with the hACE2 receptor. The SARS-CoV-2 variants and mutations might be associated with affecting the conformational plasticity of S protein, potentially linked to its altered affinity, infectivity, and immunogenicity. This review focuses on the current circulating variants of SARS-CoV-2 and the structure-function analysis of key S protein mutations linked with increased affinity, higher infectivity, enhanced transmission rates, and immune escape against this infection.
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Affiliation(s)
- Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Priyanka Sharma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Mandeep Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India.
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19
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Ramesh S, Govindarajulu M, Parise RS, Neel L, Shankar T, Patel S, Lowery P, Smith F, Dhanasekaran M, Moore T. Emerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy. Vaccines (Basel) 2021; 9:1195. [PMID: 34696303 PMCID: PMC8537675 DOI: 10.3390/vaccines9101195] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/26/2021] [Accepted: 10/08/2021] [Indexed: 12/21/2022] Open
Abstract
The widespread increase in multiple severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants is causing a significant health concern in the United States and worldwide. These variants exhibit increased transmissibility, cause more severe disease, exhibit evasive immune properties, impair neutralization by antibodies from vaccinated individuals or convalescence sera, and reinfection. The Centers for Disease Control and Prevention (CDC) has classified SARS-CoV-2 variants into variants of interest, variants of concern, and variants of high consequence. Currently, four variants of concern (B.1.1.7, B.1.351, P.1, and B.1.617.2) and several variants of interests (B.1.526, B.1.525, and P.2) are characterized and are essential for close monitoring. In this review, we discuss the different SARS-CoV-2 variants, emphasizing variants of concern circulating the world and highlight the various mutations and how these mutations affect the characteristics of the virus. In addition, we discuss the most common vaccines and the various studies concerning the efficacy of these vaccines against different variants of concern.
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Affiliation(s)
- Sindhu Ramesh
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Manoj Govindarajulu
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Rachel S. Parise
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Logan Neel
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Tharanath Shankar
- Department of Internal Medicine, Ramaiah Medical College and Hospital, Bengaluru 560054, Karnataka, India;
| | - Shriya Patel
- Department of Neuroscience, Middlebury College, Middlebury, VT 05753, USA;
| | - Payton Lowery
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Forrest Smith
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Muralikrishnan Dhanasekaran
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Timothy Moore
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
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20
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Anaclerio F, Ferrante R, Mandatori D, Antonucci I, Capanna M, Damiani V, Tomo PD, Ferrante R, Ranaudo M, De Laurenzi V, Stuppia L, De Fabritiis S. Different Strategies for the Identification of SARS-CoV-2 Variants in the Laboratory Practice. Genes (Basel) 2021; 12:genes12091428. [PMID: 34573410 PMCID: PMC8467753 DOI: 10.3390/genes12091428] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/14/2021] [Indexed: 01/24/2023] Open
Abstract
A considerable effort has been devoted in all countries to react to the COVID-19 pandemic by tracing infected individuals, containing the spread of the disease, identifying therapies, and producing and distributing vaccines. Currently, a significant concern is the appearance of variants of the virus that may frustrate these efforts by showing increased transmissibility, increased disease severity, reduced response to therapy or vaccines, and ability to escape diagnosis. All countries have therefore devoted a massive attempt to the identification and tracking of these variants, which requires a vast technological effort to sequence a large number of viral genomes. In this paper, we report our experience as one of the Italian laboratories involved in SARS-CoV-2 variant tracing. We summarize the different approaches used, and outline a potential model combining several techniques to increase tracing ability while at the same time minimizing costs.
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Affiliation(s)
- Federico Anaclerio
- Center for Advanced Studies and Technology (CAST), G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (R.F.); (I.A.); (M.C.); (V.D.); (P.D.T.); (R.F.); (M.R.); (V.D.L.); (L.S.); (S.D.F.)
| | - Rossella Ferrante
- Center for Advanced Studies and Technology (CAST), G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (R.F.); (I.A.); (M.C.); (V.D.); (P.D.T.); (R.F.); (M.R.); (V.D.L.); (L.S.); (S.D.F.)
| | - Domitilla Mandatori
- Center for Advanced Studies and Technology (CAST), G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (R.F.); (I.A.); (M.C.); (V.D.); (P.D.T.); (R.F.); (M.R.); (V.D.L.); (L.S.); (S.D.F.)
- Department of Medical Oral and Biotechnological Sciences, School of Medicine and Health Sciences, G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- Correspondence:
| | - Ivana Antonucci
- Center for Advanced Studies and Technology (CAST), G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (R.F.); (I.A.); (M.C.); (V.D.); (P.D.T.); (R.F.); (M.R.); (V.D.L.); (L.S.); (S.D.F.)
- Department of Psicological Health and Territory Science, School of Medicine and Health Sciences, G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Matteo Capanna
- Center for Advanced Studies and Technology (CAST), G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (R.F.); (I.A.); (M.C.); (V.D.); (P.D.T.); (R.F.); (M.R.); (V.D.L.); (L.S.); (S.D.F.)
| | - Verena Damiani
- Center for Advanced Studies and Technology (CAST), G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (R.F.); (I.A.); (M.C.); (V.D.); (P.D.T.); (R.F.); (M.R.); (V.D.L.); (L.S.); (S.D.F.)
- Department of Innovative Technologies in Medicine and Dentistry, School of Medicine and Health Sciences, G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Pamela Di Tomo
- Center for Advanced Studies and Technology (CAST), G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (R.F.); (I.A.); (M.C.); (V.D.); (P.D.T.); (R.F.); (M.R.); (V.D.L.); (L.S.); (S.D.F.)
- Department of Medical Oral and Biotechnological Sciences, School of Medicine and Health Sciences, G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Roberto Ferrante
- Center for Advanced Studies and Technology (CAST), G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (R.F.); (I.A.); (M.C.); (V.D.); (P.D.T.); (R.F.); (M.R.); (V.D.L.); (L.S.); (S.D.F.)
| | - Marianna Ranaudo
- Center for Advanced Studies and Technology (CAST), G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (R.F.); (I.A.); (M.C.); (V.D.); (P.D.T.); (R.F.); (M.R.); (V.D.L.); (L.S.); (S.D.F.)
| | - Vincenzo De Laurenzi
- Center for Advanced Studies and Technology (CAST), G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (R.F.); (I.A.); (M.C.); (V.D.); (P.D.T.); (R.F.); (M.R.); (V.D.L.); (L.S.); (S.D.F.)
- Department of Innovative Technologies in Medicine and Dentistry, School of Medicine and Health Sciences, G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Liborio Stuppia
- Center for Advanced Studies and Technology (CAST), G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (R.F.); (I.A.); (M.C.); (V.D.); (P.D.T.); (R.F.); (M.R.); (V.D.L.); (L.S.); (S.D.F.)
- Department of Psicological Health and Territory Science, School of Medicine and Health Sciences, G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Simone De Fabritiis
- Center for Advanced Studies and Technology (CAST), G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.A.); (R.F.); (I.A.); (M.C.); (V.D.); (P.D.T.); (R.F.); (M.R.); (V.D.L.); (L.S.); (S.D.F.)
- Department of Medicine and Aging Sciences, School of Medicine and Health Sciences, G.d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
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21
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COVID-19 and Inherited Metabolic Disorders: One-Year Experience of a Referral Center. CHILDREN-BASEL 2021; 8:children8090781. [PMID: 34572213 PMCID: PMC8464704 DOI: 10.3390/children8090781] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 11/24/2022]
Abstract
Understanding the potential risks of patients with inherited metabolic disorder (IMD) exposed to the COVID-19 pandemic is an unmet need for those involved in their management. Here, we report on the incidence of COVID-19 in a cohort of patients with IMD treated at a children’s hospital and compare them with a matched control group. Among the total number of 272 patients actively followed at a referral center, 19 (7%) tested positive for SARS-CoV-2 between March 2020 and March 2021. Their median age was 16.2 years (range 1.4–32.8 years). In two-thirds of the cases, the source of infection was a family member; 12/19 patients (63%) were asymptomatic, only one required hospitalization, and none of them died. In our single-center experience, COVID-19 had a moderate impact on a relatively large cohort of patients with IMD, including children and young adults. The clinical course was very mild in all but one case. The proportion of symptomatic cases and the clinical course were comparable in patients with IMD and in a group of matched, non-IMD COVID-19 controls from the general population.
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22
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Wilhelm A, Toptan T, Pallas C, Wolf T, Goetsch U, Gottschalk R, Vehreschild MJGT, Ciesek S, Widera M. Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Viruses 2021; 13:v13091693. [PMID: 34578275 DOI: 10.1101/2021.08.09.21261704] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/22/2021] [Indexed: 05/24/2023] Open
Abstract
The capacity of convalescent and vaccine-elicited sera and monoclonal antibodies (mAb) to neutralize SARS-CoV-2 variants is currently of high relevance to assess the protection against infections. We performed a cell culture-based neutralization assay focusing on authentic SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.427/B.1.429 (Epsilon), all harboring the spike substitution L452R. We found that authentic SARS-CoV-2 variants harboring L452R had reduced susceptibility to convalescent and vaccine-elicited sera and mAbs. Compared to B.1, Kappa and Delta showed a reduced neutralization by convalescent sera by a factor of 8.00 and 5.33, respectively, which constitutes a 2-fold greater reduction when compared to Epsilon. BNT2b2 and mRNA1273 vaccine-elicited sera were less effective against Kappa, Delta, and Epsilon compared to B.1. No difference was observed between Kappa and Delta towards vaccine-elicited sera, whereas convalescent sera were 1.51-fold less effective against Delta, respectively. Both B.1.617 variants Kappa (+E484Q) and Delta (+T478K) were less susceptible to either casirivimab or imdevimab. In conclusion, in contrast to the parallel circulating Kappa variant, the neutralization efficiency of convalescent and vaccine-elicited sera against Delta was moderately reduced. Delta was resistant to imdevimab, which, however, might be circumvented by combination therapy with casirivimab together.
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Affiliation(s)
- Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Christiane Pallas
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Timo Wolf
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Udo Goetsch
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany
| | - Rene Gottschalk
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
- Branch Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
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23
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Phosphorylation of SARS-CoV-2 Orf9b Regulates Its Targeting to Two Binding Sites in TOM70 and Recruitment of Hsp90. Int J Mol Sci 2021; 22:ijms22179233. [PMID: 34502139 PMCID: PMC8430508 DOI: 10.3390/ijms22179233] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/18/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the causative agent of the COVID19 pandemic. The SARS-CoV-2 genome encodes for a small accessory protein termed Orf9b, which targets the mitochondrial outer membrane protein TOM70 in infected cells. TOM70 is involved in a signaling cascade that ultimately leads to the induction of type I interferons (IFN-I). This cascade depends on the recruitment of Hsp90-bound proteins to the N-terminal domain of TOM70. Binding of Orf9b to TOM70 decreases the expression of IFN-I; however, the underlying mechanism remains elusive. We show that the binding of Orf9b to TOM70 inhibits the recruitment of Hsp90 and chaperone-associated proteins. We characterized the binding site of Orf9b within the C-terminal domain of TOM70 and found that a serine in position 53 of Orf9b and a glutamate in position 477 of TOM70 are crucial for the association of both proteins. A phosphomimetic variant Orf9bS53E showed drastically reduced binding to TOM70 and did not inhibit Hsp90 recruitment, suggesting that Orf9b–TOM70 complex formation is regulated by phosphorylation. Eventually, we identified the N-terminal TPR domain of TOM70 as a second binding site for Orf9b, which indicates a so far unobserved contribution of chaperones in the mitochondrial targeting of the viral protein.
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24
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Wilhelm A, Toptan T, Pallas C, Wolf T, Goetsch U, Gottschalk R, Vehreschild MJGT, Ciesek S, Widera M. Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Viruses 2021; 13:1693. [PMID: 34578275 PMCID: PMC8473269 DOI: 10.3390/v13091693] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/22/2021] [Indexed: 12/23/2022] Open
Abstract
The capacity of convalescent and vaccine-elicited sera and monoclonal antibodies (mAb) to neutralize SARS-CoV-2 variants is currently of high relevance to assess the protection against infections. We performed a cell culture-based neutralization assay focusing on authentic SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.427/B.1.429 (Epsilon), all harboring the spike substitution L452R. We found that authentic SARS-CoV-2 variants harboring L452R had reduced susceptibility to convalescent and vaccine-elicited sera and mAbs. Compared to B.1, Kappa and Delta showed a reduced neutralization by convalescent sera by a factor of 8.00 and 5.33, respectively, which constitutes a 2-fold greater reduction when compared to Epsilon. BNT2b2 and mRNA1273 vaccine-elicited sera were less effective against Kappa, Delta, and Epsilon compared to B.1. No difference was observed between Kappa and Delta towards vaccine-elicited sera, whereas convalescent sera were 1.51-fold less effective against Delta, respectively. Both B.1.617 variants Kappa (+E484Q) and Delta (+T478K) were less susceptible to either casirivimab or imdevimab. In conclusion, in contrast to the parallel circulating Kappa variant, the neutralization efficiency of convalescent and vaccine-elicited sera against Delta was moderately reduced. Delta was resistant to imdevimab, which, however, might be circumvented by combination therapy with casirivimab together.
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Affiliation(s)
- Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
| | - Christiane Pallas
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
| | - Timo Wolf
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (T.W.); (M.J.G.T.V.)
| | - Udo Goetsch
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany; (U.G.); (R.G.)
| | - Rene Gottschalk
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany; (U.G.); (R.G.)
| | - Maria J. G. T. Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (T.W.); (M.J.G.T.V.)
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
- Branch Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
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25
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Luo CH, Morris CP, Sachithanandham J, Amadi A, Gaston D, Li M, Swanson NJ, Schwartz M, Klein EY, Pekosz A, Mostafa HH. Infection with the SARS-CoV-2 Delta Variant is Associated with Higher Infectious Virus Loads Compared to the Alpha Variant in both Unvaccinated and Vaccinated Individuals. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.08.15.21262077. [PMID: 34462756 PMCID: PMC8404894 DOI: 10.1101/2021.08.15.21262077] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND The emerging SARS-CoV-2 variant of concern (VOC) B.1.6.17.2 (Delta) quickly displaced the B.1.1.7 (Alpha) and is associated with increases in COVID-19 cases nationally. The Delta variant has been associated with greater transmissibility and higher viral RNA loads in both unvaccinated and fully vaccinated individuals. Data is lacking regarding the infectious virus load in Delta infected individuals and how that compares to individuals infected with other SARS-CoV-2 lineages. METHODS Whole genome sequencing of 2,785 clinical isolates was used to characterize the prevalence of SARS-CoV-2 lineages circulating in the National Capital Region between January and July 2021. Clinical chart reviews were performed for the Delta, Alpha, and B.1.2 (a control predominant lineage prior to both VOCs) variants to evaluate disease severity and outcome and Cycle threshold values (Cts) were compared. The presence of infectious virus was determined using Vero-TMPRSS2 cells and anti-SARS-CoV-2 IgG levels were determined from upper respiratory specimen. An analysis of infection in unvaccinated and fully vaccinated populations was performed. RESULTS The Delta variant displaced the Alpha variant to constitute 88.2% of the circulating lineages in the National Capital Region by July, 2021. The Delta variant associated with increased breakthrough infections in fully vaccinated individuals that were mostly symptomatic when compared to the Alpha breakthrough infections, though it is important to note there was a significantly longer period of time between vaccination and infection with Delta infections. The recovery of infectious virus on cell culture was significantly higher with the Delta variant compared to Alpha in both vaccinated and unvaccinated groups. The impact of vaccination on reducing the recovery of infectious virus from clinical samples was only observed with Alpha variant infections but was strongly associated with low localized SARS-CoV-2 IgG for both variants. A comparison of Ct values showed a significant decrease in the Delta compared to Alpha with no significant differences between unvaccinated and vaccinated groups. CONCLUSIONS Our data indicate that the Delta variant is associated with increased infectious virus loads when compared to the Alpha variant and decreased upper respiratory antiviral IgG levels. Measures to reduce transmission in addition to increasing vaccinations rates have to be implemented to reduce Delta variant spread. FUNDING NIH/NIAID Center of Excellence in Influenza Research and Surveillance contract HHS N2772201400007C, Johns Hopkins University, Maryland department of health, Centers for Disease Control and Prevention contract 75D30121C11061.
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Affiliation(s)
- Chun Huai Luo
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - C Paul Morris
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
- National Institute of Allergy and Infectious Disease, National Institutes of Health
| | - Jaiprasath Sachithanandham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Adannaya Amadi
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - David Gaston
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Maggie Li
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Nicholas J Swanson
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Matthew Schwartz
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
| | - Eili Y Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine
- Center for Disease Dynamics, Economics, and Policy, Washington DC
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Emergency Medicine, Johns Hopkins School of Medicine
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology
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26
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Kraemer MUG, Hill V, Ruis C, Dellicour S, Bajaj S, McCrone JT, Baele G, Parag KV, Battle AL, Gutierrez B, Jackson B, Colquhoun R, O'Toole Á, Klein B, Vespignani A, Volz E, Faria NR, Aanensen DM, Loman NJ, du Plessis L, Cauchemez S, Rambaut A, Scarpino SV, Pybus OG. Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science 2021; 373:889-895. [PMID: 34301854 PMCID: PMC9269003 DOI: 10.1126/science.abj0113] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/12/2021] [Indexed: 12/24/2022]
Abstract
Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.
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Affiliation(s)
- Moritz U G Kraemer
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil.
- Department of Zoology, University of Oxford, Oxford, UK
| | - Verity Hill
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Christopher Ruis
- Department of Zoology, University of Oxford, Oxford, UK
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
| | - Simon Dellicour
- Network Science Institute, Northeastern University, Boston, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Sumali Bajaj
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - John T McCrone
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Guy Baele
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Kris V Parag
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Anya Lindström Battle
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Bernardo Gutierrez
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | - Ben Jackson
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Áine O'Toole
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Brennan Klein
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Network Science Institute, Northeastern University, Boston, USA
| | - Alessandro Vespignani
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Network Science Institute, Northeastern University, Boston, USA
| | - Erik Volz
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Nuno R Faria
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - David M Aanensen
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas J Loman
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Louis du Plessis
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - Simon Cauchemez
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Andrew Rambaut
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Samuel V Scarpino
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium.
- Network Science Institute, Northeastern University, Boston, USA
- Vermont Complex Systems Center, University of Vermont, Burlington, USA
- Santa Fe Institute, Santa Fe, USA
| | - Oliver G Pybus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil.
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
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27
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Loconsole D, Sallustio A, Centrone F, Casulli D, Ferrara MM, Sanguedolce A, Accogli M, Chironna M. An Autochthonous Outbreak of the SARS-CoV-2 P.1 Variant of Concern in Southern Italy, April 2021. Trop Med Infect Dis 2021; 6:151. [PMID: 34449757 PMCID: PMC8396329 DOI: 10.3390/tropicalmed6030151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
The SARS-CoV-2 P.1 variant of concern (VOC) was first identified in Brazil and is now spreading in European countries. It is characterized by the E484K mutation in the receptor-binding domain, which could contribute to the evasion from neutralizing antibodies. In Italy, this variant was first identified in January 2021. Here, we report an autochthonous outbreak of SARS-CoV-2 P.1 variant infections in southern Italy in subjects who had not travelled to endemic areas or outside the Apulia region. The outbreak involved seven subjects, three of whom had received a COVID-19 vaccine (one had received two doses and two had received one dose). Four patients had a mild clinical presentation. Laboratory investigations of nasopharyngeal swabs revealed that all strains were S-gene target failure-negative and molecular tests revealed they were the P.1 variant. Whole-genome sequencing confirmed that five subjects were infected with closely related strains classified as the P.1 lineage. The circulation of VOCs highlights the importance of strictly monitoring the spread of SARS-CoV-2 variants through genomic surveillance and of investigating local outbreaks. Furthermore, public health measures including social distancing, screening, and quarantine for travelers are key tools to slow down the viral transmission and to contain and mitigate the impact of VOC diffusion, and rapid scaling-up of vaccination is crucial to avoid a possible new epidemic wave.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.)
| | - Anna Sallustio
- Hygiene Unit, University Hospital Consortium Policlinico, 70124 Bari, Italy; (A.S.); (D.C.)
| | - Francesca Centrone
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.)
| | - Daniele Casulli
- Hygiene Unit, University Hospital Consortium Policlinico, 70124 Bari, Italy; (A.S.); (D.C.)
| | - Maurizio Mario Ferrara
- Local Health Unit of Bari, Department of Prevention, 70132 Bari, Italy; (M.M.F.); (A.S.)
| | - Antonio Sanguedolce
- Local Health Unit of Bari, Department of Prevention, 70132 Bari, Italy; (M.M.F.); (A.S.)
| | - Marisa Accogli
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.)
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.)
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28
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Susswein Z, Valdano E, Brett T, Rohani P, Colizza V, Bansal S. Ignoring spatial heterogeneity in drivers of SARS-CoV-2 transmission in the US will impede sustained elimination. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.08.09.21261807. [PMID: 34401885 PMCID: PMC8366803 DOI: 10.1101/2021.08.09.21261807] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To dissect the transmission dynamics of SARS-CoV-2 in the United States, we integrate parallel streams of high-resolution data on contact, mobility, seasonality, vaccination and seroprevalence within a metapopulation network. We find the COVID-19 pandemic in the US is characterized by a geographically localized mosaic of transmission along an urban-rural gradient, with many outbreaks sustained by between-county transmission. We detect a dynamic tension between the spatial scale of public health interventions and population susceptibility as pre-pandemic contact is resumed. Further, we identify regions rendered particularly at risk from invasion by variants of concern due to spatial connectivity. These findings emphasize the public health importance of accounting for the hierarchy of spatial scales in transmission and the heterogeneous impacts of mobility on the landscape of contagion risk.
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29
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Rodrigues R, Costa de Oliveira S. The Impact of Angiotensin-Converting Enzyme 2 ( ACE2) Expression Levels in Patients with Comorbidities on COVID-19 Severity: A Comprehensive Review. Microorganisms 2021; 9:1692. [PMID: 34442770 PMCID: PMC8398209 DOI: 10.3390/microorganisms9081692] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/19/2021] [Accepted: 08/06/2021] [Indexed: 01/08/2023] Open
Abstract
Angiotensin-Converting Enzyme 2 (ACE2) has been proved to be the main host cell receptor for the binding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the COVID-19 pandemic. The SARS-CoV-2 spike (S) protein binds to ACE2 to initiate the process of replication. This enzyme is widely present in human organ tissues, such as the heart and lung. The pathophysiology of ACE2 in SARS-CoV-2 infection is complex and may be associated with several factors and conditions that are more severe in COVID-19 patients, such as age, male gender, and comorbidities, namely, cardiovascular diseases, chronic respiratory diseases, obesity, and diabetes. Here we present a comprehensive review that aims to correlate the levels of expression of the ACE2 in patients with comorbidities and with a poor outcome in COVID-19 disease. Significantly higher levels of expression of ACE2 were observed in myocardial and lung tissues in heart failure and COPD patients, respectively. An age-dependent increase in SARS2-CoV-2 receptors in the respiratory epithelium may be also responsible for the increased severity of COVID-19 lung disease in elderly people. Although the role of ACE2 is highlighted regarding the damage that can arise upon the SARS-CoV-2 invasion, there was no association observed between renin-angiotensin-aldosterone system (RAAS) inhibitors and the severity of COVID-19.
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Affiliation(s)
- Rui Rodrigues
- Department of Pathology, Division of Microbiology, Faculty of Medicine, University of Porto, Al. Hernâni Monteiro, 4200-319 Porto, Portugal;
| | - Sofia Costa de Oliveira
- Department of Pathology, Division of Microbiology, Faculty of Medicine, University of Porto, Al. Hernâni Monteiro, 4200-319 Porto, Portugal;
- Center for Research in Health Technologies and Information Systems (CINTESIS), R. Dr. Plácido da Costa, 4200-450 Porto, Portugal
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30
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Goldhill DH, Barclay WS. 2020 Hindsight: Should evolutionary virologists have expected the unexpected during a pandemic? Evolution 2021; 75:2311-2316. [PMID: 34342897 PMCID: PMC8444725 DOI: 10.1111/evo.14317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022]
Affiliation(s)
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College, London, UK
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31
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Mohammad A, Abubaker J, Al-Mulla F. Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Virus Res 2021; 303:198522. [PMID: 34314772 PMCID: PMC8310422 DOI: 10.1016/j.virusres.2021.198522] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 12/18/2022]
Abstract
The B.1.1.7 SARS-CoV-2 strain that has emerged in the UK in early December presents seven mutations and three deletions on S-protein structure that could lead to a more infective strain. The P681H mutation in the “PRRAR” furin cleavage site might affect the binding affinity to furin enzyme and hence its infectivity. Therefore, in this study, various structural bioinformatics approaches were used to model the S-protein structure with the B.1.1.7 variant amino acid substitutions and deletions. In addition to modelling the binding of furin to the cleavage site of the wild-type and the B.1.1.7 variant. Conclusively the B.1.1.7 variant resulted in dynamic stability, conformational changes and variations in binding energies in the S-protein structure, resulting in a more favourable binding of furin enzyme to the SARS-CoV-2 S-protein.
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Affiliation(s)
- Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait
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32
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Tasakis RN, Samaras G, Jamison A, Lee M, Paulus A, Whitehouse G, Verkoczy L, Papavasiliou FN, Diaz M. SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts. PLoS One 2021; 16:e0255169. [PMID: 34297786 PMCID: PMC8301627 DOI: 10.1371/journal.pone.0255169] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/11/2021] [Indexed: 12/13/2022] Open
Abstract
Since the first case of COVID-19 in December 2019 in Wuhan, China, SARS-CoV-2 has spread worldwide and within a year and a half has caused 3.56 million deaths globally. With dramatically increasing infection numbers, and the arrival of new variants with increased infectivity, tracking the evolution of its genome is crucial for effectively controlling the pandemic and informing vaccine platform development. Our study explores evolution of SARS-CoV-2 in a representative cohort of sequences covering the entire genome in the United States, through all of 2020 and early 2021. Strikingly, we detected many accumulating Single Nucleotide Variations (SNVs) encoding amino acid changes in the SARS-CoV-2 genome, with a pattern indicative of RNA editing enzymes as major mutators of SARS-CoV-2 genomes. We report three major variants through October of 2020. These revealed 14 key mutations that were found in various combinations among 14 distinct predominant signatures. These signatures likely represent evolutionary lineages of SARS-CoV-2 in the U.S. and reveal clues to its evolution such as a mutational burst in the summer of 2020 likely leading to a homegrown new variant, and a trend towards higher mutational load among viral isolates, but with occasional mutation loss. The last quartile of 2020 revealed a concerning accumulation of mostly novel low frequency replacement mutations in the Spike protein, and a hypermutable glutamine residue near the putative furin cleavage site. Finally, end of the year data and 2021 revealed the gradual increase to prevalence of known variants of concern, particularly B.1.1.7, that have acquired additional Spike mutations. Overall, our results suggest that predominant viral genomes are dynamically evolving over time, with periods of mutational bursts and unabated mutation accumulation. This high level of existing variation, even at low frequencies and especially in the Spike-encoding region may become problematic when super-spreader events, akin to serial Founder Events in evolution, drive these rare mutations to prominence.
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Affiliation(s)
- Rafail Nikolaos Tasakis
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Georgios Samaras
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Program of Translational Medical Research, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Anna Jamison
- The Nightingale-Bamford School, New York, NY, United States of America
| | - Michelle Lee
- Cornell University, Ithaca, NY, United States of America
| | - Alexandra Paulus
- The Nightingale-Bamford School, New York, NY, United States of America
| | | | - Laurent Verkoczy
- San Diego Biomedical Research Institute (SDBRI), San Diego, CA, United States of America
| | - F. Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marilyn Diaz
- San Diego Biomedical Research Institute (SDBRI), San Diego, CA, United States of America
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33
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Stevanovic V, Tabain I, Vilibic-Cavlek T, Mauric Maljkovic M, Benvin I, Hruskar Z, Kovac S, Smit I, Miletic G, Hadina S, Staresina V, Radin L, Plichta V, Skrlin B, Vrbanac Z, Brkljacic M, Cvetnic M, Habus J, Martinkovic K, Zecevic I, Jurkic G, Ferencak I, Stritof Z, Perharic M, Bucic L, Barbic L. The Emergence of SARS-CoV-2 within the Dog Population in Croatia: Host Factors and Clinical Outcome. Viruses 2021; 13:1430. [PMID: 34452296 PMCID: PMC8402787 DOI: 10.3390/v13081430] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
Over a year into the COVID-19 pandemic, there is growing evidence that SARS-CoV-2 infections among dogs are more common than previously thought. In this study, the prevalence of SARS-CoV-2 antibodies was investigated in two dog populations. The first group was comprised of 1069 dogs admitted to the Veterinary Teaching Hospital for any given reason. The second group included dogs that shared households with confirmed COVID-19 cases in humans. This study group numbered 78 dogs. In COVID-19 infected households, 43.9% tested ELISA positive, and neutralising antibodies were detected in 25.64% of dogs. Those data are comparable with the secondary attack rate in the human population. With 14.69% of dogs in the general population testing ELISA positive, there was a surge of SARS-CoV-2 infections within the dog population amid the second wave of the pandemic. Noticeably seroprevalence of SARS-CoV-2 in the dog and the human population did not differ at the end of the study period. Male sex, breed and age were identified as significant risk factors. This study gives strong evidence that while acute dog infections are mostly asymptomatic, they can pose a significant risk to dog health. Due to the retrospective nature of this study, samples for viral isolation and PCR were unavailable. Still, seropositive dogs had a 1.97 times greater risk for developing central nervous symptoms.
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Affiliation(s)
- Vladimir Stevanovic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.B.); (S.K.); (G.M.); (V.S.); (L.B.)
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Irena Tabain
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (Z.H.); (I.F.)
| | - Tatjana Vilibic-Cavlek
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (Z.H.); (I.F.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Maja Mauric Maljkovic
- Department for Animal Breeding and Livestock Production, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Iva Benvin
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.B.); (S.K.); (G.M.); (V.S.); (L.B.)
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Zeljka Hruskar
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (Z.H.); (I.F.)
| | - Snjezana Kovac
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.B.); (S.K.); (G.M.); (V.S.); (L.B.)
| | - Iva Smit
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Gorana Miletic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.B.); (S.K.); (G.M.); (V.S.); (L.B.)
| | - Suzana Hadina
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Vilim Staresina
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.B.); (S.K.); (G.M.); (V.S.); (L.B.)
| | - Lada Radin
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Valentina Plichta
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Branimir Skrlin
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Zoran Vrbanac
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Mirna Brkljacic
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Marija Cvetnic
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Josipa Habus
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Kresimir Martinkovic
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Iva Zecevic
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Gabrijela Jurkic
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Ivana Ferencak
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (Z.H.); (I.F.)
| | - Zinka Stritof
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Matko Perharic
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
| | - Lovro Bucic
- Department of Epidemiology, Croatian Institute of Public Health, 10000 Zagreb, Croatia;
| | - Ljubo Barbic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.B.); (S.K.); (G.M.); (V.S.); (L.B.)
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (I.S.); (S.H.); (L.R.); (V.P.); (B.S.); (Z.V.); (M.B.); (M.C.); (J.H.); (K.M.); (I.Z.); (G.J.); (Z.S.); (M.P.)
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34
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Ulloa S, Bravo C, Ramirez E, Fasce R, Fernandez J. Inactivation of SARS-CoV-2 isolates from lineages B.1.1.7 (Alpha), P.1 (Gamma) and B.1.110 by heating and UV irradiation. J Virol Methods 2021; 295:114216. [PMID: 34171342 PMCID: PMC8219296 DOI: 10.1016/j.jviromet.2021.114216] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/19/2021] [Accepted: 06/20/2021] [Indexed: 12/24/2022]
Abstract
Currently, the rapid global spread of SARS-CoV-2 is related to G clade (including GH, GR, GRY and GV clades), which are associated with more than 98 % of sequenced viral isolates worldwide. The unprecedented velocity of spread of SARS-CoV-2 outbreak represents a critical need for prevention strategies. Vaccines are recently being available and antiviral drugs have shown limited efficacy in COVID-19 patients. Thus, it is needed to know how to reduce the infectivity of the virus by different physicochemical conditions in order to prevent exposure to contaminated material. This work describes heating and irradiating UV-C light procedures to reduce the infectivity of SARS-CoV-2 belonging to different three lineages. Results of physicochemical treatment showed no differences among viral lineages. Analytical conditions for efficient inactivation of SARS-CoV-2 were determined.
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Affiliation(s)
- S Ulloa
- Molecular Genetics Sub Department, Institute of Public Health of Chile, Santiago, Chile
| | - C Bravo
- Molecular Genetics Sub Department, Institute of Public Health of Chile, Santiago, Chile
| | - E Ramirez
- Viral Diseases Sub Department, Institute of Public Health of Chile, Santiago, Chile
| | - R Fasce
- Viral Diseases Sub Department, Institute of Public Health of Chile, Santiago, Chile
| | - J Fernandez
- Molecular Genetics Sub Department, Institute of Public Health of Chile, Santiago, Chile.
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35
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Stamatatos L, Czartoski J, Wan YH, Homad LJ, Rubin V, Glantz H, Neradilek M, Seydoux E, Jennewein MF, MacCamy AJ, Feng J, Mize G, De Rosa SC, Finzi A, Lemos MP, Cohen KW, Moodie Z, McElrath MJ, McGuire AT. mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection. Science 2021; 372:eabg9175. [PMID: 33766944 PMCID: PMC8139425 DOI: 10.1126/science.abg9175] [Citation(s) in RCA: 381] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/19/2021] [Indexed: 12/11/2022]
Abstract
Emerging SARS-CoV-2 variants have raised concerns about resistance to neutralizing antibodies elicited by previous infection or vaccination. We examined whether sera from recovered and naïve donors collected prior to, and following immunizations with existing mRNA vaccines, could neutralize the Wuhan-Hu-1 and B.1.351 variants. Pre-vaccination sera from recovered donors neutralized Wuhan-Hu-1 and sporadically neutralized B.1.351, but a single immunization boosted neutralizing titers against all variants and SARS-CoV-1 by up to 1000-fold. Neutralization was due to antibodies targeting the receptor binding domain and was not boosted by a second immunization. Immunization of naïve donors also elicited cross-neutralizing responses, but at lower titers. Our study highlights the importance of vaccinating both uninfected and previously infected persons to elicit cross-variant neutralizing antibodies.
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Affiliation(s)
- Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Julie Czartoski
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Yu-Hsin Wan
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Leah J Homad
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Vanessa Rubin
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Hayley Glantz
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Moni Neradilek
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Emilie Seydoux
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Madeleine F Jennewein
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Anna J MacCamy
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Junli Feng
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Gregory Mize
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Stephen C De Rosa
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Maria P Lemos
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Kristen W Cohen
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Zoe Moodie
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - M Juliana McElrath
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew T McGuire
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
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36
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Mukherjee R, Satardekar R. Why are some coronavirus variants more infectious? J Biosci 2021; 46:101. [PMID: 34785628 PMCID: PMC8594289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/28/2021] [Indexed: 09/22/2023]
Abstract
Since the start of the pandemic, SARS-CoV-2 has infected almost 200 million human hosts and is set to encounter and gain entry in many more in the coming months. As the coronavirus flourish, the evolutionary pressure selects those variants that can complete the infection cycle faster and reproduce in large numbers compared to others. This increase in infectivity and transmissibility coupled with the immune response from high viral load may cause moderate to severe disease. Whether this leads to enhanced virulence in the prevalent Alpha and Delta variants is still not clear. This review describes the different types of SARS-CoV-2 variants that are now prevalent, their emergence, the mutations responsible for their growth advantages, and how they affect vaccine efficacy and increase chances of reinfection. Finally, we have also summarized the efforts made to recognize and predict the mutations, which can cause immune escape and track their emergence through impactful genomic surveillance.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Binding Sites
- COVID-19/epidemiology
- COVID-19/pathology
- COVID-19/transmission
- COVID-19/virology
- COVID-19 Vaccines
- Genome, Viral
- Humans
- Immune Evasion/genetics
- Models, Molecular
- Mutation
- Phylogeny
- Protein Binding
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- SARS-CoV-2/classification
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Serine Endopeptidases/chemistry
- Serine Endopeptidases/genetics
- Serine Endopeptidases/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Virulence
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Affiliation(s)
- Raju Mukherjee
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Rohit Satardekar
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
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