key: cord-0694046-mruasoln authors: Huang, Weijuan; Cheng, Yanhui; Chen, Tao; Li, Xiyan; Tan, Minju; Wei, Hejiang; Zeng, Xiaoxu; Xie, Yiran; Liu, Jia; Xiao, Ning; Yang, Lei; Wang, Dayan title: Characterization of Influenza Viruses — China, 2019−2020 date: 2020-10-30 journal: China CDC Wkly DOI: 10.46234/ccdcw2020.228 sha: b3e1b8db273809836673860480084908647090cc doc_id: 694046 cord_uid: mruasoln Introduction: Influenza surveillance is necessary for detection of emerging variants of influenza viruses and determining their epidemiological and clinical significance. Vaccination and antiviral drugs remain the most useful ways to protect against seasonal influenza and its potentially severe consequences. This study describes the epidemiology, antigenic and genetic characteristics, and antiviral susceptibilities of influenza viruses isolated from the mainland of China during the April 1, 2019 through October 4, 2020. Methods: All viruses analyzed were isolated and submitted by Chinese National Influenza Surveillance Network laboratories. The Chinese National Influenza Center performed antigenic analysis, sequencing, and antiviral resistance testing after propagation of the viruses. Antigenic characterizations were determined by hemagglutinin inhibition assay;next-generation sequencing was used for genetic analyses;phenotypic assay and next-generation sequencing were used for determining antiviral resistance. Results: The influenza positivity rate declined significantly starting in late January 2020 and has remained low. There was no summer influenza peak season in south China. Influenza A(H3N2) and B/Victoria lineage viruses were the dominant subtype/lineage during April 1, 2019 through October 4, 2020. The majority of influenza viruses were antigenically and genetically similar to reference viruses representing components of vaccines for the 2020-2021 northern hemisphere influenza season. Nearly all seasonal influenza viruses were susceptible to oseltamivir and zanamivir. Conclusions and Implications for Public Health Practice: Since the outbreak of COVID-19, the influenza positivity rate declined with implementation of strong COVID-19 control measures. The majority of circulating viruses are well matched with the current 2020-2021 northern hemisphere influenza vaccine viruses. Circulating seasonal influenza viruses were sensitive to neuraminidase inhibitors and Baloxavir marboxil. This study provided evidence for World Health Organization (WHO) recommendations for vaccine viruses, for prevention and control of influenza, and for clinical use of antiviral medications. Influenza viruses evolve rapidly and escape natural or vaccine-induced immune responses by accumulating mutations within the surface glycoprotein genes for hemagglutinin (HA) and neuraminidase (NA) (1) . The emergence of coronavirus disease 2019 (COVID-19) has had a huge impact on the world by shifting public health challenges and changing behaviors that even affect influenza activity. Between April 2019 and September 2020, influenza activity was reported in all global regions. However, since April 2020, low levels of influenza activity have been reported -including from countries in the southern hemisphere temperate zone. Although influenza A(H1N1)pdm09, A(H3N2), and influenza B viruses co-circulated, the predominant circulating viruses varied by country and region. Overall, influenza A viruses were detected more often than influenza B viruses. Globally, co-circulation of A(H1N1)pdm09 and A(H3N2) viruses was evident in most countries, areas, and territories, but influenza A(H1N1)pdm09 viruses circulated in higher proportion than A(H3N2) viruses beginning in mid-January 2020. The B/Victoria lineage circulated in higher proportion than the B/Yamagata lineage viruses worldwide (2) (3) . Each year, the WHO recommends compositions for the northern hemisphere influenza vaccine in February and for the southern hemisphere in September. Vaccination remains the best way to protect against seasonal influenza and its potentially severe consequences. Influenza A(H3N2) and B/Victoria lineage viruses were the dominant subtype/lineage in the mainland of China during 2019-2020. To understand the variation of circulating seasonal influenza viruses and their match with vaccine virus strains, we analyzed the antigenic and genetic characteristics and antiviral susceptibilities of influenza viruses isolated from the mainland of China. The Chinese National Influenza Surveillance Network includes 410 laboratories and 554 sentinel hospitals. The influenza surveillance year typically starts on week 14, which is around April 1, and lasts for an entire year. Sentinel hospitals report influenzalike illness (ILI) cases to the Chinese National Influenza Surveillance Information System (CNISIS) and collect respiratory specimens. Network laboratories test the specimens with real-time reverse transcriptase polymerase chain reaction (RT-PCR). Influenza positive specimens are propagated in Madin-Darby canine kidney (MDCK) cells and/or embryonated chicken eggs. Viruses are submitted to the Chinese National Influenza Center (CNIC) for further characterization. Antigenic characterizations were assessed with HA inhibition (HI) assays, and genetic characterization was performed with next-generation sequencing. Influenza virus testing for antiviral resistance was conducted at CNIC using next-generation sequencing analysis, phenotypic assays, or with both tests (4). The viruses evaluated were isolated from specimens collected between week 14 in 2019 (April 1, 2019) and week 40 in 2020 (October 4, 2020). For virus surveillance during April 1, 2019 through October 4, 2020 (surveillance week 14 in 2019 to week 40 in 2020), the percentage of specimens testing positive for influenza each week ranged from 0% to 46.5% in southern China and ranged from 0% to 47.3% in northern China. The positivity rate of specimens collected from ILI cases increased starting in week 40 in 2019 reaching a peak (46.5% for southern China and 47.3% for northern China) during the first week of 2020 and decreasing substantially after that. During week 8, the positivity rate in southern China decreased to 2.0%, and by week 10 in northern China, the influenza-positive rate declined to 1.3%. The positivity rate since then has been lower than that of the same period in previous years (5) and has remained low ever since (Figures 1 and 2 Figure 1 ). Network laboratories in northern China tested 216,874 specimens between April 1, 2019 and October 4, 2020. Among these, 26,759 (12.3%) were positive for influenza viruses -influenza A and influenza B viruses were 20,203 (75.5%) and 6,556 (24.5%), respectively, of the tested viruses. Among the 20,199 seasonal influenza A viruses that were subtyped, 2,091 (10.4%) were influenza A(H1N1)pdm09 and 18,108 (89.6%) were influenza A(H3N2). Influenza B lineage information was available for 6,547 influenza B viruses; 6,460 (98.7%) were B/Victoria lineage and 87 (1.3%) were B/Yamagata lineage ( Figure 2 ). CNIC tested the antigenic and genetic characteristics of influenza viruses between April 1, 2019 and October 4, 2020. A total of 653 A(H1N1)pdm09 viruses were analyzed with HI tests, and 521 viruses were antigenically analyzed with A/Guangdong-Maonan/SWL1536/2019, and 98.3% (512/521) were well inhibited by ferret antisera raised against A/Guangdong-Maonan /SWL1536/2019, the egg-propagated reference virus representing the A(H1N1)pdm09 component for the upcoming 2020-2021 winter season's northern hemisphere influenza vaccination (2) . Among the 205 viruses sequenced, phylogenetic analysis of HA gene segments determined that 199 (97.1%) belonged to genetic clade 6B.1A ( Figure 3) ; 161 (78.5%) belonged to subclade 6B.1A5A, which evolved from clade 6B.1A. Subclade 6B.1A5A HA genes fall into 3 genetic groups: a progenitor 6B.1A5A subclade (22.9%) and 2 recently designated groups, 5A-187A (46.3%), with additional amino acid substitutions D187A and Q189E, and 5A-156K (9.3%), with an additional amino acid substitution N156K. Antigenic characterization of 1,410 A(H3N2) viruses were conducted using HI tests that used guinea pig red blood cells (RBCs) in the presence of oseltamivir, and 63 viruses underwent antigenic analysis with A/Hong Kong/2671/2019 where the results showed that 79.4% (50/63) of virus isolates were well inhibited by ferret antisera raised against A/Hong Kong/2671/2019, the egg-propagated reference virus representing the A(H3N2) component for the 2020-2021 northern hemisphere influenza vaccine -a higher proportion than the last influenza season (6 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 01 02 03 04 05 06 07 08 09 10 11 Unlike previous years, influenza activity began to decline sharply after the epidemic peaked in the first week of 2020. Lower levels of influenza activity have 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 01 02 03 04 05 06 07 08 09 10 11 12 13 also been reported globally during the April to September period in 2020 compared with recent years (3). This decrease in activity could be due to the COVID-19 pandemic response, as the government implemented a series of prevention and control measures, including home quarantine and wearing masks, to stop spread of COVID-19. In late February 2020, the WHO issued its recommendations for the 2020-2021 northern hemisphere influenza vaccines. Egg-based influenza trivalent vaccines will use an A/Guangdong- Most of these viruses belonged to subclade 6B.1A5A and contained amino acid substitutions D187A and Q189E (e.g. A/Guangdong-Maonan/SWL1536/2019) in their HA proteins. Although antigenic analyses do not detect all antigenic differences in these A(H1N1)pdm09 viruses, amino acid substitutions acquired in the circulating viruses were within the antigenic HA epitopes (8) . Almost all influenza A(H1N1)pdm09 viruses were well inhibited by ferret antisera raised against A/Guangdong-Maonan/SWL 1536/2019, but group 5A-156K viruses reacted poorly with these antisera and were antigenically distinct, and the 5A-156K group has increased rapidly in many countries since December 2019 (3). The majority of circulating A(H3N2) viruses belonged to subclade 3C.2a1b. Among A(H3N2) viruses circulating globally, there were regional differences in the proportions of subclades circulating, and viruses with 2a1b+T135K subclade (e. Based on our analysis, >99% of seasonal influenza viruses were susceptible to oseltamivir and zanamivir. Only 3 influenza A(H1N1)pdm09 viruses were resistant and included the H275Y or H275H/Y amino acid substitution in the NA protein that has previously been associated with highly reduced susceptibility to oseltamivir. The H275Y amino acid substitution in A(H1N1)pdm09 viruses is considered clinically relevant and leads to reduced treatment efficacy (4) . An influenza B/Victoria lineage virus showed reduced inhibition by oseltamivir and highly reduced inhibition by zanamivir; this virus had a G243D amino acid substitution in the NA protein, a substitution that has not been previously described. The G243S/G amino acid substitution, which was reported in B/Victorialineage viruses, is associated with reduced susceptibility to zanamivir (9) . We should conduct additional evaluation to clarify the significance of this substitution. Anti-influenza drugs are effective as postexposure prophylaxis and treatments for influenza virus infection. It is important to continuously monitor antiviral resistance of circulating influenza viruses. The COVID-19 pandemic has changed lifestyles, improved public health preventative measures, and had an impact on other respiratory infectious diseases including influenza. Surveillance and research on influenza should be strengthened, including human infection with zoonotic influenza, to better predict and prepare for the next pandemic. 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