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1.
PLoS One ; 18(5): e0284716, 2023.
Article in English | MEDLINE | ID: covidwho-20237945

ABSTRACT

Identifying the spatial patterns of genetic structure of influenza A viruses is a key factor for understanding their spread and evolutionary dynamics. In this study, we used phylogenetic and Bayesian clustering analyses of genetic sequences of the A/H1N1pdm09 virus with district-level locations in mainland China to investigate the spatial genetic structure of the A/H1N1pdm09 virus across human population landscapes. Positive correlation between geographic and genetic distances indicates high degrees of genetic similarity among viruses within small geographic regions but broad-scale genetic differentiation, implying that local viral circulation was a more important driver in the formation of the spatial genetic structure of the A/H1N1pdm09 virus than even, countrywide viral mixing and gene flow. Geographic heterogeneity in the distribution of genetic subpopulations of A/H1N1pdm09 virus in mainland China indicates both local to local transmission as well as broad-range viral migration. This combination of both local and global structure suggests that both small-scale and large-scale population circulation in China is responsible for viral genetic structure. Our study provides implications for understanding the evolution and spread of A/H1N1pdm09 virus across the population landscape of mainland China, which can inform disease control strategies for future pandemics.


Subject(s)
Influenza A Virus, H1N1 Subtype , Influenza, Human , Humans , Influenza, Human/epidemiology , Influenza, Human/genetics , Influenza A Virus, H1N1 Subtype/genetics , Phylogeny , Bayes Theorem , China/epidemiology
2.
Cell Mol Life Sci ; 80(5): 136, 2023 May 02.
Article in English | MEDLINE | ID: covidwho-2317271

ABSTRACT

Influenza A virus (IAV) is a respiratory virus that causes epidemics and pandemics. Knowledge of IAV RNA secondary structure in vivo is crucial for a better understanding of virus biology. Moreover, it is a fundament for the development of new RNA-targeting antivirals. Chemical RNA mapping using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) coupled with Mutational Profiling (MaP) allows for the thorough examination of secondary structures in low-abundance RNAs in their biological context. So far, the method has been used for analyzing the RNA secondary structures of several viruses including SARS-CoV-2 in virio and in cellulo. Here, we used SHAPE-MaP and dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) for genome-wide secondary structure analysis of viral RNA (vRNA) of the pandemic influenza A/California/04/2009 (H1N1) strain in both in virio and in cellulo environments. Experimental data allowed the prediction of the secondary structures of all eight vRNA segments in virio and, for the first time, the structures of vRNA5, 7, and 8 in cellulo. We conducted a comprehensive structural analysis of the proposed vRNA structures to reveal the motifs predicted with the highest accuracy. We also performed a base-pairs conservation analysis of the predicted vRNA structures and revealed many highly conserved vRNA motifs among the IAVs. The structural motifs presented herein are potential candidates for new IAV antiviral strategies.


Subject(s)
COVID-19 , Influenza A Virus, H1N1 Subtype , Influenza A virus , Humans , Influenza A Virus, H1N1 Subtype/genetics , SARS-CoV-2/genetics , Influenza A virus/genetics , RNA, Viral/genetics , Genomics
3.
Biosens Bioelectron ; 222: 114989, 2023 Feb 15.
Article in English | MEDLINE | ID: covidwho-2306553

ABSTRACT

For point-of-care testing (POCT), coupling isothermal nucleic acid amplification schemes (e.g., recombinase polymerase amplification, RPA) with lateral flow assay (LFA) readout is an ideal platform, since such integration offers both high sensitivity and deployability. However, isothermal schemes typically suffers from non-specific amplification, which is difficult to be differentiated by LFA and thus results in false-positives. Here, we proposed an accurate POCT platform by specific recognition of target amplicons with peptide nucleic acid (PNA, assisted by T7 Exonuclease), which could be directly plugged into the existing RPA kits and commercial LFA test strips. With SARS-CoV-2 as the model, the proposed method (RPA-TeaPNA-LFA) efficiently eliminated the false-positives, exhibiting a lowest detection concentration of 6.7 copies/µL of RNA and 90 copies/µL of virus. Using dual-gene (orf1ab and N genes of SARS-CoV-2) as the targets, RPA-TeaPNA-LFA offered a high specificity (100%) and sensitivity (RT-PCR Ct < 31, 100%; Ct < 40, 71.4%), and is valuable for on-site screening or self-testing during isolation. In addition, the dual test lines in the test strips were successfully explored for simultaneous detection of SARS-CoV-2 and H1N1, showing great potential in response to future pathogen-based pandemics.


Subject(s)
Biosensing Techniques , COVID-19 , Influenza A Virus, H1N1 Subtype , Nucleic Acids , Humans , Influenza A Virus, H1N1 Subtype/genetics , SARS-CoV-2/genetics , COVID-19/diagnosis , Nucleic Acid Amplification Techniques/methods , Point-of-Care Testing , Sensitivity and Specificity , Recombinases/genetics
4.
Viruses ; 15(4)2023 04 16.
Article in English | MEDLINE | ID: covidwho-2298859

ABSTRACT

Post-pandemic economic recovery relies on border control for safe cross-border movement. Following the COVID-19 pandemic, we investigate whether effective strategies generalize across diseases and variants. For four SARS-CoV-2 variants and influenza A-H1N1, we simulated 21 strategy families of varying test types and frequencies, quantifying expected transmission risk, relative to no control, by strategy family and quarantine length. We also determined minimum quarantine lengths to suppress relative risk below given thresholds. SARS-CoV-2 variants showed similar relative risk across strategy families and quarantine lengths, with at most 2 days' between-variant difference in minimum quarantine lengths. ART-based and PCR-based strategies showed comparable effectiveness, with regular testing strategies requiring at most 9 days. For influenza A-H1N1, ART-based strategies were ineffective. Daily ART testing reduced relative risk only 9% faster than without regular testing. PCR-based strategies were moderately effective, with daily PCR (0-day delay) testing requiring 16 days for the second-most stringent threshold. Viruses with high typical viral loads and low transmission risk given low viral loads, such as SARS-CoV-2, are effectively controlled with moderate-sensitivity tests (ARTs) and modest quarantine periods. Viruses with low typical viral loads and substantial transmission risk at low viral loads, such as influenza A-H1N1, require high-sensitivity tests (PCR) and longer quarantine periods.


Subject(s)
COVID-19 , Communicable Diseases , Influenza A Virus, H1N1 Subtype , Influenza, Human , Humans , SARS-CoV-2/genetics , COVID-19/epidemiology , COVID-19/prevention & control , Influenza A Virus, H1N1 Subtype/genetics , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Pandemics/prevention & control
5.
Sci Rep ; 13(1): 2833, 2023 02 17.
Article in English | MEDLINE | ID: covidwho-2276086

ABSTRACT

Recent reports from the World Health Organization regarding Influenza A cases of zoonotic origin in humans (H1v and H9N2) and publications describing emergence swine Influenza A cases in humans together with "G4" Eurasian avian-like H1N1 Influenza A virus have drawn global attention to Influenza A pandemic threat. Additionally, the current COVID-19 epidemic has stressed the importance of surveillance and preparedness to prevent potential outbreaks. One feature of the QIAstat-Dx Respiratory SARS-CoV-2 panel is the double target approach for Influenza A detection of seasonal strains affecting humans using a generic Influenza A assay plus the three specific human subtype assays. This work explores the potential use of this double target approach in the QIAstat-Dx Respiratory SARS-Co-V-2 Panel as a tool to detect zoonotic Influenza A strains. A set of recently recorded H9 and H1 spillover strains and the G4 EA Influenza A strains as example of recent zoonotic Flu A strains were subjected to detection prediction with QIAstat-Dx Respiratory SARS-CoV-2 Panel using commercial synthetic dsDNA sequences. In addition, a large set of available commercial human and non-human influenza A strains were also tested using QIAstat-Dx Respiratory SARS-CoV-2 Panel for a better understanding of detection and discrimination of Influenza A strains. Results show that QIAstat-Dx Respiratory SARS-CoV-2 Panel generic Influenza A assay detects all the recently recorded H9, H5 and H1 zoonotic spillover strains and all the G4 EA Influenza A strains. Additionally, these strains yielded negative results for the three-human seasonal IAV (H1, H3 and H1N1 pandemic) assays. Additional non-human strains corroborated those results of Flu A detection with no subtype discrimination, whereas human Influenza strains were positively discriminated. These results indicate that QIAstat-Dx Respiratory SARS-CoV-2 Panel could be a useful tool to diagnose zoonotic Influenza A strains and differentiate them from the seasonal strains commonly affecting humans.


Subject(s)
COVID-19 , Influenza A Virus, H1N1 Subtype , Influenza A Virus, H9N2 Subtype , Influenza, Human , Humans , SARS-CoV-2 , Influenza A Virus, H1N1 Subtype/genetics
6.
Methods Mol Biol ; 2610: 109-127, 2023.
Article in English | MEDLINE | ID: covidwho-2245117

ABSTRACT

Influenza A virus H1N1, a respiratory virus transmitted via droplets and responsible for the global pandemic in 2009, belongs to the Orthomyxoviridae family, a single-negative-stranded RNA. It possesses glycoprotein spikes neuraminidase (NA), hemagglutinin (HA), and a matrix protein named M2. The Covid-19 pandemic affected the world population belongs to the respiratory virus category is currently mutating, this can also be observed in the case of H1N1 influenza A virus. Mutations in H1N1 can enhance the viral capacity which can lead to another pandemic. This virus affects children below 5 years, pregnant women, old age people, and immunocompromised individuals due to its high viral capacity. Its early detection is necessary for the patient's recovery time. In this book chapter, we mainly focus on the detection methods for H1N1, from traditional ones to the most advance including biosensors, RT-LAMP, multi-fluorescent PCR.


Subject(s)
COVID-19 , Influenza A Virus, H1N1 Subtype , Influenza A virus , Influenza, Human , Pregnancy , Child , Humans , Female , Influenza A Virus, H1N1 Subtype/genetics , Pandemics , Sensitivity and Specificity , COVID-19/epidemiology , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Influenza A virus/genetics , Neuraminidase/genetics , RNA, Viral/genetics
7.
Influenza Other Respir Viruses ; 17(1): e13092, 2023 01.
Article in English | MEDLINE | ID: covidwho-2213680

ABSTRACT

BACKGROUND: Persons experiencing homelessness face increased risk of influenza as overcrowding in congregate shelters can facilitate influenza virus spread. Data regarding on-site influenza testing and antiviral treatment within homeless shelters remain limited. METHODS: We conducted a cluster-randomized stepped-wedge trial of point-of-care molecular influenza testing coupled with antiviral treatment with baloxavir or oseltamivir in residents of 14 homeless shelters in Seattle, WA, USA. Residents ≥3 months with cough or ≥2 acute respiratory illness (ARI) symptoms and onset <7 days were eligible. In control periods, mid-nasal swabs were tested for influenza by reverse transcription polymerase chain reaction (RT-PCR). The intervention period included on-site rapid molecular influenza testing and antiviral treatment for influenza-positives if symptom onset was <48 h. The primary endpoint was monthly influenza virus infections in the control versus intervention periods. Influenza whole genome sequencing was performed to assess transmission and antiviral resistance. RESULTS: During 11/15/2019-4/30/2020 and 11/2/2020-4/30/2021, 1283 ARI encounters from 668 participants were observed. Influenza virus was detected in 51 (4%) specimens using RT-PCR (A = 14; B = 37); 21 influenza virus infections were detected from 269 (8%) intervention-eligible encounters by rapid molecular testing and received antiviral treatment. Thirty-seven percent of ARI-participant encounters reported symptom onset < 48 h. The intervention had no effect on influenza virus transmission (adjusted relative risk 1.73, 95% confidence interval [CI] 0.50-6.00). Of 23 influenza genomes, 86% of A(H1N1)pdm09 and 81% of B/Victoria sequences were closely related. CONCLUSION: Our findings suggest feasibility of influenza test-and-treat strategies in shelters. Additional studies would help discern an intervention effect during periods of increased influenza activity.


Subject(s)
Ill-Housed Persons , Influenza A Virus, H1N1 Subtype , Influenza, Human , Orthomyxoviridae Infections , Humans , Influenza, Human/diagnosis , Influenza, Human/drug therapy , Influenza, Human/epidemiology , Influenza A Virus, H1N1 Subtype/genetics , Oseltamivir/therapeutic use , Antiviral Agents/therapeutic use , Orthomyxoviridae Infections/drug therapy
8.
Mol Biol Evol ; 40(2)2023 02 03.
Article in English | MEDLINE | ID: covidwho-2189385

ABSTRACT

Some viruses (e.g., human immunodeficiency virus 1 and severe acute respiratory syndrome coronavirus 2) have been experimentally proposed to accelerate features of human aging and of cellular senescence. These observations, along with evolutionary considerations on viral fitness, raised the more general puzzling hypothesis that, beyond documented sources in human genetics, aging in our species may also depend on virally encoded interactions distorting our aging to the benefits of diverse viruses. Accordingly, we designed systematic network-based analyses of the human and viral protein interactomes, which unraveled dozens of viruses encoding proteins experimentally demonstrated to interact with proteins from pathways associated with human aging, including cellular senescence. We further corroborated our predictions that specific viruses interfere with human aging using published experimental evidence and transcriptomic data; identifying influenza A virus (subtype H1N1) as a major candidate age distorter, notably through manipulation of cellular senescence. By providing original evidence that viruses may convergently contribute to the evolution of numerous age-associated pathways through co-evolution, our network-based and bipartite network-based methodologies support an ecosystemic study of aging, also searching for genetic causes of aging outside a focal aging species. Our findings, predicting age distorters and targets for anti-aging therapies among human viruses, could have fundamental and practical implications for evolutionary biology, aging study, virology, medicine, and demography.


Subject(s)
Aging , Influenza A Virus, H1N1 Subtype , Influenza A virus , Humans , Aging/genetics , Influenza A virus/genetics , Influenza A Virus, H1N1 Subtype/genetics , Viral Proteins/genetics , Biological Coevolution , Cellular Senescence
9.
Anal Chim Acta ; 1242: 340812, 2023 Feb 15.
Article in English | MEDLINE | ID: covidwho-2164922

ABSTRACT

Currently, the coronavirus disease 2019 (COVID-19) caused by the outbreak of a novel coronavirus (SARS-CoV-2) is spreading rapidly worldwide. Due to the high incidence of influenza coinciding with SARS-CoV-2, rapid detection is crucial to prevent spreading. Here, we present an integrated dual-layer microfluidic platform for specific and highly sensitive SARS-CoV-2, influenza viruses A (FluA) H1N1, H3N2, and influenza virus B (FluB) simultaneous detection. The platform includes a dual microchip (Dµchip) and a portable detection device for real-time fluorescence detection, temperature control and online communication. The Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) and Cas12a cleavage were performed on the Dµchip. The limit of detection (LoD) of the Dµchip assay was 10 copies for SARS-CoV-2, FluA H1N1, H3N2, and FluB RNAs. The Dµchip assay yielded no cross-reactivity against other coronaviruses, so it was suitable for the screening of multiple viruses. Moreover, the positive percentage agreement (PPA) and negative percentage agreement (NPA) of the assay were 97.9% and 100%, respectively, in 75 clinical samples compared to data from RT-PCR-based assays. Furthermore, the assay allowed the detection SARS-CoV-2 and influenza viruses in spiked samples. Overall, the present platform would provide a rapid method for the screening of multiple viruses in hospital emergency, community and primary care settings and facilitate the remote diagnosis and outbreak control of the COVID-19.


Subject(s)
COVID-19 , Influenza A Virus, H1N1 Subtype , Humans , COVID-19/diagnosis , SARS-CoV-2 , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H3N2 Subtype/genetics , Microfluidics , Nucleic Acid Amplification Techniques/methods , Sensitivity and Specificity , RNA, Viral
10.
Eur J Clin Microbiol Infect Dis ; 41(12): 1445-1449, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2085399

ABSTRACT

With the COVID-19 pandemic still ongoing, the annual season of influenza and other respiratory virus epidemics has arrived. Specimens from patients suspected of respiratory viruses infection were collected. Viral detection was performed following RNA extraction and real-time RT-PCR. During the study period, we received and tested a total of 606 specimens. Rhinovirus virus was the viral type most prevalent, detected in 186 (45.47%) specimens. The age range of patients positive for influenza A, influenza A (H1N1), and influenza B was 18 days to 13 years. With female prevalence for this viral type, cough and asthma were the main clinical manifestations presented by this viral type. Our results indicate that rhinoviruses, adenoviruses, metapneumoviruses, and influenza are among the most important agents of ARI in pediatrics. The epidemic period of respiratory infections observed in Goiânia can be useful for planning and implementing some prevention strategies.


Subject(s)
COVID-19 , Influenza A Virus, H1N1 Subtype , Influenza, Human , Respiratory Tract Infections , Viruses , Child , Humans , Female , Influenza, Human/epidemiology , Influenza A Virus, H1N1 Subtype/genetics , Prevalence , Pandemics , Viruses/genetics , Rhinovirus/genetics
11.
Lab Chip ; 22(20): 3933-3941, 2022 10 11.
Article in English | MEDLINE | ID: covidwho-2028739

ABSTRACT

For rapid detection of the COVID-19 infection, the digital polymerase chain reaction (dPCR) with higher sensitivity and specificity has been presented as a promising method of point-of-care testing (POCT). Unlike the conventional real-time PCR (qPCR), the dPCR system allows absolute quantification of the target DNA without a calibration curve. Although a number of dPCR systems have previously been reported, most of these previous assays lack multiplexing capabilities. As different variants of COVID-19 have rapidly emerged, there is an urgent need for highly specific multiplexed detection systems. Additionally, the advances in the Internet of Things (IoT) technology have enabled the onsite detection of infectious diseases. Here, we present an IoT-integrated multiplexed dPCR (IM-dPCR) system involving sample compartmentalization, DNA amplification, fluorescence imaging, and quantitative analysis. This IM-dPCR system comprises three modules: a plasmonic heating-based thermal cycler, a multi-color fluorescence imaging set-up, and a firmware control module. Combined with a custom-developed smartphone application built on an IoT platform, the IM-dPCR system enabled automatic processing, data collection, and cloud storage. Using a self-priming microfluidic chip, 9 RNA groups (e.g., H1N1, H3N2, IFZ B, DENV2, DENV3, DENV4, OC43, 229E, and NL63) associated with three infectious diseases (e.g., influenza, dengue, and human coronaviruses) were analyzed with higher linearity (>98%) and sensitivity (1 copy per µL). The IM-dPCR system exhibited comparable analytical accuracy to commercial qPCR platforms. Therefore, this IM-dPCR system plays a crucial role in the onsite detection of infectious diseases.


Subject(s)
COVID-19 , Communicable Diseases , Influenza A Virus, H1N1 Subtype , COVID-19/diagnosis , COVID-19 Testing , Communicable Diseases/diagnosis , DNA/genetics , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H3N2 Subtype/genetics , RNA , Real-Time Polymerase Chain Reaction/methods
12.
Viruses ; 14(8)2022 07 30.
Article in English | MEDLINE | ID: covidwho-2024273

ABSTRACT

Annual vaccination against influenza is the best tool to prevent deaths and hospitalizations. Regular updates of trivalent inactivated influenza vaccines (TIV) are necessary due to high mutation rates in influenza viruses. TIV effectiveness is affected by antigenic mismatches, age, previous immunity, and other host factors. Studying TIV effectiveness annually in different populations is critical. The serological responses to Southern-Hemisphere TIV and circulating influenza strains were evaluated in 2018-2020 among Brazilian volunteers, using hemagglutination inhibition (HI) assays. Post-vaccination titers were corrected to account for pre-vaccination titers. Our population achieved >83% post-vaccination seroprotection levels, whereas seroconversion rates ranged from 10% to 46%. TIV significantly enhanced antibody titers and seroprotection against all prior and contemporary vaccine and circulating strains tested. Strong cross-reactive responses were detected, especially between H1N1 subtypes. A/Singapore/INFIMH-16-0019/2016, included in the 2018 TIV, induced the poorest response. Significant titer and seroprotection reductions were observed 6 and 12 months after vaccination. Age had a slight effect on TIV response, whereas previous vaccination was associated with lower seroconversion rates and titers. Despite this, TIV induced high seroprotection for all strains, in all groups. Regular TIV evaluations, based on regional influenza strain circulation, should be conducted and the factors affecting response studied.


Subject(s)
Influenza A Virus, H1N1 Subtype , Influenza Vaccines , Influenza, Human , Adult , Antibodies, Viral , Brazil/epidemiology , Hemagglutination Inhibition Tests , Humans , Influenza A Virus, H1N1 Subtype/genetics , Seasons , Vaccines, Inactivated
13.
Viruses ; 14(9)2022 08 29.
Article in English | MEDLINE | ID: covidwho-2006223

ABSTRACT

Influenza circulation was substantially reduced after March 2020 in the European region and globally due to the wide introduction of non-pharmaceutical interventions (NPIs) against COVID-19. The virus, however, has been actively circulating in natural reservoirs. In summer 2021, NPIs were loosened in Russia, and influenza activity resumed shortly thereafter. Here, we summarize the epidemiological and virological data on the influenza epidemic in Russia in 2021-2022 obtained by the two National Influenza Centers. We demonstrate that the commonly used baseline for acute respiratory infection (ARI) is no longer sufficiently sensitive and BL for ILI incidence was more specific for early recognition of the epidemic. We also present the results of PCR detection of influenza, SARS-CoV-2 and other respiratory viruses as well as antigenic and genetic analysis of influenza viruses. Influenza A(H3N2) prevailed this season with influenza B being detected at low levels at the end of the epidemic. The majority of A(H3N2) viruses were antigenically and genetically homogenous and belonged to the clade 3C.2a1b.2a.2 of the vaccine strain A/Darwin/9/2021 for the season 2022-2023. All influenza B viruses belonged to the Victoria lineage and were similar to the influenza B/Austria/1359417/2021 virus. No influenza A(H1N1)pdm09 and influenza B/Yamagata lineage was isolated last season.


Subject(s)
COVID-19 , Influenza A Virus, H1N1 Subtype , Influenza Vaccines , Influenza, Human , COVID-19/epidemiology , COVID-19/prevention & control , Epidemiological Monitoring , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H3N2 Subtype/genetics , Influenza B virus/genetics , Influenza, Human/epidemiology , Influenza, Human/prevention & control , RNA, Viral/genetics , SARS-CoV-2/genetics , Seasons
14.
Signal Transduct Target Ther ; 7(1): 266, 2022 08 03.
Article in English | MEDLINE | ID: covidwho-1972575

ABSTRACT

Defective interfering genes (DIGs) are short viral genomes and interfere with wild-type viral replication. Here, we demonstrate that the new designed SARS-CoV-2 DIG (CD3600) can significantly inhibit the replication of SARS-CoV-2 including Alpha, Delta, Kappa and Omicron variants in human HK-2 cells and influenza DIG (PAD4) can significantly inhibit influenza virus replication in human A549 cells. One dose of influenza DIGs prophylactically protects 90% mice from lethal challenge of A(H1N1)pdm09 virus and CD3600 inhibits SARS-CoV-2 replication in hamster lungs when DIGs are administrated to lungs one day before viral challenge. To further investigate the gene delivery vector in the respiratory tract, a peptidic TAT2-P1&LAH4, which can package genes to form small spherical nanoparticles with high endosomal escape ability, is demonstrated to dramatically increase gene expression in the lung airway. TAT2-P1&LAH4, with the dual-functional TAT2-P1 (gene-delivery and antiviral), can deliver CD3600 to significantly inhibit the replication of Delta and Omicron SARS-CoV-2 in hamster lungs. This peptide-based nanoparticle system can effectively transfect genes in lungs and deliver DIGs to inhibit SARS-CoV-2 variants and influenza virus in vivo, which provides the new insight into the drug delivery system for gene therapy against respiratory viruses.


Subject(s)
COVID-19 , Influenza A Virus, H1N1 Subtype , Influenza A virus , Influenza, Human , Nanoparticles , Animals , COVID-19/genetics , Cricetinae , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza, Human/prevention & control , Mice , Peptides/genetics , Peptides/pharmacology , SARS-CoV-2/genetics
15.
EMBO Rep ; 23(8): e55393, 2022 08 03.
Article in English | MEDLINE | ID: covidwho-1955118

ABSTRACT

In 1977, the world witnessed both the eradication of smallpox and the beginning of the modern age of genomics. Over the following half-century, 7 epidemic viruses of international concern galvanized virologists across the globe and led to increasingly extensive virus genome sequencing. These sequencing efforts exerted over periods of rapid adaptation of viruses to new hosts, in particular, humans provide insight into the molecular mechanisms underpinning virus evolution. Investment in virus genome sequencing was dramatically increased by the unprecedented support for phylogenomic analyses during the COVID-19 pandemic. In this review, we attempt to piece together comprehensive molecular histories of the adaptation of variola virus, HIV-1 M, SARS, H1N1-SIV, MERS, Ebola, Zika, and SARS-CoV-2 to the human host. Disruption of genes involved in virus-host interaction in animal hosts, recombination including genome segment reassortment, and adaptive mutations leading to amino acid replacements in virus proteins involved in host receptor binding and membrane fusion are identified as the key factors in the evolution of epidemic viruses.


Subject(s)
COVID-19 , Influenza A Virus, H1N1 Subtype , Zika Virus Infection , Zika Virus , Animals , COVID-19/epidemiology , COVID-19/genetics , Evolution, Molecular , Genome, Viral , Humans , Influenza A Virus, H1N1 Subtype/genetics , Pandemics , SARS-CoV-2/genetics , Zika Virus/genetics
17.
J Med Virol ; 94(11): 5325-5335, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-1935706

ABSTRACT

Establishment of rapid on-site detection technology capable of concurrently detecting SARS-Cov-2 and influenza A virus is urgent to effectively control the epidemic from these two types of important viruses. Accordingly, we developed a reusable dual-channel optical fiber immunosensor (DOFIS), which utilized the evanescent wave-sensing properties and tandem detection mode of the mobile phase, effectively accelerating the detection process such that it can be completed within 10 min. It could detect the nucleoprotein of multiple influenza A viruses (H1N1, H3N2, and H7N9), as well as the spike proteins of the SARS-CoV-2 Omicron and Delta variants, and could respond to 20 TCID50 /ml SARS-CoV-2 pseudovirus and 100 TCID50 /ml influenza A (A/PR/8/H1N1), presenting lower limit of detection and wider linear range than enzyme-linked immunosorbent assay. The detection results on 26 clinical samples for SARS-CoV-2 demonstrated its specificity (100%) and sensitivity (94%), much higher than the sensitivity of commercial colloidal gold test strip (35%). Particularly, DOFIS might be reused more than 80 times, showing not only cost-saving but also potential in real-time monitoring of the pathogenic viruses. Therefore, this newly-developed DOFIS platform is low cost, simple to operate, and has broad spectrum detection capabilities for SARS-CoV-2 mutations and multiple influenza A strains. It may prove suitable for deployment as a rapid on-site screening and surveillance technique for infectious disease.


Subject(s)
Biosensing Techniques , COVID-19 , Influenza A Virus, H1N1 Subtype , Influenza A Virus, H7N9 Subtype , Influenza, Human , Humans , Immunoassay , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H3N2 Subtype/genetics , Influenza, Human/diagnosis , SARS-CoV-2/genetics
18.
Int J Infect Dis ; 121: 195-202, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1851259

ABSTRACT

OBJECTIVES: Because of the spread of the Omicron variant, many countries have experienced COVID-19 case numbers unseen since the start of the pandemic. We aimed to compare the epidemiological characteristics of Omicron with previous variants and different strains of influenza to provide context for public health responses. METHODS: We developed transmission models for SARS-CoV-2 variants and influenza, in which transmission, death, and vaccination rates were taken to be time-varying. We fit our model based on publicly available data in South Africa, the United States, and Canada. We used this model to evaluate the relative transmissibility and mortality of Omicron compared with previous variants and influenza. RESULTS: We found that Omicron is more transmissible and less fatal than both seasonal and 2009 H1N1 influenza and the Delta variant; these characteristics make Omicron epidemiologically more similar to influenza than it is to Delta. We estimate that as of February 7, 2022, booster doses have prevented 4.29×107 and 1.14×106 Omicron infections in the United States and Canada, respectively. CONCLUSION: Our findings indicate that the high infectivity of Omicron will keep COVID-19 endemic, similar to influenza. However, because of Omicron's lower fatality rate, our work suggests that human populations living with SARS-CoV-2 are most likely.


Subject(s)
COVID-19 , Influenza A Virus, H1N1 Subtype , Influenza, Human , Mutation , SARS-CoV-2 , COVID-19/epidemiology , COVID-19/virology , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza, Human/prevention & control , Influenza, Human/virology , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , United States/epidemiology
19.
J Virol ; 96(5): e0179121, 2022 03 09.
Article in English | MEDLINE | ID: covidwho-1799229

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and seasonal influenza viruses are cocirculating in the human population. However, only a few cases of viral coinfection with these two viruses have been documented in humans with some people having severe disease and others mild disease. To examine this phenomenon, ferrets were coinfected with SARS-CoV-2 and human seasonal influenza A viruses (IAVs; H1N1 or H3N2) and were compared to animals that received each virus alone. Ferrets were either immunologically naive to both viruses or vaccinated with the 2019 to 2020 split-inactivated influenza virus vaccine. Coinfected naive ferrets lost significantly more body weight than ferrets infected with each virus alone and had more severe inflammation in both the nose and lungs compared to that of ferrets that were single infected with each virus. Coinfected, naive animals had predominantly higher IAV titers than SARS-CoV-2 titers, and IAVs were efficiently transmitted by direct contact to the cohoused ferrets. Comparatively, SARS-CoV-2 failed to transmit to the ferrets that cohoused with coinfected ferrets by direct contact. Moreover, vaccination significantly reduced IAV titers and shortened the viral shedding but did not completely block direct contact transmission of the influenza virus. Notably, vaccination significantly ameliorated influenza-associated disease by protecting vaccinated animals from severe morbidity after IAV single infection or IAV and SARS-CoV-2 coinfection, suggesting that seasonal influenza virus vaccination is pivotal to prevent severe disease induced by IAV and SARS-CoV-2 coinfection during the COVID-19 pandemic. IMPORTANCE Influenza A viruses cause severe morbidity and mortality during each influenza virus season. The emergence of SARS-CoV-2 infection in the human population offers the opportunity to potential coinfections of both viruses. The development of useful animal models to assess the pathogenesis, transmission, and viral evolution of these viruses as they coinfect a host is of critical importance for the development of vaccines and therapeutics. The ability to prevent the most severe effects of viral coinfections can be studied using effect coinfection ferret models described in this report.


Subject(s)
Antibodies, Viral/blood , COVID-19/prevention & control , Coinfection/prevention & control , Influenza Vaccines/immunology , Orthomyxoviridae Infections/prevention & control , Animals , COVID-19/immunology , Female , Ferrets/immunology , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H3N2 Subtype/genetics , Influenza A Virus, H3N2 Subtype/immunology , Orthomyxoviridae Infections/immunology , Vaccination , Virus Shedding
20.
Microb Biotechnol ; 15(5): 1301-1317, 2022 05.
Article in English | MEDLINE | ID: covidwho-1752469

ABSTRACT

The COVID-19 pandemic goes into its third year and the world population is longing for an end to the pandemic. Computer simulations of the future development of the pandemic have wide error margins and predictions on the evolution of new viral variants of SARS-CoV-2 are uncertain. It is thus tempting to look into the development of historical viral respiratory pandemics for insight into the dynamic of pandemics. The Spanish flu pandemic of 1918 caused by the influenza virus H1N1 can here serve as a potential model case. Epidemiological observations on the shift of influenza mortality from very young and old subjects to high mortality in young adults delimitate the pandemic phase of the Spanish flu from 1918 to 1920. The identification and sequencing of the Spanish flu agent allowed following the H1N1 influenza virus after the acute pandemic phase. During the 1920s H1N1 influenza virus epidemics with substantial mortality were still observed. As late as 1951, H1N1 strains of high virulence evolved but remained geographically limited. Until 1957, the H1N1 virus evolved by accumulation of mutations ('antigenic drift') and some intratypic reassortment. H1N1 viruses were then replaced by the pandemic H2N2 influenza virus from 1957, which was in 1968 replaced by the pandemic H3N2 influenza virus; both viruses were descendants from the Spanish flu agent but showed the exchange of entire gene segments ('antigenic shift'). In 1977, H1N1 reappeared from an unknown source but caused only mild disease. However, H1N1 achieved again circulation in the human population and is now together with the H3N2 influenza virus an agent of seasonal influenza winter epidemics.


Subject(s)
COVID-19 , Influenza A Virus, H1N1 Subtype , Influenza A virus , Influenza Pandemic, 1918-1919 , Influenza, Human , History, 20th Century , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H3N2 Subtype/genetics , Influenza A virus/genetics , Pandemics , SARS-CoV-2 , Young Adult
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