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1.
J Med Virol ; 95(2): e28489, 2023 02.
Article in English | MEDLINE | ID: covidwho-2267040

ABSTRACT

Social distancing, mask-wearing, and travel restrictions during the COVID-19 pandemic have significantly impacted the spread of influenza viruses. The objectives of this study were to analyze the pattern of influenza virus circulation with respect to that of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Bulgaria during the 2021-2022 season and to perform a phylogenetic/molecular analysis of the hemagglutinin (HA) and neuraminidase (NA) sequences of representative influenza strains. Influenza infection was confirmed using real-time reverse transcription polymerase chain reaction in 93 (4.2%) of the 2193 patients with acute respiratory illness tested wherein all detected viruses were subtyped as A(H3N2). SARS-CoV-2 was identified in 377 (24.3%) of the 1552 patients tested. Significant differences in the incidence of influenza viruses and SARS-CoV-2 were found between individual age groups, outpatients/inpatients, and in the seasonal distribution of cases. Two cases of coinfections were identified. In hospitalized patients, the Ct values of influenza viruses at admission were lower in adults aged ≥65 years (indicating higher viral load) than in children aged 0-14 years (p < 0.05). In SARS-CoV-2-positive inpatients, this association was not statistically significant. HA genes of all A(H3N2) viruses analyzed belonged to subclade 3C.2a1b.2a. The sequenced viruses carried 11 substitutions in HA and 5 in NA, in comparison to the vaccine virus A/Cambodia/e0826360/2020, including several substitutions in the HA antigenic sites B and C. This study revealed extensive changes in the typical epidemiology of influenza infection, including a dramatic reduction in the number of cases, diminished genetic diversity of circulating viruses, changes in age, and seasonal distribution of cases.


Subject(s)
COVID-19 , Influenza Vaccines , Influenza, Human , Adult , Child , Humans , Influenza A Virus, H3N2 Subtype/genetics , SARS-CoV-2/genetics , Seasons , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Bulgaria/epidemiology , Phylogeny , Prevalence , Pandemics , COVID-19/epidemiology , RNA, Viral/genetics , Sequence Analysis, DNA , Hemagglutinins , Neuraminidase/genetics
2.
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
3.
Vaccine ; 40(38): 5569-5578, 2022 09 09.
Article in English | MEDLINE | ID: covidwho-2016159

ABSTRACT

Alphavirus-derived RNA replicon particle (RP) vaccines represent the next generation of swine influenza A virus (IAV) vaccines, as they were shown to be safe, effective, and offer advantages over traditional vaccine platforms. IAV is a significant respiratory pathogen of swine and there is a critical need to improve current commercial swine IAV vaccine platforms. Adjuvanted whole inactivated virus (WIV) IAV swine vaccines provide limited heterologous protection and may lead to vaccine-associated enhanced respiratory disease (VAERD). This study investigated the ability of RP IAV hemagglutinin (HA) vaccines to avoid VAERD and evaluated experimental multivalent HA and neuraminidase (NA) RP vaccines. RP vaccines were formulated with HA or NA heterologous or homologous to the challenge virus in monovalent HA or HA and NA bivalent combinations (HA/NA bivalent). Pigs were vaccinated with an HA RP, HA/NA bivalent RP, or heterologous HA WIV, followed by IAV challenge and necropsy 5 days post infection. RP vaccines provided homologous protection from challenge and induced robust peripheral and local antibody responses. The RP vaccine did not induce VAERD after challenge with a virus containing the heterologous HA, in contrast to the traditional WIV vaccine. The HA monovalent and HA/NA bivalent RP vaccines showed superior protection compared to traditional WIV. Additionally, the RP platform allows greater flexibility to adjust HA and NA content to reflect circulating IAV in swine antigenic diversity.


Subject(s)
Influenza A virus , Influenza Vaccines , Influenza, Human , Orthomyxoviridae Infections , Respiratory Tract Diseases , Swine Diseases , Animals , Antibodies, Viral , Hemagglutinins , Humans , Neuraminidase/genetics , Replicon , Swine
5.
Infect Dis Poverty ; 11(1): 74, 2022 Jun 29.
Article in English | MEDLINE | ID: covidwho-1910355

ABSTRACT

BACKGROUND: During the coronavirus disease 2019 (COVID-19) pandemic, seasonal influenza activity declined globally and remained below previous seasonal levels, but intensified in China since 2021. Preventive measures to COVID-19 accompanied by different epidemic characteristics of influenza in different regions of the world. To better respond to influenza outbreaks under the COVID-19 pandemic, we analyzed the epidemiology, antigenic and genetic characteristics, and antiviral susceptibility of influenza viruses in the mainland of China during 2020-2021. METHODS: Respiratory specimens from influenza like illness cases were collected by sentinel hospitals and sent to network laboratories in Chinese National Influenza Surveillance Network. Antigenic mutation analysis of influenza virus isolates was performed by hemagglutination inhibition assay. Next-generation sequencing was used for genetic analyses. We also conducted molecular characterization and phylogenetic analysis of circulating influenza viruses. Viruses were tested for resistance to antiviral medications using phenotypic and/or sequence-based methods. RESULTS: In the mainland of China, influenza activity recovered in 2021 compared with that in 2020 and intensified during the traditional influenza winter season, but it did not exceed the peak in previous years. Almost all viruses isolated during the study period were of the B/Victoria lineage and were characterized by genetic diversity, with the subgroup 1A.3a.2 viruses currently predominated. 37.8% viruses tested were antigenically similar to reference viruses representing the components of the vaccine for the 2020-2021 and 2021-2022 Northern Hemisphere influenza seasons. In addition, China has a unique subgroup of 1A.3a.1 viruses. All viruses tested were sensitive to neuraminidase inhibitors and endonuclease inhibitors, except two B/Victoria lineage viruses identified to have reduced sensitivity to neuraminidase inhibitors. CONCLUSIONS: Influenza activity increased in the mainland of China in 2021, and caused flu season in the winter of 2021-2022. Although the diversity of influenza (sub)type decreases, B/Victoria lineage viruses show increased genetic and antigenic diversity. The world needs to be fully prepared for the co-epidemic of influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus globally.


Subject(s)
COVID-19 , Influenza, Human , Orthomyxoviridae , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19/epidemiology , China/epidemiology , Humans , Influenza, Human/epidemiology , Neuraminidase/genetics , Orthomyxoviridae/genetics , Pandemics , Phylogeny , SARS-CoV-2 , Seasons
6.
Emerg Infect Dis ; 28(3): 639-649, 2022 03.
Article in English | MEDLINE | ID: covidwho-1770988

ABSTRACT

Evaluating the stability of highly pathogenic avian influenza viruses on human skin and measuring the effectiveness of disinfectants are crucial for preventing contact disease transmission. We constructed an evaluation model using autopsy skin samples and evaluated factors that affect the stability and disinfectant effectiveness for various subtypes. The survival time of the avian influenza A(H5N1) virus on plastic surfaces was ≈26 hours and on skin surfaces ≈4.5 hours, >2.5-fold longer than other subtypes. The effectiveness of a relatively low ethanol concentration (32%-36% wt/wt) against the H5N1 subtype was substantially reduced compared with other subtypes. Moreover, recombinant viruses with the neuraminidase gene of H5N1 survived longer on plastic and skin surfaces than other recombinant viruses and were resistant to ethanol. Our results imply that the H5N1 subtype poses a higher contact transmission risk because of its higher stability and ethanol resistance, which might depend on the neuraminidase protein.


Subject(s)
Influenza A Virus, H5N1 Subtype , Influenza A virus , Influenza in Birds , Influenza, Human , Animals , Ethanol/pharmacology , Humans , Influenza A Virus, H5N1 Subtype/genetics , Neuraminidase/genetics
7.
Curr Opin Pulm Med ; 28(3): 199-204, 2022 05 01.
Article in English | MEDLINE | ID: covidwho-1672375

ABSTRACT

PURPOSE OF REVIEW: To review the clinico-epidemiological aspects of influenza in the context of the Coronavirus Disease 2019 (COVID-19) pandemic; the recent advances in point-of-care molecular diagnostics and co-detection of influenza and coronaviruses, and the development of new influenza therapeutics. RECENT FINDINGS: Rates of influenza have declined globally since the 2020-2021 season; waning population immunity and uncertainty in vaccine strains could pose a risk in its significant resurgence, especially where pandemic public health interventions start being lifted. As symptoms are similar for influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, accurate, rapid diagnostics are needed to guide management. In addition to neuraminidase inhibitors, newer class of antivirals including polymerase inhibitors show promise in treating influenza infections in adults, children, and high-risk individuals. SUMMARY: This review summarizes the most recent data on rapid molecular diagnostics, including point-of-care tests and co-detection of influenza and SARS-CoV-2 viruses. The implications to inform clinical and infection control practices, and detection of antiviral resistance are discussed. The latest clinical trial data on neuraminidase inhibitors and polymerase inhibitors, their efficacy, limitations, and resistance concerns are reviewed.


Subject(s)
COVID-19 , Influenza Vaccines , Influenza, Human , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19/diagnosis , COVID-19/epidemiology , Child , Humans , Influenza Vaccines/therapeutic use , Influenza, Human/diagnosis , Influenza, Human/drug therapy , Influenza, Human/epidemiology , Neuraminidase/genetics , Pandemics , SARS-CoV-2
8.
Euro Surveill ; 26(27)2021 07.
Article in English | MEDLINE | ID: covidwho-1577032

ABSTRACT

BackgroundInfluenza virus presents a considerable challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid infection diagnosis, rationalising antimicrobial therapy, and supporting infection-control interventions.AimTo evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings.MethodsWe conducted Oxford Nanopore Technologies (Oxford, United Kingdom (UK)) metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic standards (Xpert Xpress Flu/RSV assay; BioFire FilmArray Respiratory Panel 2 assay). We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data.ResultsCompared to standard testing, Nanopore metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses. Of 59 samples with haemagglutinin subtype determined, 40 were H1 and 19 H3. We identified an influenza A(H3N2) genome encoding the oseltamivir resistance S331R mutation in neuraminidase, potentially associated with an emerging distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in a ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant community-circulating strain. We also detected other potentially pathogenic viruses and bacteria from the metagenome.ConclusionNanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Full genome generation can help investigate and manage nosocomial outbreaks.


Subject(s)
Cross Infection , Influenza, Human , Nanopores , Antiviral Agents/therapeutic use , Cross Infection/diagnosis , Cross Infection/drug therapy , Drug Resistance , Drug Resistance, Viral/genetics , Humans , Influenza A Virus, H3N2 Subtype/genetics , Influenza, Human/diagnosis , Influenza, Human/drug therapy , Influenza, Human/epidemiology , Metagenome , Neuraminidase/genetics , Seasons , United Kingdom
9.
Infect Genet Evol ; 81: 104270, 2020 07.
Article in English | MEDLINE | ID: covidwho-1452334

ABSTRACT

In the endemic settings of India, high CFR (3.6-7.02%) was observed in the consecutive 2009, 2015 and 2017 A/H1N1pdm09 outbreaks, though in eastern India CFR varied between 0 and 5.5% during same period. Recurrent outbreaks of pandemic Influenza A/H1N1pdm09, fragmented nationwide incidence data, lack of national policy for Influenza vaccination in India underscores the necessity for generating regional level data. Thus, during 2017-19, 4106 referred samples from patients hospitalized with severe acute respiratory illness (SARI) in eastern India were tested for A/H1N1pdm09 infection. Among which 16.5% (n = 677/4106) were found A/H1N1pdm09 positive. Individuals <20 years and middle-aged persons (40-60 years) were most susceptible to A/H1N1pdm09 infection. The vaccine strain (A/human/California/07/2009) which was globally used before 2017, clustered in a different lineage away from the representative eastern Indian strains in the phylogenetic dendrogram. The vaccine strain (A/human/Michigan/45/2015) used in India during the study period and the WHO recommended strain (A/human/Brisbane/02/2018) for 2019-20 flu season for the northern hemisphere, clustered with the circulating isolates in the same lineage-6b. Dissimilarities in the amino acids encompassing the antigenic epitopes were seen to be highest with the vaccine strain- A/human/California/07/2009. The significant amino acid variations in the circulating strains with the current WHO recommended vaccine strain, implies the exigency of continuous pandemic A/H1N1pdm09 surveillance studies in this epidemiological setting. The absence of any Oseltamivir resistant mutation (H275Y) in the neuraminidase gene of the current isolates suggests continuing use of Tamiflu® as an antiviral therapy in suspected subjects in this region.


Subject(s)
Antigenic Variation/genetics , Antigenic Variation/immunology , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/immunology , Influenza Vaccines/immunology , Influenza, Human/immunology , Adolescent , Adult , Amino Acid Substitution/genetics , Amino Acid Substitution/immunology , Child , Child, Preschool , Drug Resistance, Viral/genetics , Female , Humans , India , Influenza, Human/virology , Male , Middle Aged , Neuraminidase/genetics , Oseltamivir/therapeutic use , Phylogeny , Viral Proteins/genetics , Young Adult
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