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Trobajo-Sanmartín C, Miqueleiz A, Guevara M, Fernández-Huerta M, Burgui C, Casado I, Baigorria F, Navascués A, Ezpeleta C, Castilla J. Comparison of the Risk of Hospitalization and Severe Disease Among Co-circulating Severe Acute Respiratory Syndrome Coronavirus 2 Variants. J Infect Dis 2023; 227:332-338. [PMID: 36179126 DOI: 10.1093/infdis/jiac385] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/18/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND We compare the risk of coronavirus disease 2019 (COVID-19) outcomes among co-circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants between January 2021 and May 2022 in Navarra, Spain. METHODS We compared the frequency of hospitalization and severe disease (intensive care unit admission or death) due to COVID-19 among the co-circulating variants. Variants analyzed were nonvariants of concern (non-VOCs), Alpha, Delta, Omicron BA.1, and Omicron BA.2. Logistic regression models were used to estimate adjusted odds ratio (aOR). RESULTS The Alpha variant had a higher risk of hospitalization (aOR, 1.86 [95 confidence interval {CI}, 1.282.71]) and severe disease (aOR, 2.40 [95 CI, 1.314.40]) than non-VOCs. The Delta variant did not show a significantly different risk of hospitalization (aOR, 0.73 [95 CI, .401.30]) and severe disease (aOR, 3.04 [95 CI, .5716.22]) compared to the Alpha variant. The Omicron BA.1 significantly reduced both risks relative to the Delta variant (aORs, 0.28 [95 CI, .16.47] and 0.23 [95 CI, .12.46], respectively). The Omicron BA.2 reduced the risk of hospitalization compared to BA.1 (aOR, 0.52 [95 CI, .29.95]). CONCLUSIONS The Alpha and Delta variants showed an increased risk of hospitalization and severe disease, which decreased considerably with the Omicron BA.1 and BA.2. Surveillance of variants can lead to important differences in severity.
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Affiliation(s)
- Camino Trobajo-Sanmartín
- Instituto de Salud Pblica de Navarra, Pamplona, Spain
- CIBER Epidemiologa y Salud Pblica, Madrid, Spain
- Navarra Institute for Health Research, Pamplona, Spain
| | - Ana Miqueleiz
- Navarra Institute for Health Research, Pamplona, Spain
- Clinical Microbiology Department, Hospital Universitario de Navarra, Pamplona, Spain
| | - Marcela Guevara
- Instituto de Salud Pblica de Navarra, Pamplona, Spain
- CIBER Epidemiologa y Salud Pblica, Madrid, Spain
- Navarra Institute for Health Research, Pamplona, Spain
| | - Miguel Fernández-Huerta
- Navarra Institute for Health Research, Pamplona, Spain
- Clinical Microbiology Department, Hospital Universitario de Navarra, Pamplona, Spain
| | - Cristina Burgui
- Instituto de Salud Pblica de Navarra, Pamplona, Spain
- CIBER Epidemiologa y Salud Pblica, Madrid, Spain
- Navarra Institute for Health Research, Pamplona, Spain
| | - Itziar Casado
- Instituto de Salud Pblica de Navarra, Pamplona, Spain
- CIBER Epidemiologa y Salud Pblica, Madrid, Spain
- Navarra Institute for Health Research, Pamplona, Spain
| | | | - Ana Navascués
- Navarra Institute for Health Research, Pamplona, Spain
- Clinical Microbiology Department, Hospital Universitario de Navarra, Pamplona, Spain
| | - Carmen Ezpeleta
- Navarra Institute for Health Research, Pamplona, Spain
- Clinical Microbiology Department, Hospital Universitario de Navarra, Pamplona, Spain
| | - Jesús Castilla
- Instituto de Salud Pblica de Navarra, Pamplona, Spain
- CIBER Epidemiologa y Salud Pblica, Madrid, Spain
- Navarra Institute for Health Research, Pamplona, Spain
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Hanifa M, Salman M, Fatima M, Mukhtar N, Almajhdi FN, Zaman N, Suleman M, Ali SS, Waheed Y, Khan A. Mutational analysis of the spike protein of SARS-COV-2 isolates revealed atomistic features responsible for higher binding and infectivity. Front Cell Dev Biol 2023; 10:940863. [PMID: 36733340 PMCID: PMC9888553 DOI: 10.3389/fcell.2022.940863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023] Open
Abstract
Introduction: The perpetual appearance of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2), and its new variants devastated the public health and social fabric around the world. Understanding the genomic patterns and connecting them to phenotypic attributes is of great interest to devise a treatment strategy to control this pandemic. Materials and Methods: In this regard, computational methods to understand the evolution, dynamics and mutational spectrum of SARS-CoV-2 and its new variants are significantly important. Thus, herein, we used computational methods to screen the genomes of SARS-CoV-2 isolated from Pakistan and connect them to the phenotypic attributes of spike protein; we used stability-function correlation methods, protein-protein docking, and molecular dynamics simulation. Results: Using the Global initiative on sharing all influenza data (GISAID) a total of 21 unique mutations were identified, among which five were reported as stabilizing while 16 were destabilizing revealed through mCSM, DynaMut 2.0, and I-Mutant servers. Protein-protein docking with Angiotensin-converting enzyme 2 (ACE2) and monoclonal antibody (4A8) revealed that mutation G446V in the receptor-binding domain; R102S and G181V in the N-terminal domain (NTD) significantly affected the binding and thus increased the infectivity. The interaction pattern also revealed significant variations in the hydrogen bonding, salt bridges and non-bonded contact networks. The structural-dynamic features of these mutations revealed the global dynamic trend and the finding energy calculation further established that the G446V mutation increases the binding affinity towards ACE2 while R102S and G181V help in evading the host immune response. The other mutations reported supplement these processes indirectly. The binding free energy results revealed that wild type-RBD has a TBE of -60.55 kcal/mol while G446V-RBD reported a TBE of -73.49 kcal/mol. On the other hand, wild type-NTD reported -67.77 kcal/mol of TBE, R102S-NTD reported -51.25 kcal/mol of TBE while G181V-NTD reported a TBE of -63.68 kcal/mol. Conclusions: In conclusion, the current findings revealed basis for higher infectivity and immune evasion associated with the aforementioned mutations and structure-based drug discovery against such variants.
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Affiliation(s)
- Muhammad Hanifa
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | | | | | - Naila Mukhtar
- Department of Botany, University of Okara, Punjab, Pakistan
| | - Fahad N. Almajhdi
- COVID-19 Virus Research Chair, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nasib Zaman
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Yasir Waheed
- Office of Research, Innovation and Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan,Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon,*Correspondence: Yasir Waheed, ; Abbas Khan,
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Yasir Waheed, ; Abbas Khan,
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Andrés C, Piñana M, Borràs-Bermejo B, González-Sánchez A, García-Cehic D, Esperalba J, Rando A, Zules-Oña RG, Campos C, Codina MG, Blanco-Grau A, Colomer-Castell S, Martín MC, Castillo C, García-Comuñas K, Vásquez-Mercado R, Martins-Martins R, Saubi N, Campins-Martí M, Pumarola T, Quer J, Antón A. A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). Emerg Microbes Infect 2022; 11:172-181. [PMID: 34842496 PMCID: PMC8741249 DOI: 10.1080/22221751.2021.2011617] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/23/2021] [Indexed: 12/24/2022]
Abstract
Herein, we describe the genetic diversity of circulating SARS-CoV-2 viruses by whole-genome sequencing (WGS) in Barcelona city (Catalonia, Spain) throughout the first four pandemic waves. From weeks 11/2020-24/2021, SARS-CoV-2-positive respiratory samples were randomly selected per clinical setting (80% from primary care or 20% from the hospital), age group, and week. WGS was performed following the ARTICv3 protocol on MiSeq or NextSeq2000 Illumina platforms. Nearly complete consensus sequences were used for genetic characterization based on GISAID and PANGOLIN nomenclatures. From 2475 samples, 2166 (87%) were fully sequenced (78% from primary care and 22% from hospital settings). Multiple genetic lineages were co-circulating, but four were predominant at different periods. While B.1.5 (50.68%) and B.1.1 (32.88%) were the major lineages during the first pandemic wave, B.1.177 (66.85%) and B.1.1.7 (83.80%) were predominant during the second, third, and fourth waves, respectively. Almost all (96.4%) were carrying D614G mutation in the S protein, with additional mutations that define lineages or variants. But some mutations of concern, such as E484K from B.1.351 and P.1 lineages are currently under monitoring, together with those observed in the receptor-binding domain or N-terminal domain, such as L452R and T478K from B.1.617.2 lineage. The fact that a predominant lineage was observed in each pandemic wave suggests advantageous properties over other contemporary co-circulating variants. This genetic variability should be monitored, especially when a massive vaccination campaign is ongoing because the potential selection and emergence of novel antigenic SARS-CoV-2 strains related to immunological escapement events.
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Affiliation(s)
- Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Maria Piñana
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Blanca Borràs-Bermejo
- Preventive Medicine and Epidemiology Department, Vall d´Hebron Research Institute (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Alejandra González-Sánchez
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Damir García-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Juliana Esperalba
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Ariadna Rando
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Ricardo-Gabriel Zules-Oña
- Preventive Medicine and Epidemiology Department, Vall d´Hebron Research Institute (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maria Gema Codina
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Albert Blanco-Grau
- Clinical Biochemistry (Clinical Laboratories), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maria Carmen Martín
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Carla Castillo
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Karen García-Comuñas
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Rodrigo Vásquez-Mercado
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Reginaldo Martins-Martins
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Narcís Saubi
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain
| | - Magda Campins-Martí
- Preventive Medicine and Epidemiology Department, Vall d´Hebron Research Institute (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Tomàs Pumarola
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
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Valleriani F, Jurisic L, Di Pancrazio C, Irelli R, Ciarrocchi E, Martino M, Cocco A, Di Felice E, Colaianni ML, Decaro N, Bonfini B, Lorusso A, Di Teodoro G. A Deletion Encompassing the Furin Cleavage Site in the Spike Encoding Gene Does Not Alter SARS-CoV-2 Replication in Lung Tissues of Mink and Neutralization by Convalescent Human Serum Samples. Pathogens 2022; 11:1152. [PMID: 36297209 PMCID: PMC9609486 DOI: 10.3390/pathogens11101152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023] Open
Abstract
SARS-CoV-2 has been shown to lose the furin polybasic cleavage site (FCS) following adaptation on cell culture. Deletion occurring in this region, which may include also the FCS flanking regions, seem not to affect virus replication in vitro; however, a chimeric SARS-CoV-2 virus without the sole FCS motif has been associated with lower virulence in mice and lower neutralization values. Moreover, SARS-CoV-2 virus lacking the FCS was shed to lower titers from experimentally infected ferrets and was not transmitted to cohoused sentinel animals, unlike wild-type virus. In this study, we investigated the replication kinetics and cellular tropism of a SARS-CoV-2 isolate carrying a 10-amino acid deletion in the spike protein spanning the FCS in lung ex vivo organ cultures of mink. Furthermore, we tested the neutralization capabilities of human convalescent SARS-CoV-2 positive serum samples against this virus. We showed that this deletion did not significantly hamper neither ex vivo replication nor neutralization activity by convalescent serum samples. This study highlights the importance of the preliminary phenotypic characterization of emerging viruses in ex vivo models and demonstrates that mink lung tissues are permissive to the replication of a mutant form of SARS-CoV-2 showing a deletion spanning the FCS. Notably, we also highlight the need for sequencing viral stocks before any infection study as large deletions may occur leading to the misinterpretation of results.
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Affiliation(s)
- Fabrizia Valleriani
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Lucija Jurisic
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
- Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy
| | - Chiara Di Pancrazio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Roberta Irelli
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Eugenia Ciarrocchi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Michele Martino
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Antonio Cocco
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Elisabetta Di Felice
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | | | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari, 70010 Bari, Italy
| | - Barbara Bonfini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
| | - Giovanni Di Teodoro
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy
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DEMİRCİ Ş. Examination with Cross-Correlation Analysis of the Time-Lagged Relationship Between COVID-19 Cases of Turkey and Some Countries. İSTANBUL GELIŞIM ÜNIVERSITESI SAĞLIK BILIMLERI DERGISI 2022. [DOI: 10.38079/igusabder.987254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Amaç: Bu çalışmada, Dünya’da COVID-19 vaka sayısında üçüncü dalganın yaşandığı dönemde Türkiye’ye en fazla ziyaretçinin geldiği ülkeler ile Türkiye’nin günlük bir milyon kişi başına düşen COVID-19 vaka sayıları arasındaki gecikmeli ilişkinin incelenmesi amaçlanmıştır.Yöntem: Bütün ulaşım yolları dahil olmak üzere Türkiye’ye en fazla ziyaretçinin geldiği ilk 30 ülke çalışma kapsamına alınmıştır. Vaka sayıları arasındaki gecikmeli ilişki çapraz korelasyon analizi kullanılarak belirlenmiştir.Bulgular: Ukrayna (r=0,80), Polonya (r=0,81), Makedonya (r=0,78), Romanya (r=0,77), Sırbistan (r=0,76), Bulgaristan (r=0,73), Avusturya (r=0,71), Moldova (r=0,71), Birleşik Krallık (r=0,53), Fransa (r=0,52), Belçika (r=0,57), Amerika Birleşik Devletleri (r=0,57), Ürdün (r=0,81), Libya (r=0,74) ve Lübnan’da (r=0,64) vaka sayılarının pik yapmasından haftalar sonra Türkiye’de de pik gerçekleştirdiği ve gecikmeli ilişkinin olduğu saptanmıştır. Türkiye’de vaka sayılarının Almanya (r=0,69), Azerbaycan (r=0,93), Irak (r=0,88), İran (r=0,87) ve Hollanda (r=0,77) ile benzer zaman aralıklarında benzer bir trend sergilediği tespit edilmiştir. Sonuçlar istatistiki açıdan anlamlıdır (p<0,05).Sonuç: Türkiye’de vaka sayılarında üçüncü dalganın yaşandığı dönemde, çalışma kapsamında gecikmeli ilişki tespit edilen ülkelerden gelen ziyaretçilerin hastalığın toplum içerisinde yayılımında etkisi olabilir. Bu bakımdan vaka sayılarında ciddi artışların olduğu ülkelerden Türkiye’ye gelen ziyaretçilerin ülkeye girişlerine izin verilmemesi, karantinada kalma koşulu ile girişine izin verilmesi, ülkeye girişten sonra semptom takibinin yapılması gibi farklı çözümler ile farklı ülkelerden hastalığın taşınması kısmi olarak engellenebilir.
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Affiliation(s)
- Şenol DEMİRCİ
- HACETTEPE ÜNİVERSİTESİ, İKTİSADİ VE İDARİ BİLİMLER FAKÜLTESİ, SAĞLIK YÖNETİMİ BÖLÜMÜ
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6
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Mello M, Moscelli G. Voting, contagion and the trade-off between public health and political rights: Quasi-experimental evidence from the Italian 2020 polls. JOURNAL OF ECONOMIC BEHAVIOR & ORGANIZATION 2022; 200:1025-1052. [PMID: 35873867 PMCID: PMC9295382 DOI: 10.1016/j.jebo.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/30/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Natural disasters raise challenging trade-offs between public health safety and inalienable rights like the active involvement in political choices through voting. We exploit a quasi-experimental setting provided by multiple ballots across regions and municipalities during the Italian 2020 elections to estimate the effect of voters' turnout on the spread of COVID-19. By employing an event-study design with a two-stage Control Function strategy, we find that post-poll new COVID infections increased by an average of 1.1% for each additional percentage point of turnout. Based on these estimates and real political events, we also show through a simulation that in-person voting during a high-infection regime may have a large impact on public health outcomes, more than doubling new infections, deaths and hospitalizations. These findings suggest that policy-makers' responses to natural disasters should be flexible and contingent to the emergency severity, in order to minimize social costs for citizens.
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Affiliation(s)
- Marco Mello
- School of Economics, University of Surrey, GU2 7XH, Guildford, United Kingdom
| | - Giuseppe Moscelli
- School of Economics, University of Surrey, GU2 7XH, Guildford, United Kingdom
- IZA, Bonn, Germany
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7
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Full Genome Characterization of Respiratory Syncytial Virus Causing a Fatal Infection in an Immunocompromised Patient in Tunisia. Pathogens 2022; 11:pathogens11070758. [PMID: 35890000 PMCID: PMC9315832 DOI: 10.3390/pathogens11070758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/13/2022] [Accepted: 06/25/2022] [Indexed: 01/27/2023] Open
Abstract
Human orthopneumovirus (HRSV) is a virus belonging to the Pneumovirus genus that causes lower respiratory tract infections (LRTI) in infants worldwide. In Tunisia, thousands of infants hospitalized for LRTI are found to be positive for HRSV but no whole genome sequences of HRSV strains circulating in this country are available thus far. In this study, five nasal swab samples collected at different time points from a three-month-old female baby with severe immunodeficiency that was hospitalized for acute bronchiolitis were investigated by next generation sequencing. The Tunisian sequences from this study originated from samples collected in 2021, belong to the ON1 genotype of HRSV-A, and are clustered with European sequences from 2019 and not from 2020 or 2021. This is most likely related to local region-specific transmission of different HRSV-A variants due to the COVID-19 related travel restrictions. Overall, this is the first report describing the whole genome sequence of HRSV from Tunisia. However, more sequence data is needed to better understand the genetic diversity and transmission dynamic of HRSV.
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8
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Hoteit R, Yassine HM. Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences. Vaccines (Basel) 2022; 10:919. [PMID: 35746526 PMCID: PMC9230982 DOI: 10.3390/vaccines10060919] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that belongs to the coronavirus family and is the cause of coronavirus disease 2019 (COVID-19). As of May 2022, it had caused more than 500 million infections and more than 6 million deaths worldwide. Several vaccines have been produced and tested over the last two years. The SARS-CoV-2 virus, on the other hand, has mutated over time, resulting in genetic variation in the population of circulating variants during the COVID-19 pandemic. It has also shown immune-evading characteristics, suggesting that vaccinations against these variants could be potentially ineffective. The purpose of this review article is to investigate the key variants of concern (VOCs) and mutations of the virus driving the current pandemic, as well as to explore the transmission rates of SARS-CoV-2 VOCs in relation to epidemiological factors and to compare the virus's transmission rate to that of prior coronaviruses. We examined and provided key information on SARS-CoV-2 VOCs in this study, including their transmissibility, infectivity rate, disease severity, affinity for angiotensin-converting enzyme 2 (ACE2) receptors, viral load, reproduction number, vaccination effectiveness, and vaccine breakthrough.
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Affiliation(s)
- Reem Hoteit
- Clinical Research Institute, Faculty of Medicine, American University of Beirut, Beirut 110236, Lebanon;
| | - Hadi M. Yassine
- Biomedical Research Center and College of Health Sciences-QU Health, Qatar University, Doha 2713, Qatar
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9
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Bonura F, Genovese D, Amodio E, Calamusa G, Sanfilippo GL, Cacioppo F, Giammanco GM, De Grazia S, Ferraro D. Neutralizing Antibodies Response against SARS-CoV-2 Variants of Concern Elicited by Prior Infection or mRNA BNT162b2 Vaccination. Vaccines (Basel) 2022; 10:vaccines10060874. [PMID: 35746482 PMCID: PMC9229788 DOI: 10.3390/vaccines10060874] [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: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/25/2022] [Indexed: 12/21/2022] Open
Abstract
In order to determine the humoral protective response against SARS-CoV-2, the vaccine-induced and naturally induced neutralizing antibodies (NtAbs) responses against SARS-CoV-2 variants circulating in Italy through in vitro live virus neutralization assay were evaluated. A total of 39 SARS-CoV-2 recovered subjects (COVID-19+) and 63 subjects with a two-dose cycle of the BNT16262 vaccine were enrolled. A single serum sample was tested for COVID-19+ at 35–52 days post-positive swab, while vaccinees blood samples were taken at one (V1) and at three months (V3) after administration of the second vaccine dose. Significantly higher NtAb titers were found against B.1 and Alpha in both COVID-19+ and vaccinees, while lower NtAb titers were detected against Delta, Gamma, and Omicron variants. A comparison between groups showed that NtAb titers were significantly higher in both V1 and V3 than in COVID-19+, except against the Omicron variant where no significant difference was found. COVID-19+ showed lower neutralizing titers against all viral variants when compared to the vaccinees. Two-dose vaccination induced a sustained antibody response against each analyzed variant, except for Omicron. The evolution process of SARS-CoV-2, through variants originating from an accumulation of mutations, can erode the neutralizing effectiveness of natural and vaccine-elicited immunity. Therefore, a need for new vaccines should be evaluated to contain the ongoing pandemic.
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10
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Antonini C, Calandrini S, Bianconi F. Robustness analysis for quantitative assessment of vaccination effects and SARS-CoV-2 lineages in Italy. BMC Infect Dis 2022; 22:415. [PMID: 35488251 PMCID: PMC9051820 DOI: 10.1186/s12879-022-07395-2] [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: 10/26/2021] [Accepted: 04/08/2022] [Indexed: 11/25/2022] Open
Abstract
Background In Italy, the beginning of 2021 was characterized by the emergence of new variants of SARS-CoV-2 and by the availability of effective vaccines that contributed to the mitigation of non-pharmaceutical interventions and to the avoidance of hospital collapse. Methods We analyzed the COVID-19 propagation in Italy starting from September 2021 with a Susceptible-Exposed-Infected-Recovered (SEIR) model that takes into account SARS-CoV-2 lineages, intervention measures and efficacious vaccines. The model was calibrated with the Bayesian method Conditional Robust Calibration (CRC) using COVID-19 data from September 2020 to May 2021. Here, we apply the Conditional Robustness Analysis (CRA) algorithm to the calibrated model in order to identify model parameters that most affect the epidemic diffusion in the long-term scenario. We focus our attention on vaccination and intervention parameters, which are the key parameters for long-term solutions for epidemic control. Results Our model successfully describes the presence of new variants and the impact of vaccinations and non-pharmaceutical interventions in the Italian scenario. The CRA analysis reveals that vaccine efficacy and waning immunity play a crucial role for pandemic control, together with asymptomatic transmission. Moreover, even though the presence of variants may impair vaccine effectiveness, virus transmission can be kept low with a constant vaccination rate and low restriction levels. Conclusions In the long term, a policy of booster vaccinations together with contact tracing and testing will be key strategies for the containment of SARS-CoV-2 spread. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07395-2.
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Affiliation(s)
| | - Sara Calandrini
- ICT4Life srl, Perugia, Italy.,Department of Engineering, University of Perugia, Perugia, Italy
| | - Fortunato Bianconi
- COVID-19 Epidemiological Unit, Regional Government of Umbria, Perugia, Italy
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11
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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: 10] [Impact Index Per Article: 5.0] [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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12
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Pascucci I, Paniccià M, Giammarioli M, Biagetti M, Duranti A, Campomori P, Smilari V, Ancora M, Scialabba S, Secondini B, Cammà C, Lorusso A. SARS-CoV-2 Delta VOC in a Paucisymptomatic Dog, Italy. Pathogens 2022; 11:pathogens11050514. [PMID: 35631035 PMCID: PMC9143276 DOI: 10.3390/pathogens11050514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 11/30/2022] Open
Abstract
Since the very beginning of the COVID-19 pandemic, SARS-CoV-2 detection has been described in several animal species. A total of 625 outbreaks in animals have been reported globally, affecting 17 species in 32 countries and the human source of infection has been recognized including pet owners, zookeepers, and farmers. In this report, we describe the case of a paucisymptomatic dog in Italy infected with SARS-CoV-2 from a household with three confirmed human cases of COVID-19 living in Pesaro (Marche region, Italy). The dog showed high viral RNA titers in the nasal and oropharyngeal swabs. In the nasal swab, SARS-CoV-2 RNA lasted for a least a week. By sequencing, the strain was assigned to the AY.23 lineage (PANGO), one of the sub-lineages of the major SARS-CoV-2 Delta variant of concern (VOC). Although we did not process the swabs of the three human cases, we strongly suspect a human origin for the dog infection. In this regard, AY.23 sequences, although never released thus far in the Marche region, were detected in the neighboring regions. Our findings highlight once more the need for a One Health approach for SARS-CoV-2 surveillance, management, and control, thus preventing viral spillover from animals to humans.
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Affiliation(s)
- Ilaria Pascucci
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche—Togo Rosati, 06126 Perugia, Italy; (M.P.); (M.G.); (M.B.); (A.D.)
- Correspondence: ; Tel.:+39-0721-281677
| | - Marta Paniccià
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche—Togo Rosati, 06126 Perugia, Italy; (M.P.); (M.G.); (M.B.); (A.D.)
| | - Monica Giammarioli
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche—Togo Rosati, 06126 Perugia, Italy; (M.P.); (M.G.); (M.B.); (A.D.)
| | - Massimo Biagetti
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche—Togo Rosati, 06126 Perugia, Italy; (M.P.); (M.G.); (M.B.); (A.D.)
| | - Anna Duranti
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche—Togo Rosati, 06126 Perugia, Italy; (M.P.); (M.G.); (M.B.); (A.D.)
| | - Pamela Campomori
- Servizio Veterinario Sanità Animale Area Vasta 1-ASUR Marche, 61121 Pesaro, Italy; (P.C.); (V.S.)
| | - Valerio Smilari
- Servizio Veterinario Sanità Animale Area Vasta 1-ASUR Marche, 61121 Pesaro, Italy; (P.C.); (V.S.)
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy; (M.A.); (S.S.); (B.S.); (C.C.); (A.L.)
| | - Silvia Scialabba
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy; (M.A.); (S.S.); (B.S.); (C.C.); (A.L.)
| | - Barbara Secondini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy; (M.A.); (S.S.); (B.S.); (C.C.); (A.L.)
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy; (M.A.); (S.S.); (B.S.); (C.C.); (A.L.)
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise, 64100 Teramo, Italy; (M.A.); (S.S.); (B.S.); (C.C.); (A.L.)
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13
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SARS-CoV-2 Pandemic Tracing in Italy Highlights Lineages with Mutational Burden in Growing Subsets. Int J Mol Sci 2022; 23:ijms23084155. [PMID: 35456974 PMCID: PMC9029933 DOI: 10.3390/ijms23084155] [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: 03/02/2022] [Revised: 03/31/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023] Open
Abstract
Tracing the appearance and evolution of virus variants is essential in the management of the COVID-19 pandemic. Here, we focus on SARS-CoV-2 spread in Italian patients by using viral sequences deposited in public databases and a tracing procedure which is used to monitor the evolution of the pandemic and detect the spreading, within the infected population of emergent sub-clades with a potential positive selection. Analyses of a collection of monthly samples focused on Italy highlighted the appearance and evolution of all the main viral sub-trees emerging at the end of the first year of the pandemic. It also identified additional expanding subpopulations which spread during the second year (i.e., 2021). Three-dimensional (3D) modelling of the main amino acid changes in mutated viral proteins, including ORF1ab (nsp3, nsp4, 2’-o-ribose methyltransferase, nsp6, helicase, nsp12 [RdRp]), N, ORF3a, ORF8, and spike proteins, shows the potential of the analysed structural variations to result in epistatic modulation and positive/negative selection pressure. These analyzes will be of importance to the early identification of emerging clades, which can develop into new “variants of concern” (i.e., VOC). These analyses and settings will also help SARS-CoV-2 coronet genomic centers in other countries to trace emerging worldwide variants.
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14
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Marcotte H, Piralla A, Zuo F, Du L, Cassaniti I, Wan H, Kumagai-Braesh M, Andréll J, Percivalle E, Sammartino JC, Wang Y, Vlachiotis S, Attevall J, Bergami F, Ferrari A, Colaneri M, Vecchia M, Sambo M, Zuccaro V, Asperges E, Bruno R, Oggionni T, Meloni F, Abolhassani H, Bertoglio F, Schubert M, Calzolai L, Varani L, Hust M, Xue Y, Hammarström L, Baldanti F, Pan-Hammarström Q. Immunity to SARS-CoV-2 up to 15 months after infection. iScience 2022; 25:103743. [PMID: 35018336 PMCID: PMC8736281 DOI: 10.1016/j.isci.2022.103743] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/20/2021] [Accepted: 01/05/2022] [Indexed: 11/25/2022] Open
Abstract
Information concerning the longevity of immunity to SARS-CoV-2 following natural infection may have considerable implications for durability of immunity induced by vaccines. Here, we monitored the SARS-CoV-2 specific immune response in COVID-19 patients followed up to 15 months after symptoms onset. Following a peak at day 15–28 postinfection, the IgG antibody response and plasma neutralizing titers gradually decreased over time but stabilized after 6 months. Compared to G614, plasma neutralizing titers were more than 8-fold lower against variants Beta, Gamma, and Delta. SARS-CoV-2-specific memory B and T cells persisted in the majority of patients up to 15 months although a significant decrease in specific T cells, but not B cells, was observed between 6 and 15 months. Antiviral specific immunity, especially memory B cells in COVID-19 convalescent patients, is long-lasting, but some variants of concern may at least partially escape the neutralizing activity of plasma antibodies. Plasma neutralizing antibodies persist in the majority of patients up to 15 months Neutralizing activity is lower against variants of concern Delta, Beta, and Gamma Specific memory B and T cells were present in 95% of patients up to 15 months Specific T cells, but not B cells, were decreased between 6 and 15 months
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Affiliation(s)
- Harold Marcotte
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Fanglei Zuo
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Likun Du
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Irene Cassaniti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Hui Wan
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Makiko Kumagai-Braesh
- Division of Transplantation Surgery, CLINTEC, Karolinska Institutet at Karolinska University Hospital, Stockholm, Sweden
| | - Juni Andréll
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Elena Percivalle
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Josè Camilla Sammartino
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Yating Wang
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Stelios Vlachiotis
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Janine Attevall
- Division of Transplantation Surgery, CLINTEC, Karolinska Institutet at Karolinska University Hospital, Stockholm, Sweden
| | - Federica Bergami
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Alessandro Ferrari
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marta Colaneri
- Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Italy
| | - Marco Vecchia
- Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Italy
| | - Margherita Sambo
- Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Italy
| | - Valentina Zuccaro
- Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Italy
| | - Erika Asperges
- Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Italy
| | - Raffaele Bruno
- Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Italy
| | - Tiberio Oggionni
- Unit of Respiratory Diseases, Department of Medical Sciences and Infective Diseases, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Federica Meloni
- Section of Pneumology, Department of Internal Medicine, University of Pavia, Pavia, Italy
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Federico Bertoglio
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Braunschweig, Germany
| | - Maren Schubert
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Braunschweig, Germany
| | - Luigi Calzolai
- European Commission, Joint Research Centre, Ispra, Italy
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Michael Hust
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Department of Biotechnology, Braunschweig, Germany
| | - Yintong Xue
- Department of Immunology, Peking University Health Science Center, Beijing, China
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Qiang Pan-Hammarström
- Division of Transplantation Surgery, CLINTEC, Karolinska Institutet at Karolinska University Hospital, Stockholm, Sweden
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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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Stadtmüller M, Laubner A, Rost F, Winkler S, Patrasová E, Šimůnková L, Reinhardt S, Beil J, Dalpke AH, Yi B. OUP accepted manuscript. Virus Evol 2022; 8:veac010. [PMID: 35494175 PMCID: PMC9048873 DOI: 10.1093/ve/veac010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/05/2022] [Accepted: 02/14/2022] [Indexed: 11/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution plays a significant role in shaping the dynamics of the coronavirus disease 2019 pandemic. To monitor the evolution of SARS-CoV-2 variants, through international collaborations, we performed genomic epidemiology analyses on a weekly basis with SARS-CoV-2 samples collected from a border region between Germany, Poland, and the Czech Republic in a global background. For identified virus mutant variants, active viruses were isolated and functional evaluations were performed to test their replication fitness and neutralization sensitivity against vaccine-elicited serum neutralizing antibodies. Thereby we identified a new B.1.1.7 sub-lineage carrying additional mutations of nucleoprotein G204P and open-reading-frame-8 K68stop. Of note, this B.1.1.7 sub-lineage is the predominant B.1.1.7 variant in several European countries such as Czech Republic, Austria, and Slovakia. The earliest samples belonging to this sub-lineage were detected in November 2020 in a few countries in the European continent, but not in the UK. We have also detected its further evolution with extra spike mutations D138Y and A701V, which are signature mutations shared with the Gamma and Beta variants, respectively. Antibody neutralization assay of virus variant isolations has revealed that the variant with extra spike mutations is 3.2-fold less sensitive to vaccine-elicited antibodies as compared to the other B.1.1.7 variants tested, indicating potential for immune evasion, but it also exhibited reduced replication fitness, suggesting lower transmissibility. The wide spread of this B.1.1.7 sub-lineage was related to the pandemic waves in early 2021 in various European countries. These findings about the emergence, spread, evolution, infection, and transmission abilities of this B.1.1.7 sub-lineage add to our understanding about the pandemic development in Europe and highlight the importance of international collaboration on virus mutant surveillance.
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Affiliation(s)
| | - Alexa Laubner
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, Saxony 01307, Germany
| | - Fabian Rost
- DRESDEN concept Genome Center, Technische Universität Dresden, Fetscherstraße 105, Dresden, Saxony 01307, Germany
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstraße 105, Dresden, Saxony 01307, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and DRESDEN concept Genome Center, Technische Universität Dresden, Pfotenhauerstraße 108, Dresden, Saxony 01307, Germany
| | - Eva Patrasová
- Department of Epidemiology, Regional Public Health Authority for Ustecky Kraj, Moskevská 15, Ústí nad Labem 400 01, Czech Republic
- Third Faculty of Medicine, Charles University in Prague, Ruská 2411/87, Prague 100 00, Czech Republic
| | - Lenka Šimůnková
- Department of Epidemiology, Regional Public Health Authority for Ustecky Kraj, Moskevská 15, Ústí nad Labem 400 01, Czech Republic
| | | | - Johanna Beil
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and DRESDEN concept Genome Center, Technische Universität Dresden, Pfotenhauerstraße 108, Dresden, Saxony 01307, Germany
| | - Alexander H Dalpke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, Saxony 01307, Germany
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Mio C, Dal Secco C, Marzinotto S, Bruno C, Pimpo S, Betto E, Bertoni M, Pipan C, Sozio E, Tascini C, Damante G, Curcio F. Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. PLoS One 2021; 16:e0261229. [PMID: 34905574 PMCID: PMC8670677 DOI: 10.1371/journal.pone.0261229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/24/2021] [Indexed: 11/27/2022] Open
Abstract
In-depth study of the entire SARS-CoV-2 genome has uncovered many mutations, which have replaced the lineage that characterized the first wave of infections all around the world. In December 2020, the outbreak of variant of concern (VOC) 202012/01 (lineage B.1.1.7) in the United Kingdom defined a turning point during the pandemic, immediately posing a worldwide threat on the Covid-19 vaccination campaign. Here, we reported the evolution of B.1.1.7 lineage-related infections, analyzing samples collected from January 1st 2021, until April 15th 2021, in Friuli Venezia Giulia, a northeastern region of Italy. A cohort of 1508 nasopharyngeal swabs was analyzed by High Resolution Melting (HRM) and 479 randomly selected samples underwent Next Generation Sequencing analysis (NGS), uncovering a steady and continuous accumulation of B.1.1.7 lineage-related specimens, joined by sporadic cases of other known lineages (i.e. harboring the Spike glycoprotein p.E484K mutation). All the SARS-CoV-2 genome has been analyzed in order to highlight all the rare mutations that may eventually result in a new variant of interest. This work suggests that a thorough monitoring of the SARS-CoV-2 genome by NGS is essential to contain any new variant that could jeopardize all the efforts that have been made so far to resolve the emergence of the pandemic.
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Affiliation(s)
- Catia Mio
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Chiara Dal Secco
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Stefania Marzinotto
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Claudio Bruno
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Santa Pimpo
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Elena Betto
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Martina Bertoni
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Corrado Pipan
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Emanuela Sozio
- Infectious Diseases Clinic, University Hospital of Udine, Udine, Italy
| | - Carlo Tascini
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Infectious Diseases Clinic, University Hospital of Udine, Udine, Italy
| | - Giuseppe Damante
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Francesco Curcio
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
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18
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Boshier FAT, Venturini C, Stirrup O, Guerra-Assunção JA, Alcolea-Medina A, Becket AH, Byott M, Charalampous T, Filipe ADS, Frampton D, Glaysher S, Khan T, Kulasegara-Shylini R, Kele B, Monahan IM, Mollett G, Parker M, Pelosi E, Randell P, Roy S, Taylor JF, Weller SJ, Wilson-Davies E, Wade P, Williams R, Copas AJ, Cutino-Moguel T, Freemantle N, Hayward AC, Holmes A, Hughes J, Mahungu TW, Nebbia G, Nastouli E, Partridge DG, Pope CF, Price JR, Robson SC, Saeed K, Shin GY, de Silva TI, Snell LB, Thomson EC, Witney AA, Breuer J. The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study. J Infect 2021; 83:693-700. [PMID: 34610391 PMCID: PMC8487101 DOI: 10.1016/j.jinf.2021.09.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 09/12/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Recently emerging SARS-CoV-2 variants have been associated with an increased rate of transmission within the community. We sought to determine whether this also resulted in increased transmission within hospitals. METHODS We collected viral sequences and epidemiological data of patients with community and healthcare associated SARS-CoV-2 infections, sampled from 16th November 2020 to 10th January 2021, from nine hospitals participating in the COG-UK HOCI study. Outbreaks were identified using ward information, lineage and pairwise genetic differences between viral sequences. RESULTS Mixed effects logistic regression analysis of 4184 sequences showed healthcare-acquired infections were no more likely to be identified as the Alpha variant than community acquired infections. Nosocomial outbreaks were investigated based on overlapping ward stay and SARS-CoV-2 genome sequence similarity. There was no significant difference in the number of patients involved in outbreaks caused by the Alpha variant compared to outbreaks caused by other lineages. CONCLUSIONS We find no evidence to support it causing more nosocomial transmission than previous lineages. This suggests that the stringent infection prevention measures already in place in UK hospitals contained the spread of the Alpha variant as effectively as other less transmissible lineages, providing reassurance of their efficacy against emerging variants of concern.
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Affiliation(s)
- Florencia A T Boshier
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Cristina Venturini
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Oliver Stirrup
- Institute for Global Health, University College London, London, United Kingdom
| | - José Afonso Guerra-Assunção
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; Infection Sciences, Viapath, London, United Kingdom
| | - Angela H Becket
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom; School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Matthew Byott
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom; The Francis Crick Institute, London, United Kingdom
| | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Dan Frampton
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom; Division of Infection and Immunity, University College London, London, United Kingdom
| | - Sharon Glaysher
- Portsmouth Hospitals University NHS Trust, Queen Alexandra Hospital, Portsmouth PO6 3LY, United Kingdom
| | - Tabassum Khan
- Division of Infection, The Royal London Hospital, Barts Health, United Kingdom
| | | | - Beatrix Kele
- Division of Infection, The Royal London Hospital, Barts Health, United Kingdom
| | - Irene M Monahan
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom
| | - Guy Mollett
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Matthew Parker
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, United Kingdom; Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom; Sheffield Biomedical Research Centre, The University of Sheffield, Sheffield, United Kingdom
| | - Emanuela Pelosi
- Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Paul Randell
- Department of Infection and Immunity, North West London Pathology, London, United Kingdom
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Joshua F Taylor
- Department of Microbiology, South West London Pathology, Jenner Wing, St. George's Hospital, Blackshaw Road, London SW17 0QT, United Kingdom
| | - Sophie J Weller
- Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Eleri Wilson-Davies
- Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Phillip Wade
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Rachel Williams
- Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Andrew J Copas
- Institute for Global Health, University College London, London, United Kingdom
| | | | - Nick Freemantle
- Institute for Clinical Trials and Methodology, University College London, London, United Kingdom
| | - Andrew C Hayward
- Institute of Epidemiology and Health Care, University College London, London, United Kingdom
| | - Alison Holmes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, United Kingdom; Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Tabitha W Mahungu
- Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, United Kingdom
| | - Eleni Nastouli
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom; Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom; The Francis Crick Institute, London, United Kingdom
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Cassie F Pope
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom; Infection Care Group, St George's University Hospitals NHS Foundation Trust, Blackshaw Road, London SW17 0QT, United Kingdom
| | - James R Price
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Samuel C Robson
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom; School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom; School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
| | - Kordo Saeed
- Department of Infection, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, United Kingdom; Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Tremona Road, Southampton, United Kingdom
| | - Gee Yen Shin
- Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom; Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, United Kingdom
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Adam A Witney
- Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Microbiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.
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19
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Changing Features of COVID-19: Characteristics of Infections with the SARS-CoV-2 Delta (B.1.617.2) and Alpha (B.1.1.7) Variants in Southern Italy. Vaccines (Basel) 2021; 9:vaccines9111354. [PMID: 34835285 PMCID: PMC8624869 DOI: 10.3390/vaccines9111354] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Differences in the demographic and clinical characteristics of patients infected with the Alpha and Delta SARS-CoV-2 variants of concern in a large region of Southern Italy were assessed. Two cohorts of positive patients were compared. The Alpha group consisted of 11,135 subjects diagnosed between 21 March and 21 April 2021, and the Delta group consisted of 499 positive subjects diagnosed between 21 July and 21 August 2021. A descriptive and statistical analysis of the demographic and clinical characteristics of the two groups was performed. The proportion of patients with mild and moderate infections was significantly higher in the Delta than in the Alpha group (p < 0.001). In fully vaccinated patients, the proportion of symptomatic individuals was significantly higher in the Delta than in the Alpha group. The Delta group showed odds ratios of 3.08 (95% CI, 2.55-3.72) for symptomatic infection and 2.66 (95% CI, 1.76-3.94) for hospitalization. Improving COVID-19 vaccination rates is a priority, since infection with the SARS-CoV-2 Delta variant has a significant impact on patient outcomes. Additional targeted prevention strategies such as social distancing, the use of masks in indoor settings irrespective of vaccination status, and the use of a sanitary passport could be crucial to contain further spread of SARS-CoV-2 infection.
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20
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Di Pasquale A, Radomski N, Mangone I, Calistri P, Lorusso A, Cammà C. SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels. BMC Genomics 2021; 22:782. [PMID: 34717546 PMCID: PMC8556844 DOI: 10.1186/s12864-021-08112-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/20/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Faced with the ongoing global pandemic of coronavirus disease, the 'National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis' (GENPAT) formally established at the 'Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise' (IZSAM) in Teramo (Italy) is in charge of the SARS-CoV-2 surveillance at the genomic scale. In a context of SARS-CoV-2 surveillance requiring correct and fast assessment of epidemiological clusters from substantial amount of samples, the present study proposes an analytical workflow for identifying accurately the PANGO lineages of SARS-CoV-2 samples and building of discriminant minimum spanning trees (MST) bypassing the usual time consuming phylogenomic inferences based on multiple sequence alignment (MSA) and substitution model. RESULTS GENPAT constituted two collections of SARS-CoV-2 samples. The first collection consisted of SARS-CoV-2 positive swabs collected by IZSAM from the Abruzzo region (Italy), then sequenced by next generation sequencing (NGS) and analyzed in GENPAT (n = 1592), while the second collection included samples from several Italian provinces and retrieved from the reference Global Initiative on Sharing All Influenza Data (GISAID) (n = 17,201). The main results of the present work showed that (i) GENPAT and GISAID detected the same PANGO lineages, (ii) the PANGO lineages B.1.177 (i.e. historical in Italy) and B.1.1.7 (i.e. 'UK variant') are major concerns today in several Italian provinces, and the new MST-based method (iii) clusters most of the PANGO lineages together, (iv) with a higher dicriminatory power than PANGO lineages, (v) and faster that the usual phylogenomic methods based on MSA and substitution model. CONCLUSIONS The genome sequencing efforts of Italian provinces, combined with a structured national system of NGS data management, provided support for surveillance SARS-CoV-2 in Italy. We propose to build phylogenomic trees of SARS-CoV-2 variants through an accurate, discriminant and fast MST-based method avoiding the typical time consuming steps related to MSA and substitution model-based phylogenomic inference.
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Affiliation(s)
- Adriano Di Pasquale
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Nicolas Radomski
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Iolanda Mangone
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Paolo Calistri
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Alessio Lorusso
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Cesare Cammà
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
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21
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da Silva Francisco Junior R, Lamarca AP, de Almeida LGP, Cavalcante L, Machado DT, Martins Y, Brustolini O, Gerber AL, de C Guimarães AP, Gonçalves RB, Alves C, Mariani D, Cruz TF, de Souza IV, de Carvalho EM, Ribeiro MS, Carvalho S, da Silva FD, de Oliveira Garcia MH, de Souza LM, da Silva CG, Ribeiro CLP, Cavalcanti AC, de Mello CMB, Struchiner CJ, Tanuri A, Vasconcelos ATR. Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil. Viruses 2021; 13:2013. [PMID: 34696443 PMCID: PMC8537965 DOI: 10.3390/v13102013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/23/2021] [Accepted: 09/29/2021] [Indexed: 01/02/2023] Open
Abstract
In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the pandemic was characterized by three different phases driven by a successive replacement of lineages. Interestingly, we noticed that viral supercarriers accounted for the overwhelming majority of the circulating virus (>90%) among symptomatic individuals in the state. Moreover, SARS-CoV-2 genomic surveillance also revealed the emergence and spread of two new variants (P.5 and P.1.2), firstly reported in this study. Our findings provided important lessons learned from the different epidemiological aspects of the SARS-CoV-2 dynamic in Rio de Janeiro. Altogether, this might have a strong potential to shape future decisions aiming to improve public health management and understanding mechanisms underlying virus dispersion.
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Affiliation(s)
- Ronaldo da Silva Francisco Junior
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Alessandra P Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Luiz G P de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Liliane Cavalcante
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Douglas Terra Machado
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Yasmmin Martins
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Otávio Brustolini
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Alexandra L Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Ana Paula de C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Reinaldo Bellini Gonçalves
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Cassia Alves
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil; (C.A.); (D.M.); (T.F.C.); (A.T.)
| | - Diana Mariani
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil; (C.A.); (D.M.); (T.F.C.); (A.T.)
| | - Thais Felix Cruz
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil; (C.A.); (D.M.); (T.F.C.); (A.T.)
| | | | - Erika Martins de Carvalho
- Unidades de Apoio ao Diagnóstico da COVID-19, Rio de Janeiro 21040-900, Brazil; (I.V.d.S.); (E.M.d.C.)
| | - Mario Sergio Ribeiro
- Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro 20031-142, Brazil; (M.S.R.); (S.C.); (C.M.B.d.M.)
| | - Silvia Carvalho
- Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro 20031-142, Brazil; (M.S.R.); (S.C.); (C.M.B.d.M.)
| | - Flávio Dias da Silva
- Secretaria Municipal de Saúde Rio de Janeiro, Rio de Janeiro 20211-901, Brazil; (F.D.d.S.); (M.H.d.O.G.); (C.L.P.R.)
| | | | - Leandro Magalhães de Souza
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro 20231-092, Brazil; (L.M.d.S.); (C.G.d.S.); (A.C.C.)
| | - Cristiane Gomes da Silva
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro 20231-092, Brazil; (L.M.d.S.); (C.G.d.S.); (A.C.C.)
| | - Caio Luiz Pereira Ribeiro
- Secretaria Municipal de Saúde Rio de Janeiro, Rio de Janeiro 20211-901, Brazil; (F.D.d.S.); (M.H.d.O.G.); (C.L.P.R.)
| | - Andréa Cony Cavalcanti
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro 20231-092, Brazil; (L.M.d.S.); (C.G.d.S.); (A.C.C.)
| | - Claudia Maria Braga de Mello
- Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro 20031-142, Brazil; (M.S.R.); (S.C.); (C.M.B.d.M.)
| | | | - Amilcar Tanuri
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil; (C.A.); (D.M.); (T.F.C.); (A.T.)
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
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22
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Valleriani F, Mancuso E, Vincifori G, Teodori L, Di Marcantonio L, Spedicato M, Leone A, Savini G, Morelli D, Bonfini B, Lorusso A. Neutralization of SARS-CoV-2 Variants by Serum from BNT162b2 Vaccine Recipients. Viruses 2021; 13:v13102011. [PMID: 34696441 PMCID: PMC8540752 DOI: 10.3390/v13102011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 02/02/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved rapidly, leading to viral lineages characterized by multiple mutations in the spike protein, which could potentially confer to the virus the ability to avoid the vaccine-induced immune response, making the vaccines less effective or ineffective. Here, we initially evaluated the neutralization capabilities in vitro by serum neutralization (SN) of six serum samples collected from recipients of the BNT162b2 vaccine against 11 SARS-CoV-2 isolates belonging to the major SARS-CoV-2 lineages that had been circulating in Italy. Then, we considered 30 additional serum samples by SN assay against the dominant B.1.617.2 (Delta) variant. A B.1 lineage isolate was used as a reference. In the first analysis, significant differences when compared with the reference strain (p > 0.05) were not evidenced; instead, when the panel of 30 sera was tested against the B.1.617.2 (Delta) variant, a significant (p = 0.0015) 2.38-fold reduction in neutralizing titres compared with the reference after the first vaccine dose was demonstrated. After the second vaccine dose, the reduction was not significant (p = 0.1835). This study highlights that the BNT162b2 vaccine stimulates a humoral response able to neutralize all tested SARS-CoV-2 variants, thus suggesting a prominent role in mitigating the impact of the SARS-CoV-2 pandemic in real-world conditions. Long-term follow-up is currently ongoing.
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23
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Messali S, Campisi G, Giovanetti M, Ciccozzi M, Caruso A, Caccuri F. The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. J Med Virol 2021; 94:413-416. [PMID: 34515998 PMCID: PMC8661962 DOI: 10.1002/jmv.27333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 11/12/2022]
Abstract
In December 2020, Italy experienced the first case of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) B.1.1.7 lineage. In January 2021, we identified 21 cases of this variant in Corzano, defining the first outbreak of SARS-CoV-2 B.1.1.7 lineage in Italy. The high transmissibility of the B.1.1.7 variant represented an important benefit for the virus, which became rapidly dominant on the territory. Containment measures induced the epidemic curve onto a decreasing trajectory underlining the importance of appropriate control and surveillance for restraint of virus spread. Highlights The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage occurred in Lombardy in January 2021. The outbreak originated by a single introduction of the B.1.1.7 lineage. The genomic sequencing revealed, for the first time, the presence of the V551F mutation in the B.1.1.7 lineage in Italy. Surveillance, prompt sequencing and tracing efforts were fundamental to identify and to quickly contain the outbreak.
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Affiliation(s)
- Serena Messali
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giovanni Campisi
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo, Cruz, Brazil.,Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Arnaldo Caruso
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Francesca Caccuri
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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24
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A Modeling Study on Vaccination and Spread of SARS-CoV-2 Variants in Italy. Vaccines (Basel) 2021; 9:vaccines9080915. [PMID: 34452040 PMCID: PMC8402493 DOI: 10.3390/vaccines9080915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/29/2021] [Accepted: 08/12/2021] [Indexed: 12/16/2022] Open
Abstract
From the end of 2020, different vaccines against COVID-19 have been approved, offering a glimmer of hope and relief worldwide. However, in late 2020, new cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) started to re-surge, worsened by the emergence of highly infectious variants. To study this scenario, we extend the Susceptible-Exposed-Infectious-Removed model with lockdown measures used in our previous work with the inclusion of new lineages and mass vaccination campaign. We estimate model parameters using the Bayesian method Conditional Robust Calibration in two case studies: Italy and the Umbria region, the Italian region being worse affected by the emergence of variants. We then use the model to explore the dynamics of COVID-19, given different vaccination paces and a policy of gradual reopening. Our findings confirm the higher reproduction number of Umbria and the increase of transmission parameters due to the presence of new variants. The results illustrate the importance of preserving population-wide interventions, especially during the beginning of vaccination. Finally, under the hypothesis of waning immunity, the predictions show that a seasonal vaccination with a constant rate would probably be necessary to control the epidemic.
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25
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Abstract
A growing number of emerging SARS-CoV-2 variants is being identified worldwide, potentially impacting the effectiveness of current vaccines. We report the data obtained in several Italian regions involved in the SARS-CoV-2 variant monitoring from the beginning of the epidemic and spanning the period from October 2020 to March 2021.
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26
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Hogan CA, Jassem AN, Sbihi H, Joffres Y, Tyson JR, Noftall K, Taylor M, Lee T, Fjell C, Wilmer A, Galbraith J, Romney MG, Henry B, Krajden M, Galanis E, Prystajecky N, Hoang LM. Rapid Increase in SARS-CoV-2 P.1 Lineage Leading to Codominance with B.1.1.7 Lineage, British Columbia, Canada, January-April 2021. Emerg Infect Dis 2021; 27:2802-2809. [PMID: 34388358 PMCID: PMC8544957 DOI: 10.3201/eid2711.211190] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Several severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) emerged in late 2020; lineage B.1.1.7 initially dominated globally. However, lineages B.1.351 and P.1 represent potentially greater risk for transmission and immune escape. In British Columbia, Canada, B.1.1.7 and B.1.351 were first identified in December 2020 and P.1 in February 2021. We combined quantitative PCR and whole-genome sequencing to assess relative contribution of VOCs in nearly 67,000 infections during the first 16 weeks of 2021 in British Columbia. B.1.1.7 accounted for <10% of screened or sequenced specimens early on, increasing to >50% by week 8. P.1 accounted for <10% until week 10, increased rapidly to peak at week 12, and by week 13 codominated within 10% of rates of B.1.1.7. B.1.351 was a minority throughout. This rapid expansion of P.1 but suppression of B.1.351 expands our understanding of population-level VOC patterns and might provide clues to fitness determinants for emerging VOCs.
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27
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An Autochthonous Outbreak of the SARS-CoV-2 P.1 Variant of Concern in Southern Italy, April 2021. Trop Med Infect Dis 2021; 6:tropicalmed6030151. [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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28
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Cross-neutralization of SARS-CoV-2 B.1.1.7 and P.1 variants in vaccinated, convalescent and P.1 infected. J Infect 2021; 83:467-472. [PMID: 34320390 PMCID: PMC8310664 DOI: 10.1016/j.jinf.2021.07.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/17/2021] [Accepted: 07/21/2021] [Indexed: 11/24/2022]
Abstract
Objectives The emergence of new variants of concern (VOCs) of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) around the world significantly complicated the exit from Coronavirus disease 2019 (COVID-19) pandemic. The aim of this study was to evaluate the serum neutralizing activity of three cohorts. Methods BNT162b2-elicited serum (N = 103), candidates as hyper-immune plasma donors (N = 90) and patients infected with the SARS-CoV-2 P1 variant (N = 22) were enrolled. Three strains of SARS-CoV-2 have been tested: 20A.EU1, B.1.1.7 (alpha) and P.1 (gamma). Neutralizing antibodies (NT-Abs) titers against SARS-CoV-2 were evaluated. Results B.1.1.7 and P.1 are less efficiently neutralized by convalescent wild-type infected serums if compared to 20A.EU1 strain (mean titer 1.6 and 6.7-fold lower respectively). BNT162b2 vaccine-elicited human sera show an equivalent neutralization potency on the B.1.1.7 but it is significantly lower for the P.1 variant (mean titer 3.3-fold lower). Convalescent P.1 patients are less protected from other SARS-CoV-2 strains with an important reduction of neutralizing antibodies against 20A.EU1 and B.1.1.7, about 12.2 and 10.9-fold, respectively. Conclusions BNT162b2 vaccine confers immunity against all the tested VOCs, while previous SARS-CoV-2 infection may be less protective.
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29
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Chakraborty C, Bhattacharya M, Sharma AR. Present variants of concern and variants of interest of severe acute respiratory syndrome coronavirus 2: Their significant mutations in S‐glycoprotein, infectivity, re‐infectivity, immune escape and vaccines activity. Rev Med Virol 2021. [PMCID: PMC8420283 DOI: 10.1002/rmv.2270] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Newly arising variants of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) are now a threat to global public health and are creating COVID‐19 surges in different countries. At the same time, there is limited knowledge about these emerging variants. Even if research data are available, it is varyingly scattered. In this review, we have discussed the appearance of significant alarming SARS‐CoV‐2 variants in the entire world. The study also discusses the properties of the substantial variant of concern (VOC) variants such as B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.427 (Epsilon) and B.1.429 (Epsilon). At the same time, the characteristic properties of some significant variant of interest (VOI) variants like B.1.525 (Eta), B.1.526 (Iota) (sublineage B.1.526.1), B.1.617 (sublineages B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.617.3), P.2 (Zeta), P.3 (Theta), B.1.616 and B.1.427 have also been discussed. Here, we have explained some essential mutations for the VOC and VOI variants such as K417T/N, L452R, E484K, N501Y, D614G and P681R. Consecutively, we also highlighted the crucial clinical characteristics of the variants, such as transmissibility, infectivity, re‐infectivity, immune escape, vaccine activity and vaccine escape. Our comprehensive review will provide updated information on the newly appearing variants of SARS‐CoV‐2 and help the researchers to formulate strategies to curtail the COVID‐19 pandemic.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology School of Life Science and Biotechnology Adamas University Kolkata West Bengal India
| | | | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery Hallym University‐Chuncheon Sacred Heart Hospital Chuncheon‐si Gangwon‐do South Korea
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