No evidence of SARS-CoV-2 in hospitalized patients with severe acute respiratory syndrome in five Italian hospitals from 1st November 2019 to 29th February 2020

Background On 9th January 2020, China CDC reported a novel coronavirus (later named SARS-CoV-2) as the causative agent of the coronavirus disease 2019 (COVID-19). Identifying the first appearance of virus is of epidemiological importance to tracking and mapping the spread of SARS-CoV-2 in a country. We therefore conducted a retrospective observational study to detect SARS-CoV-2 in oropharyngeal samples collected from hospitalized patients with a Severe Acute Respiratory Infection (SARI) enrolled in the DRIVE (Development of Robust and Innovative Vaccine Effectiveness) study in five Italian hospitals (CIRI-IT BIVE hospitals network) (1st November 2019 – 29th February 2020). Objectives To acquire new information on the real trend in SARS-CoV-2 infection during pandemic phase I and to determine the possible early appearance of the virus in Italy. Materials and methods Samples were tested for influenza [RT-PCR assay (A/H1N1, A/H3N2, B/Yam, B/Vic)] in accordance with the DRIVE study protocol. Subsequently, swabs underwent molecular testing for SARS-COV-2. [one-step real-time multiplex retro-transcription (RT) PCR]. Results In the 1683 samples collected, no evidence of SARS-CoV-2 was found. Moreover, 28.3% (477/1683) of swabs were positive for influenza viruses, the majority being type A (358 vs 119 type B). A/H3N2 was predominant among influenza A viruses (55%); among influenza B viruses, B/Victoria was prevalent. The highest influenza incidence rate was reported in patients aged 0–17 years (40.3%) followed by those aged 18–64 years (24.4%) and ≥65 years (14.8%). Conclusions In Italy, some studies have shown the early circulation of SARS-CoV-2 in northern regions, those most severely affected during phase I of the pandemic. In central and southern regions, by contrast no early circulation of the virus was registered. These results are in line with ours. These findings highlight the need to continue to carry out retrospective studies, in order to understand the epidemiology of the novel coronavirus, to better identify the clinical characteristics of COVID-19 in comparison with other acute respiratory illnesses (ARI), and to evaluate the real burden of COVID-19 on the healthcare system.

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A multiplex one-step real-time RT-PCR assay for influenza surveillance

Eurosurveillance ◽

10.2807/ese.16.07.19798-en ◽

2011 ◽

Vol 16 (7) ◽

Author(s):

I Huber ◽

H Campe ◽

D Sebah ◽

C Hartberger ◽

R Konrad ◽

...

Keyword(s):

Real Time ◽

High Throughput ◽

Influenza A ◽

Multiplex Assay ◽

Influenza Viruses ◽

Influenza Surveillance ◽

Influenza B ◽

Rt Pcr ◽

Influenza A H1n1 ◽

One Step

For surveillance purposes real-time PCR assays for influenza viruses had to be adapted to the pandemic influenza A(H1N1)2009 strain. We combined published primers and probes for influenza A, influenza B and an internal amplification control with a detection system for influenza A(H1N1)2009 to set up a rapid, reliable, simple and cost-effective high-throughput multiplex one-step real-time RT-PCR. The workflow also includes automated sample preparation for high-throughput screening. The lower limit of detection of the multiplex assay was 3.5x102 RNA copies per PCR reaction. The diagnostic sensitivity of the multiplex assay was 87.7%, but increased to 99.4% for influenza-positive samples yielding Ct values of less than 34 cycles in the respective diagnostic assay. High specificity was confirmed by sequencing and correct detection of 15 reference samples from two quality assurance studies. The multiplex PCR was introduced for surveillance of samples from a network of general practitioners and paediatricians in Bavaria, Germany during the influenza pandemic of 2009. Comparison with surveillance data from reported cases proved the reliability of the multiplex assay for influenza surveillance programmes.

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Poor Vaccine Effectiveness against Influenza B-Related Severe Acute Respiratory Infection in a Temperate North Indian State (2019–2020): A Call for Further Data for Possible Vaccines with Closer Match

Vaccines ◽

10.3390/vaccines9101094 ◽

2021 ◽

Vol 9 (10) ◽

pp. 1094

Author(s):

Hyder Mir ◽

Inaamul Haq ◽

Parvaiz A. Koul

Keyword(s):

Influenza Vaccine ◽

Influenza A ◽

Respiratory Illness ◽

Vaccine Effectiveness ◽

Influenza Viruses ◽

Vaccine Uptake ◽

Influenza B ◽

Severe Acute Respiratory Infection ◽

Influenza A H1n1 ◽

Indian State

Influenza vaccine uptake in India is poor, and scant data exist regarding the effectiveness of influenza vaccine against hospitalization. Methods: From October 2019 to March 2020, vaccination status of 1219 patients (males n = 571, aged 5–107 years; median, 50 years) hospitalized with severe acute respiratory illness (SARI) was assessed. The patients were tested for influenza viruses and their subtypes by RT PCR. Sequencing of the HA gene was performed. Vaccine effectiveness (VE) against influenza subtypes was estimated by the test negative design. Results: A total of 336 (27.5%) patients were influenza-positive, with influenza B/Victoria accounting for 49.7% (n = 167), followed by influenza A/H1N1 (47.6%; n = 155) and influenza A/H3N2 (4.4%; n = 15). About 6.8% and 8.6% of the influenza-positive and influenza-negative patients, respectively, had been vaccinated. Adjusted VE for any influenza strain was 13% (95% CI −42 to 47), which for influenza B was 0%. HA sequencing revealed that influenza B samples mainly belonged to subclade V1A.3/133R with deletion of residues 163–165, as against the 2-aa deletion in influenza B/Colorado/06/2017 strain, contained in the vaccine. VE for influenza A/H1N1 was 55%. Conclusions: Poor VE due to a genetic mismatch between the circulating strain and the vaccine strain calls for efforts to reduce the mismatch.

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Sensitivity of influenza viruses to specific drugs in Russia during 2017−2020. The rare finds and perspective antivirals

Epidemiology and Infectious Diseases (Russian Journal) ◽

10.17816/eid46440 ◽

2020 ◽

Vol 25 (2) ◽

pp. 65-77

Author(s):

Natalia V. Breslav ◽

Kirill G. Krasnoslobotsev ◽

Evgeniya A. Mukasheva ◽

Elena S. Kirillova ◽

Alexandra G. Rosatkevich ◽

...

Keyword(s):

Influenza A ◽

Influenza Viruses ◽

Epidemiological Surveillance ◽

Influenza B Virus ◽

Influenza B ◽

Neuraminidase Inhibitors ◽

Chemotherapy Drugs ◽

Pdm09 Virus ◽

Severe Acute Respiratory Infection ◽

Influenza A H1n1

BACKGROUND: The article presents the results of studying the effectiveness of anti-influenza drugs in Russia in the period 20172020. The sensitivity of circulating strains of influenza viruses A(H1N1)pdm09, A(H3N2) and B to neuraminidase inhibitors oseltamivir, zanamivir and rimantadine was determined. The analysis of scientific articles by both domestic and foreign researchers on new promising chemotherapy drugs for influenza viruses was carried out. AIMS: study of the sensitivity of influenza viruses circulating strains to specific anti-influenza drugs in the framework of monitoring in the period 20172020. MATERIALS AND METHODS: The study was conducted within the framework of epidemiological surveillance of the influenza viruses circulation using the collection of the influenza etiology and epidemiology laboratory with the following criteria for selecting strains isolated from pregnant women, patients with complicated flu infection and severe acute respiratory infection (SARI), lethal outcomes, as well as patients undergoing treatment with specific drugs. Virological, immunological, and molecular genetic methods were used in the study, and following drugs substances were used: oseltamivir carboxylate, zanamivir, and rimantadine. RESULTS: For the period 20172020, the sensitivity of 541 influenza A and B viruses epidemic strains to anti-influenza drugs was studied. Most of the studied strains remained sensitive to neuraminidase inhibitors. The exceptions were: in 2017/2018 5 strains of the influenza A(H1N1)pdm09 virus resistant to oseltamivir and 2 strains of the influenza B virus, one with reduced sensitivity to oseltamivir, the second to zanamivir; in 2019/2020 influenza A(H1N1)pdm09 virus strain with reduced sensitivity to both drugs. In the 2018/2019 season, an influenza A/Moscow/246/2018 A(H1N1)pdm09 strain was found to be sensitive to rimantadine. CONCLUSIONS: The main and most common genetic markers of influenza viruses resistance to specific drugs are: for oseltamivir substitution H274Y in the influenza A(H1N1)pdm09 virus NA; for rimantadine substitution S31N in the influenza A(H1N1)pdm09 and A(H3N2) viruses M2 protein. Taking into account the low frequency of strains with reduced sensitivity to drugs with antineuraminidase activity, can confidently approve that they remain the drugs of choice for the treatment and prevention of influenza infection.

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DETECTION OF INFLUENZA VIRUSES AMONG HOSPITALIZED CASES SUFFERING FROM SEVERE ACUTE RESPIRATORY ILLNESS (SARI) IN SANA’A CITY, YEMEN

Universal Journal of Pharmaceutical Research ◽

10.22270/ujpr.v4i4.296 ◽

2019 ◽

Author(s):

Dina Abdulljabbar Abdullah Al-Ademi ◽

Abdulilah Hussein Al-Harazi ◽

Hassan A. Al-Shamahy ◽

Bushra Mohammed Jaadan

Keyword(s):

Mortality Rate ◽

Influenza A ◽

Respiratory Illness ◽

Hospitalized Patients ◽

Influenza Viruses ◽

Influenza Surveillance ◽

Influenza B ◽

Acute Respiratory Illness ◽

Influenza A H1n1 ◽

Severe Acute Respiratory Illness

Influenza is a major cause of morbidity and mortality around the world. So national influenza surveillance have been important for understanding the epidemiology of influenza over time. The aims of this study were to determine the prevalence rate of influenza viruses among hospitalized patients with severe acute respiratory illness (SARI), identify circulating types and subtypes of influenza viruses among them, and determine the risk factors associated with SARI. A total of 320 hospitalized patients suffering from SARI at Al Joumhouri University hospital in Sana’a city were enrolled; and their age was ranged from < 1 year to ≥ 56 years. Both nasopharyngeal and oro-pharyngeal swabs were collected from each patient and tested by using rRT-PCR technique for the detection of influenza A, influenza B and subtypes of influenza A viruses (A/H1N1(2009) and A/H3N2). The crude prevalent rate of influenza viruses among SARI patients was 10.9%;the female rate was 12.4%, and the male rate was 9.9%. The rate of Flu A in the total SARI cases was 5.9% and for Flu B was 5%. In addition 3.8% of SARI patients were suffering from influenza A/H3N2, 2.2% from influenza A/H1N1(2009) infections; and the mortality rate for influenza infections was 17.1%. Also, a high mortality rate was occurred in influenza infections in age groups 36-45 years and 6-15 years. Also, there was a significant association between flu infection; and 46-55 years group (OR=2.8), Winter time (OR=17.5), cardiac diseases (OR=9.1), and diabetic mellitus (OR=3.7). In conclusion: both influenza A and B were represented as a causative agents of SARI, and Influenza A/H3N2 was present subtype followed by A/H1N1(2009). The frequency of influenza viruses ascertain among SARI patients in Yemen highlights the need for health authorities to develop strategies to reduce morbidity among at-risk population in the course of vaccine recommendation.

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Comparison of the Sofia and Veritor Direct Antigen Detection Assay Systems for Identification of Influenza Viruses from Patient Nasopharyngeal Specimens

Journal of Clinical Microbiology ◽

10.1128/jcm.03441-14 ◽

2015 ◽

Vol 53 (4) ◽

pp. 1345-1347 ◽

Cited By ~ 10

Author(s):

G. P. Leonardi ◽

A. M. Wilson ◽

I. Mitrache ◽

A. R. Zuretti

Keyword(s):

Reverse Transcriptase ◽

Influenza A ◽

Point Of Care ◽

Antigen Detection ◽

Influenza Viruses ◽

Nasopharyngeal Swab ◽

Influenza B ◽

Rt Pcr ◽

Point Of Care Testing ◽

Detection Assay

Influenza antigen detection assays (Sofia fluorescent immunoassay [FIA] and Veritor) yield objective results, which are potentially useful for point-of-care testing. The assays were evaluated with reverse transcriptase PCR (RT-PCR) using 411 nasopharyngeal swab specimens. Sensitivity and specificity values (percentages) of 79.0/99.0 and 64.0/99.4 for influenza A and 92.9/96.7 and 78.6/98.7 for influenza B were obtained for the Sofia and Veritor assays, respectively.

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Sensitivity and Specificity of the Quidel Sofia Influenza A+B FIA Rapid Influenza Detection Test in Long-Term Care Facilities

Open Forum Infectious Diseases ◽

10.1093/ofid/ofx163.859 ◽

2017 ◽

Vol 4 (suppl_1) ◽

pp. S355-S355 ◽

Cited By ~ 1

Author(s):

Jonathan Temte ◽

Mary Checovich ◽

Shari Barlow ◽

Peter Shult ◽

Erik Reisdorf ◽

...

Keyword(s):

Sensitivity And Specificity ◽

Symptom Onset ◽

Influenza A ◽

Long Term Care ◽

Respiratory Viruses ◽

Influenza Viruses ◽

Influenza B ◽

Rt Pcr ◽

Term Care

Abstract Background Influenza is a significant pathogen for long-term care facility (LTCF) residents. As part of a randomized controlled trial to assess early detection of influenza in LTCFs, we deployed rapid influenza detection tests (RIDTs) at intervention LTCFs. Our primary objectives for this interim analysis were to evaluate the sensitivity and specificity of the Quidel Sofia® Influenza A+B Fluorescent Immunoassay RIDT in a high-risk, nontraditional population, and to describe the virology of acute respiratory infections (ARI) in LTCF residents. Methods Personnel at LCTFs identified cases of ARI, collected nasal specimens, and ran RIDTs from 10/21/2016 to 4/28/2017. The residual nasal swab and leftover lysis buffer were placed into a viral transport medium tube and sent to the Wisconsin State Laboratory of Hygiene for confirmatory influenza RT-PCR testing. In addition, all specimens were tested for other viruses using the Luminex NxTAG® Respiratory Pathogen Panel. Sensitivity and specificity of the Sofia RIDT were calculated using RT-PCR results as the reference standard. Results Specimens were collected from 228 residents (mean age = 71.3 ± 22.4 years). The mean time from symptom onset to specimen collection was 1.4 ± 1.6 days (range: 0-7 days). Respiratory viruses were identified in 134/228 cases (58.8%); influenza viruses (A: 7.5% and B: 14.5%) were the most commonly detected virus by PCR, followed by rhinovirus/enterovirus (13.2%), RSV (11.0%) and coronaviruses (10.1%). The sensitivities of Sofia RIDT for influenza A and influenza B were 77.8% (95% CI: 52.4–93.6%) and 80.0% (95% CI: 61.4–92.3%), respectively, with specificities of 98.4% (95.3–99.7%) and 97.1% (93.4–99.1%), respectively. Overall performance assessment for influenza A or B yielded a sensitivity of 79.2% (65.0–89.5%) and specificity of 96.1% (91.7–98.6%). The estimated likelihood of discovering one of the first two influenza cases at a LTCF using this RIDT is estimated to be ≥95.7%. Conclusion Although a wide constellation of respiratory viruses cause ARIs within LTCF populations, influenza is very common. Early ARI recognition in residents, with testing shortly after symptom onset, likely contributed to high performance of the Sofia RIDT. Use of RIDTs allows early identification of influenza with high sensitivity and specificity in elderly LTCF residents. Disclosures J. Temte, Quidel: Investigator, Research support

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Clinical evaluation of a fully automated, laboratory-developed multiplex RT-PCR assay integrating dual-target SARS-CoV-2 and influenza A/B detection on a high-throughput platform

Journal of Medical Microbiology ◽

10.1099/jmm.0.001295 ◽

2021 ◽

Author(s):

Dominik Nörz ◽

Armin Hoffmann ◽

Martin Aepfelbacher ◽

Susanne Pfefferle ◽

Marc Lütgehetmann

Keyword(s):

Clinical Evaluation ◽

High Throughput ◽

Influenza A ◽

Influenza Season ◽

Influenza Viruses ◽

Analytical Performance ◽

Influenza B ◽

Rt Pcr ◽

Pcr Assay ◽

Dual Target

Introduction. Laboratories worldwide are facing high demand for molecular testing during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, which might be further aggravated by the upcoming influenza season in the northern hemisphere. Gap Statement. Given that the symptoms of influenza are largely indistinguishable from those of coronavirus disease 2019 (COVID-19), both SARS-CoV-2 and the influenza viruses require concurrent testing by RT-PCR in patients presenting with symptoms of respiratory tract infection. Aim. We adapted and evaluated a laboratory-developed multiplex RT-PCR assay for simultaneous detection of SARS-CoV-2 (dual target), influenza A and influenza B (SC2/InflA/InflB-UCT) on a fully automated high-throughput system (cobas6800). Methodology. Analytical performance was assessed by serial dilution of quantified reference material and cell culture stocks in transport medium, including pretreatment for chemical inactivation. For clinical evaluation, residual portions of 164 predetermined patient samples containing SARS-CoV-2 (n=52), influenza A (n=43) or influenza B (n=19), as well as a set of negative samples, were subjected to the novel multiplex assay. Results. The assay demonstrated comparable analytical performance to currently available commercial tests, with limits of detection of 94.9 cp ml−1 for SARS-CoV-2, 14.6 cp ml−1 for influenza A and 422.3 cp ml−1 for influenza B. Clinical evaluation showed excellent agreement with the comparator assays (sensitivity of 98.1, 97.7 and 100 % for Sars-CoV-2 and influenza A and B, respectively). Conclusion. The SC2/InflA/InflB-UCT allows for efficient high-throughput testing for all three pathogens and thus provides streamlined diagnostics while conserving resources during the influenza season.

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An evaluation of the InDevR FluChip-8G insight microarray assay in characterizing influenza a viruses

Tropical Diseases Travel Medicine and Vaccines ◽

10.1186/s40794-021-00133-7 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Emily S. Bailey ◽

Xinye Wang ◽

Mai-juan Ma ◽

Guo-lin Wang ◽

Gregory C. Gray

Keyword(s):

Influenza A ◽

Influenza Viruses ◽

Time Range ◽

Influenza B ◽

Influenza A Viruses ◽

Laboratory Methods ◽

Duke University ◽

Multiple Viral Strains ◽

Rapid Characterization

AbstractInfluenza viruses are an important cause of disease in both humans and animals, and their detection and characterization can take weeks. In this study, we sought to compare classical virology techniques with a new rapid microarray method for the detection and characterization of a very diverse, panel of animal, environmental, and human clinical or field specimens that were molecularly positive for influenza A alone (n = 111), influenza B alone (n = 3), both viruses (n = 13), or influenza negative (n = 2) viruses. All influenza virus positive samples in this study were first subtyped by traditional laboratory methods, and later evaluated using the FluChip-8G Insight Assay (InDevR Inc. Boulder, CO) in laboratories at Duke University (USA) or at Duke Kunshan University (China). The FluChip-8G Insight multiplexed assay agreed with classical virologic techniques 59 (54.1%) of 109 influenza A-positive, 3 (100%) of the 3 influenza B-positive, 0 (0%) of 10 both influenza A- and B-positive samples, 75% of 24 environmental samples including those positive for H1, H3, H7, H9, N1, and N9 strains, and 80% of 22 avian influenza samples. It had difficulty with avian N6 types and swine H3 and N2 influenza specimens. The FluChip-8G Insight assay performed well with most human, environmental, and animal samples, but had some difficulty with samples containing multiple viral strains and with specific animal influenza strains. As classical virology methods are often iterative and can take weeks, the FluChip-8G Insight Assay rapid results (time range 8 to 12 h) offers considerable time savings. As the FluChip-8G analysis algorithm is expected to improve over time with addition of new subtypes and sample matrices, the FluChip-8G Insight Assay has considerable promise for rapid characterization of novel influenza viruses affecting humans or animals.

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Influenza: An Emerging and Re-emerging Public Health Threat in Nepal

Annals of Clinical Chemistry and Laboratory Medicine ◽

10.3126/acclm.v3i2.20737 ◽

2018 ◽

Vol 3 (2) ◽

pp. 1-2

Author(s):

Bishnu Prasad Upadhyay

Keyword(s):

Influenza Virus ◽

Influenza A ◽

Winter Season ◽

Emerging Infectious Diseases ◽

Influenza Viruses ◽

Influenza B ◽

Influenza A Viruses ◽

Influenza A H1n1 ◽

New Variant ◽

Seasonal Epidemics

Influenza virus type A and B are responsible for seasonal epidemics as well as pandemics in human. Influenza A viruses are further divided into two major groups namely, low pathogenic seasonal influenza (A/H1N1, A/H1N1 pdm09, A/H3N2) and highly pathogenic influenza virus (H5N1, H5N6, H7N9) on the basis of two surface antigens: hemagglutinin (HA) and neuraminidase (NA). Mutations, including substitutions, deletions, and insertions, are one of the most important mechanisms for producing new variant of influenza viruses. During the last 30 years; more than 50 viral threat has been evolved in South-East Asian countriesof them influenza is one of the major emerging and re-emerging infectious diseases of global concern. Similar to tropical and sub-tropical countries of Southeast Asia; circulation of A/H1N1 pdm09, A/H3N2 and influenza B has been circulating throughout the year with the peak during July-November in Nepal. However; the rate of infection transmission reach peak during the post-rain and winter season of Nepal.

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Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018–2019

Viruses ◽

10.3390/v13060977 ◽

2021 ◽

Vol 13 (6) ◽

pp. 977

Author(s):

Kobporn Boonnak ◽

Chayasin Mansanguan ◽

Dennis Schuerch ◽

Usa Boonyuen ◽

Hatairat Lerdsamran ◽

...

Keyword(s):

Amino Acid ◽

Influenza A ◽

Seasonal Influenza ◽

Influenza Viruses ◽

Surface Proteins ◽

Antigenic Drift ◽

Influenza B ◽

Receptor Binding Site ◽

Antigenic Sites ◽

Ha Protein

Influenza viruses continue to be a major public health threat due to the possible emergence of more virulent influenza virus strains resulting from dynamic changes in virus adaptability, consequent of functional mutations and antigenic drift in surface proteins, especially hemagglutinin (HA) and neuraminidase (NA). In this study, we describe the genetic and evolutionary characteristics of H1N1, H3N2, and influenza B strains detected in severe cases of seasonal influenza in Thailand from 2018 to 2019. We genetically characterized seven A/H1N1 isolates, seven A/H3N2 isolates, and six influenza B isolates. Five of the seven A/H1N1 viruses were found to belong to clade 6B.1 and were antigenically similar to A/Switzerland/3330/2017 (H1N1), whereas two isolates belonged to clade 6B.1A1 and clustered with A/Brisbane/02/2018 (H1N1). Interestingly, we observed additional mutations at antigenic sites (S91R, S181T, T202I) as well as a unique mutation at a receptor binding site (S200P). Three-dimensional (3D) protein structure analysis of hemagglutinin protein reveals that this unique mutation may lead to the altered binding of the HA protein to a sialic acid receptor. A/H3N2 isolates were found to belong to clade 3C.2a2 and 3C.2a1b, clustering with A/Switzerland/8060/2017 (H3N2) and A/South Australia/34/2019 (H3N2), respectively. Amino acid sequence analysis revealed 10 mutations at antigenic sites including T144A/I, T151K, Q213R, S214P, T176K, D69N, Q277R, N137K, N187K, and E78K/G. All influenza B isolates in this study belong to the Victoria lineage. Five out of six isolates belong to clade 1A3-DEL, which relate closely to B/Washington/02/2009, with one isolate lacking the three amino acid deletion on the HA segment at position K162, N163, and D164. In comparison to the B/Colorado/06/2017, which is the representative of influenza B Victoria lineage vaccine strain, these substitutions include G129D, G133R, K136E, and V180R for HA protein. Importantly, the susceptibility to oseltamivir of influenza B isolates, but not A/H1N1 and A/H3N2 isolates, were reduced as assessed by the phenotypic assay. This study demonstrates the importance of monitoring genetic variation in influenza viruses regarding how acquired mutations could be associated with an improved adaptability for efficient transmission.

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