Persons who work in close contact with dairy cattle and poultry that are infected with highly pathogenic avian influenza (HPAI) A(H5N1) virus are at increased risk for infection. In July 2024, the Colorado Department of Public Health & Environment responded to two poultry facilities with HPAI A(H5N1) virus detections in poultry. Across the two facilities, 663 workers assisting with poultry depopulation (i.e., euthanasia) received screening for illness; 109 (16.4%) reported symptoms and consented to testing. Among those who received testing, nine (8.3%) received a positive influenza A(H5) virus test result, and 19 (17.4%) received a positive SARS-CoV-2 test result. All nine workers who received positive influenza A(H5) test results had conjunctivitis, experienced mild illness, and received oseltamivir. This poultry exposure-associated cluster of human cases of influenza A(H5) is the first reported in the United States. The identification of these cases highlights the ongoing risk to persons who work in close contact with infected animals. Early response to each facility using multidisciplinary, multilingual teams facilitated case-finding, worker screening, and treatment. As the prevalence of HPAI A(H5N1) virus clade 2.3.4.4b genotype B3.13 increases, U.S. public health agencies should prepare to rapidly investigate and respond to illness in agricultural workers, including workers with limited access to health care.
During May 19-September 28, 2019,* low levels of influenza activity were reported in the United States, with cocirculation of influenza A and influenza B viruses. In the Southern Hemisphere seasonal influenza viruses circulated widely, with influenza A(H3) predominating in many regions; however, influenza A(H1N1)pdm09 and influenza B viruses were predominant in some countries. In late September, the World Health Organization (WHO) recommended components for the 2020 Southern Hemisphere influenza vaccine and included an update to the A(H3N2) and B/Victoria-lineage components. Annual influenza vaccination is the best means for preventing influenza illness and its complications, and vaccination before influenza activity increases is optimal. Health care providers should recommend vaccination for all persons aged ≥6 months who do not have contraindications to vaccination (1).
Abstract Influenza B/Yamagata viruses have not been detected globally since 2020 and will be removed from U.S. 2024/25 seasonal influenza vaccines. We inferred impacts of vaccination against B/Yamagata from 2016/17–2019/20 by combining B/Yamagata prevalence data with model-based estimates of disease burden prevented by vaccination against all influenza B viruses. B/Yamagata comprised approximately 16–22% of positive virus specimens in 2016/17 and 2017/18, compared to 1% in 2018/19 and 2019/20. Across all seasons, we estimated that vaccination against B/Yamagata prevented 4.15 million illnesses, 58,500 hospitalizations, and 4,070 deaths, and that 22.9 million B/Yamagata-associated illnesses, 340,000 hospitalizations, and 25,100 deaths would have occurred without vaccination. Vaccination prevented the most B/Yamagata hospitalizations among adults ≥65 years but prevented the greatest percentage of B/Yamagata hospitalizations among children 6 months–4 years. Our results may help assess the potential impact if B/Yamagata were to recirculate in the absence of vaccination.
Since April 2024, sporadic infections with highly pathogenic avian influenza (HPAI) A(H5) viruses have been detected among dairy farm workers in the United States. To date, infections have mostly been detected through worker monitoring, and have been mild despite the possibility of more severe illness. During June-August 2024, CDC collaborated with the Michigan Department of Health and Human Services and the Colorado Department of Public Health and Environment to implement cross-sectional serologic surveys to ascertain the prevalence of recent infection with HPAI A(H5) virus among dairy workers. In both states, a convenience sample of persons who work in dairies was interviewed, and blood specimens were collected. Among 115 persons, eight (7%; 95% CI = 3.6%-13.1%) had serologic evidence of recent infection with A(H5) virus; all reported milking cows or cleaning the milking parlor. Among persons with serologic evidence of infection, four recalled being ill around the time cows were ill; symptoms began before or within a few days of A(H5) virus detections among cows. This finding supports the need to identify and implement strategies to prevent transmission among dairy cattle to reduce worker exposures and for education and outreach to dairy workers concerning prevention, symptoms, and where to seek medical care if the workers develop symptoms. Timely identification of infected herds can support rapid initiation of monitoring, testing, and treatment for human illness, including mild illness, among exposed dairy workers.
The COVID-19 pandemic and subsequent implementation of nonpharmaceutical interventions (e.g., cessation of global travel, mask use, physical distancing, and staying home) reduced transmission of some viral respiratory pathogens (1). In the United States, influenza activity decreased in March 2020, was historically low through the summer of 2020 (2), and remained low during October 2020-May 2021 (<0.4% of respiratory specimens with positive test results for each week of the season). Circulation of other respiratory pathogens, including respiratory syncytial virus (RSV), common human coronaviruses (HCoVs) types OC43, NL63, 229E, and HKU1, and parainfluenza viruses (PIVs) types 1-4 also decreased in early 2020 and did not increase until spring 2021. Human metapneumovirus (HMPV) circulation decreased in March 2020 and remained low through May 2021. Respiratory adenovirus (RAdV) circulated at lower levels throughout 2020 and as of early May 2021. Rhinovirus and enterovirus (RV/EV) circulation decreased in March 2020, remained low until May 2020, and then increased to near prepandemic seasonal levels. Circulation of respiratory viruses could resume at prepandemic levels after COVID-19 mitigation practices become less stringent. Clinicians should be aware of increases in some respiratory virus activity and remain vigilant for off-season increases. In addition to the use of everyday preventive actions, fall influenza vaccination campaigns are an important component of prevention as COVID-19 mitigation measures are relaxed and schools and workplaces resume in-person activities.
Before the emergence of SARS-CoV-2, the virus that causes COVID-19, influenza activity in the United States typically began to increase in the fall and peaked in February. During the 2021-22 season, influenza activity began to increase in November and remained elevated until mid-June, featuring two distinct waves, with A(H3N2) viruses predominating for the entire season. This report summarizes influenza activity during October 3, 2021-June 11, 2022, in the United States and describes the composition of the Northern Hemisphere 2022-23 influenza vaccine. Although influenza activity is decreasing and circulation during summer is typically low, remaining vigilant for influenza infections, performing testing for seasonal influenza viruses, and monitoring for novel influenza A virus infections are important. An outbreak of highly pathogenic avian influenza A(H5N1) is ongoing; health care providers and persons with exposure to sick or infected birds should remain vigilant for onset of symptoms consistent with influenza. Receiving a seasonal influenza vaccine each year remains the best way to protect against seasonal influenza and its potentially severe consequences.
Abstract Four cases of oseltamivir-resistant influenza A(H1N1)pdm09 virus infection were detected among inhabitants of a border detention center in Texas, USA. Hemagglutinin of these viruses belongs to 6B.1A5A-156K subclade, which may enable viral escape from preexisting immunity. Our finding highlights the necessity to monitor both drug resistance and antigenic drift of circulating viruses.
The COVID-19 pandemic and subsequent implementation of nonpharmaceutical interventions (e.g., cessation of global travel, mask use, physical distancing, and staying home) reduced the transmission of some viral respiratory pathogens.1Haddadin Z Schuster JE Spieker AJ et al.Acute respiratory illnesses in children in the SARS-CoV-2 pandemic: prospective multicenter study.Pediatrics. 2021; 148 (doi: 10.1542/Peds.2021-051462): 202Crossref Scopus (31) Google Scholar In the United States, influenza activity decreased in March 2020, was historically low through the summer of 2020,2Olsen SJ Azziz-Baumgartner E Budd AP et al.Decreased influenza activity during the COVID-19 pandemic—United States, Australia, Chile, and South Africa, 2020.MMWR Morb Mortal Wkly Rep. 2020; 69 (doi: 10.15585/mmwr.mm6937a6): 1305-1309Crossref PubMed Scopus (271) Google Scholar and remained low during October 2020–May 2021 (<0.4% of respiratory specimens with positive test results for each week of the season). Circulation of other respiratory pathogens, including respiratory syncytial virus (RSV), common human coronaviruses (HCoVs) types OC43, NL63, 229E, and HKU1, and parainfluenza viruses (PIVs) types 1–4 also decreased in early 2020 and did not increase until spring 2021. Human metapneumovirus (HMPV) circulation decreased in March 2020 and remained low through May 2021. Respiratory adenovirus (RAdV) circulated at lower levels throughout 2020 and as of early May 2021. Rhinovirus and enterovirus (RV/EV) circulation decreased in March 2020, remained low until May 2020, and then increased to near prepandemic seasonal levels. Circulation of respiratory viruses could resume at prepandemic levels after COVID-19 mitigation practices become less stringent. Clinicians should be aware of increases in some respiratory virus activity and remain vigilant for off-season increases. In addition to the use of everyday preventive actions, fall influenza vaccination campaigns are an important component of prevention as COVID-19 mitigation measures are relaxed and schools and workplaces resume in-person activities. CDC analyzed virologic data* from U.S. laboratories available through the U.S. World Health Organization Collaborating Laboratories System† (influenza only) and CDC's National Respiratory and Enteric Virus Surveillance System§ (NREVSS) (multiple respiratory viruses). Reporting bias on the part of participating laboratories was minimized by requiring the following pathogen-specific inclusion criteria for noninfluenza viruses: 1) an average of ≥10 tests and ≥36 of 52 weeks of tests for RSV, RAdV, and HMPV or 2) ≥1 detection for each of the virus types for PIV (types 1–4) and HCoV (OC43, NL63, 229E, and HKU1). Hospitalization rates for influenza and RSV were calculated with data from the Influenza Hospitalization Surveillance Network (FluSurv-NET) and RSV Hospitalization Surveillance Network (RSV-NET).¶ Antigenic analyses for influenza viruses were conducted using hemagglutination inhibition or neutralization-based assays; viruses were tested for resistance to antiviral medications.**** Influenza activity during October 3, 2020–May 22, 2021, and activity of other viruses during January 4, 2020–May 22, 2021 were described; data from 4 previous years were used for comparisons. Each date is the Saturday marking the week's end.†† This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy.§§ During October 3, 2020–May 22, 2021, influenza activity was lower than during any previous influenza season since at least 1997, the first season for which data are publicly available (Figure 1) (Figure 2). Among 1,095,080 clinical specimens tested, 1921 (0.2%) specimens were positive for an influenza virus: 721 (37.5%) for influenza A and 1200 (62.5%) for influenza B. During this period, public health laboratories tested 502,782 specimens; 255 (0.05%) were positive for influenza, 153 (60.0%) were positive for influenza A, and 102 (40.0%) were positive for influenza B virus. Among 39 (25.5%) seasonal influenza A viruses subtyped, 18 (46.2%) were A(H1N1)pdm09, and 21 (53.8%) were A(H3N2). Of the 25 (24.5%) influenza B viruses with B lineage results, 17 (68.0%) were B/Victoria and 8 (32.0%) were B/Yamagata. The cumulative incidence of laboratory-confirmed, influenza-associated hospitalizations during this period was 0.8 per 100,000 (range = 62.0–102.9 during the previous four seasons). Five human infections with variant influenza A(H1N1)v, (H1N2)v, or (H3N2)v viruses¶¶ were reported from four U.S. states during the 2020–21 season. In each case, the patient reported direct contact with swine or living or working on a farm where swine were present before illness onset.FIGURE 2Percentage of specimens testing positive for influenza viruses, respiratory syncytial virus, common human coronaviruses, parainfluenza viruses, human metapneumovirus, respiratory adenoviruses, and rhinoviruses/enteroviruses, by month—United States, 2016–2017 through 2020–2021View Large Image Figure ViewerDownload Hi-res image Download (PPT) Sixteen influenza viruses were genetically characterized. Phylogenetic analysis of influenza hemagglutinin (HA) genes indicated that of three influenza A(H1N1)pdm09 viruses, all HA genes belonged to the 6B.1A clade (two in 5A1 and one in 5B subclades); all five A(H3N2) viruses belonged to the 3C.2a1b2a subclade, and all eight B/Victoria viruses belonged to the V1A.3 clade. Fifteen viruses were antigenically characterized by hemagglutination inhibition or virus neutralization-based methods. The three A(H1N1)pdm09 viruses were similar to the cell-based A(H1) component of the 2020–21 Northern Hemisphere influenza vaccines and two of these were also similar to the egg-based A(H1) component*****; all eight B/Victoria lineage viruses were antigenically similar to the egg- and cell-based B/Victoria components of the vaccine. One of the four A(H3N2) viruses was similar to the cell-based A(H3) component of the vaccine (i.e., reacted within fourfold of homologous titer); none of the viruses were as antigenically similar to the egg-based component. All 10 viruses tested for susceptibility to therapeutics were susceptible to neuraminidase (NA) inhibitors and Baloxavir. During January 4–April 4, 2020, the weekly percentage of positive RSV results decreased from 15.3% to 1.4%, then remained at historically low levels (<1.0% per week) for the next year (Figure 1) (Figure 2). During the previous 4 years, the weekly percentage of positive RSV results exceeded 3.0% beginning in October with peaks ranging from 12.5% to 16.7% in late December. During April 17–May 22, 2021, the weekly percentage of positive results increased from 1.1% to 2.8% (increases occurred predominantly within the southeastern United States in U.S. Department of Health and Human Services [HHS] regions 4 and 6†††). The cumulative incidence of RSV-associated hospitalization was 0.3 per 100,000 persons during October 2020–April 2021 (compared with 27.1 and 33.4, respectively, during the previous two seasons); 173 (76.5%) of 226 RSV-associated hospitalizations reported during October 1, 2020–May 22, 2021 occurred in April and May 2021. From January 2020 to January 2021, HCoVs and PIVs circulated at lower levels than during the preceding 4 years (Figure 1). From January 4, 2020 to April 18, 2020, the weekly percentage of HCoV-positive results declined from 7.5% to 1.3%, remained <1.0% until February 27, 2021, and increased to 6.6% by May 22, 2021 (led by types OC43 and NL63). During the previous 4 years, HCoV circulation peaks occurred during December–January and ranged from 7.7% to 11.4%. From January 4, 2020 to March 28, 2020, the weekly percentage of positive PIV test results decreased from 2.6% to 1.0%, then remained <1.0% until April 3, 2021, followed by an increase to 10.9% by May 22, 2021 (led by type PIV3). During the previous 4 years, PIV circulation peaked during the fall (October–November) and spring (May–June). The current increase could represent a return to prepandemic seasonality. From January 4, 2020 to March 14, 2020, the weekly percentage of HMPV-positive results rose from 4.2% to 7.0%, dropped to 1.9% during the week of April 11, 2020, and remained <1.0% through May 22, 2021 (Figure 2). During the previous 4 years, HMPV circulation peaked between 6.2% and 7.7% in March and April. SummaryWhat is already known about this topic?Nonpharmaceutical interventions introduced to mitigate the impact of COVID-19 reduced transmission of common respiratory viruses in the United States.What is added by this report?Influenza viruses and human metapneumovirus circulated at historic lows through May 2021. In April 2021, respiratory syncytial virus activity increased. Common human coronaviruses, parainfluenza viruses, and respiratory adenoviruses have been increasing since January or February 2021. Rhinoviruses and enteroviruses began to increase in June 2020.What are the implications for public health practice?Clinicians should be aware of increased circulation, sometimes off season, of some respiratory viruses and consider multipathogen testing. In addition to recommended preventive actions, fall influenza vaccination campaigns are important as schools and workplaces resume in-person activities with relaxed COVID-19 mitigation practices. Nonpharmaceutical interventions introduced to mitigate the impact of COVID-19 reduced transmission of common respiratory viruses in the United States. Influenza viruses and human metapneumovirus circulated at historic lows through May 2021. In April 2021, respiratory syncytial virus activity increased. Common human coronaviruses, parainfluenza viruses, and respiratory adenoviruses have been increasing since January or February 2021. Rhinoviruses and enteroviruses began to increase in June 2020. Clinicians should be aware of increased circulation, sometimes off season, of some respiratory viruses and consider multipathogen testing. In addition to recommended preventive actions, fall influenza vaccination campaigns are important as schools and workplaces resume in-person activities with relaxed COVID-19 mitigation practices. From January 2020 to April 2021, the weekly percentage of RAdV-positive results decreased to lower ranges (1.2%–2.6%) than those observed historically. The weekly percentage of positive results increased steadily to 3% by May 22, 2021, a level observed during previous surveillance years. The weekly percentage of positive RV/EV results declined from late March (14.9%) through early May 2020 (3.2%), levels lower than those typically observed during spring peaks (Figure 2). Weekly percentage of positive results then increased steadily until October 17, 2020, peaking at a lower level (21.7%) compared with fall peaks in previous years (median = 32.8%). In 2021, weekly percentage of RV/EV-positive results declined to 9.9% by January 16, 2021, before increasing to 19.1% on May 22, 2021; this could reflect the usual spring peak that has occurred in previous years (Figure 2). In the United States, the circulation of respiratory viruses was disrupted during the COVID-19 pandemic, but the magnitude, timing, and duration of this effect varied among viruses. During 2020, influenza viruses and RSV circulated at historically low levels. In 2021, influenza continues to circulate at low levels, whereas RSV activity has been increasing since April 2021, indicating an unusually timed increase in some regions of the country.‡‡‡ HCoV and PIV activity is rising to prepandemic levels after notably low circulation, but this HCoV activity is inconsistent with the timing for a typical season. HPMV activity has remained low since March 2020. Although RAdV and RV/EV activity decreased in spring 2020, circulation has reverted to the week-to-week fluctuations at levels similar to those observed before the pandemic. Among each group of viruses, changes in the circulation of specific species and types warrant further assessment. The duration of the effect of the COVID-19 pandemic and associated mitigation measures on respiratory virus circulation is unknown. Circulation of other respiratory viruses might continue to change as pandemic mitigation measures are adjusted and as prevalence of and immunity to both SARS-CoV-2, the virus that causes COVID-19, and immunity to these other viruses waxes and wanes. In 2020, influenza continued to circulate in the tropics; therefore, resumption of circulation in the United States is possible as global travel resumes.3Mott JA Fry AM Kondor R Wentworth DE Olsen SJ. Re-emergence of influenza virus circulation during 2020 in parts of tropical Asia: implications for other countries.Influenza Other Respir Viruses. 2021; 15 (doi: 10.1111/irv.12844): 415-418Crossref PubMed Scopus (16) Google Scholar Every year, it is difficult to predict which influenza viruses might circulate during the next season.4Laurie KL, Rockman S. Which influenza viruses will emerge following the SARS-CoV-2 pandemic? Influenza Other Respir Viruses. 2021. Epub May 6, 2021. doi: 10.1111/irv.12844Google Scholar In the United States, influenza A (H3N2) viruses continue to be identified, but the diversity of the subclades co-circulating was reduced relative to recent seasons, and globally, few detections of influenza B viruses of the Yamagata lineage were detected during the pandemic. Reduced circulation of influenza viruses during the past year might affect the severity of the upcoming influenza season given the prolonged absence of ongoing natural exposure to influenza viruses. Lower levels of population immunity, especially among younger children, could portend more widespread disease and a potentially more severe epidemic when influenza virus circulation resumes. As the fall season approaches with schools and workplaces reopening, in addition to the use of recommended everyday preventive actions, clinicians should encourage influenza vaccination for all persons aged ≥6 months.5Grohskopf LA Alyanak E Broder KR et al.Prevention and control of seasonal influenza with vaccines: recommendations of the advisory committee on immunization practices—United States, 2020–21 influenza season.MMWR Recomm Rep. 2020; 69 (doi: 10.15585/mmwr.rr6908a1): 1-24Crossref PubMed Google Scholar RAdV and RV/EV activity continued during 2020 and might be returning to prepandemic circulation patterns.6Huang QS, Wood T, Jelley L, et al. Impact of the COVID-19 nonpharmaceutical interventions on influenza and other respiratory viral infections in New Zealand. Nat Commun. 2021. Epub February 12, 2021. doi: 10.1038/s41467-021-21157-9Google Scholar,7Yum S Hong K Sohn S Kim J Chun BC. Trends in viral respiratory infections during COVID-19 pandemic, South Korea.Emerg Infect Dis. 2021; 27 (doi: 10.3201/eid2706.210135): 1685-1688Crossref PubMed Scopus (29) Google Scholar Factors contributing to this distinct circulation are unclear but might include the relative importance of different transmission mechanisms, such as aerosol, droplet, or contact, the role of asymptomatic transmission, and prolonged survival of these nonenveloped viruses on surfaces, all of which might make these viruses less susceptible to nonpharmaceutical interventions, such as mask-wearing and surface cleaning.8Leung NHL Chu DKW Shiu EYC et al.Respiratory virus shedding in exhaled breath and efficacy of face masks.Nat Med. 2020; 26 (doi: 10.1038/s41591-020-0843-2): 676-680Crossref PubMed Scopus (1321) Google Scholar,9Lin Q Lim JYC Xue K et al.Sanitizing agents for virus inactivation and disinfection.VIEW. 2020; 1 (doi: 10.1002/viw2.16externalicon): e16Google Scholar The delay in circulation of PIVs and HCoVs, which circulate at high levels among children, could be related to some schools suspending in-person classes until late winter. However, the relative absence of HMPV, which affects a similar age group as RSV (i.e., children aged <2 years) is unexplained. The unusual timing of rising RSV detections was also observed in Western Australia.10Foley DA, Yeoh DK, Minney-Smith CA, et al. The interseasonal resurgence of respiratory syncytial virus in Australian children following the reduction of coronavirus disease 2019-related public health measures. Clin Infect Dis. 2021;ciaa1906. doi: 10.1093/cid/ciaa1906Google Scholar The findings in this report are subject to at least three limitations. First, changes in health-seeking behaviors during the pandemic (e.g., designated testing sites for COVID-19) might have contributed to a decrease in reported respiratory virus activity if routine health care visits were not made to health care providers who participate in surveillance. Testing for respiratory viruses was somewhat reduced during 2020–2021 but was higher than typically seen during periods of low virus activity. In addition, the detection of sporadic novel influenza viruses and increases in levels of circulation of other respiratory viruses attest to systems' effectiveness. Second, each test result was independently reported, therefore the role of virus-virus interactions on activity could not be examined. Finally, some viral groupings (e.g., RV/EV) are large and might obscure type-specific patterns. The different epidemiologic patterns of respiratory viruses observed during the COVID-19 pandemic in this U.S. surveillance summary raise questions about transmission and prevention, such as the contribution of birth cohort effects, natural immunity, and interventions. Clinicians should be aware that respiratory viruses might not exhibit typical seasonal circulation patterns and that a resumption of circulation of certain respiratory viruses is occurring, therefore an increased index of suspicion and testing for multiple respiratory pathogens remain important. Improved understanding of the role that nonpharmaceutical interventions play on the transmission dynamics of respiratory viruses can guide future prevention recommendations. Charisse Cummings, Rachel Holstein, Stacy Huang, Alissa O'Halloran, Rishika Parikh, Kyung Park, Carrie Reed, Sandra Seby, Dawud Ujamaa, Influenza Division, National Center for Immunization and Respiratory Diseases, CDC; Rebecca Dahl, Meredith McMorrow, Michael Whitaker, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, CDC. All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. John Steel reported intellectual property from patent positions on universal influenza virus vaccines; he receives no income from the patent positions. No other potential conflicts of interest were disclosed. * Influenza data as of July 7, 2021. † https://www.cdc.gov/flu/weekly/overview.htm § Some influenza clinical laboratory data and all other respiratory virus data are aggregate, weekly numbers of nucleic acid amplification tests and detections reported to NREVSS, a passive, voluntary surveillance network of clinical, commercial, and public health laboratories. NREVSS aggregate, weekly tests are reported specifically for each pathogen. NREVSS participating laboratories' testing capabilities vary annually, and testing intentions vary for each pathogen. A range of 50–178 laboratories met the pathogen-specific criteria for inclusion criteria during a given surveillance year. https://www.cdc.gov/surveillance/nrevss/index.html ¶ FluSurv-NET and RSV-NET use similar methods; unadjusted cumulative incidence rates are calculated using CDC's National Center for Health Statistics bridged-race postcensal population estimates for the counties included in the surveillance catchment area. Laboratory confirmation is dependent on clinician-ordered testing and cases identified through surveillance are likely an underestimation of the actual number of persons hospitalized with both pathogens. https://www.cdc.gov/flu/weekly/influenza-hospitalization-surveillance.htm; https://www.cdc.gov/ncezid/dpei/eip/eip-network-activities.html ** Genetic characterization was carried out using next-generation sequencing, and the genomic data were analyzed and submitted to public databases (GenBank or EpiFlu). Antigenic characterizations were carried out by hemagglutination inhibition assays or virus neutralization–based focus reduction assays to evaluate whether genetic changes in circulating viruses affected antigenicity; substantial differences could affect vaccine effectiveness. Testing of seasonal influenza viruses for resistance to the neuraminidase (NA) and polymerase inhibitors was performed at CDC using next-generation sequencing analysis, a functional assay, or both. NA sequences of viruses are examined for the presence of amino acid substitutions previously associated with reduced or highly reduced inhibition by any of the three NA inhibitors. https://www.who.int/influenza/gisrs_laboratory/antiviral_susceptibility/NAI_Reduced_Susceptibility_Marker_Table_WHO.pdf?uapdf iconexternal icon †† MMWR week numbers were used corresponding to week 40 in 2020 through week 39 in 2021. https://ndc.services.cdc.gov/wp-content/uploads/MMWR_Week_overview.pdfpdf icon §§ 45 C.F.R. part 46, 21 C.F.R. part 56; 42 U.S.C. Sect. 241(d); 5 U.S.C. Sect. 552a; 44 U.S.C. Sect. 3501 et seq. ¶¶ Phylogenetic lineage classification of variant swine viruses indicated that one A(H1N1)v influenza virus was reported from North Carolina and one A(H1N2)v was reported from Wisconsin. Each virus had an hemagglutinin (HA) gene closely related to the 1A.3.3.3 lineage of swine influenza virus. Another (H1N1)v influenza virus was reported from Iowa that had an HA gene derived from a seasonal A(H1N1)pdm09 virus that was likely introduced into swine by reverse zoonosis. In addition, an influenza A(H1N1)v virus was reported from a patient in Ohio. However, only partial HA and NA gene sequences could be obtained from the sample, thus no detailed lineage classification or antigenic characterization was possible. An A(H3N2)v influenza virus was reported from Wisconsin that had an HA gene closely related to H3N2 viruses currently circulating in the swine population, which was likely introduced into swine from humans in 2010. *** https://www.who.int/influenza/vaccines/virus/recommendations/202002_recommendation.pdfpdf iconexternal icon ††† HHS Region 4: Alabama, Florida, Georgia, Kentucky, Mississippi, North Carolina, South Carolina, and Tennessee. Region 6: Arkansas, Louisiana, New Mexico, Oklahoma, and Texas. ‡‡‡ https://emergency.cdc.gov/han/2021/han00443.asp
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