Update: Influenza Activity — United States and Worldwide, May 20–October 13, 2018

Eric J. Chow, MD; C. Todd Davis, PhD; Anwar Isa Abd Elal; Noreen Alabi, MPH; Eduardo Azziz-Baumgartner, MD; John Barnes, PhD; Lenee Blanton, MPH; Lynnette Brammer, MPH; Alicia P. Budd, MPH; Erin Burns, MA; William W. Davis, DrPH; Vivien G. Dugan, PhD; Alicia M. Fry, MD; Rebecca Garten, PhD; Lisa A. Grohskopf, MD; Larisa Gubareva, PhD; Yunho Jang, PhD; Joyce Jones, MS; Krista Kniss, MPH; Stephen Lindstrom, PhD; Desiree Mustaquim, MPH; Rachael Porter, MPH; Melissa Rolfes, PhD; Wendy Sessions, MPH; Calli Taylor, MPH; David E. Wentworth, PhD; Xiyan Xu, MD; Natosha Zanders, MS; Jacqueline Katz, PhD; Daniel Jernigan, MD

Disclosures

Morbidity and Mortality Weekly Report. 2018;67(42):1178-1185. 

In This Article

Genetic and Antigenic Characterization of Influenza Viruses

The components for the Northern Hemisphere 2018–19 influenza vaccines were selected in February 2018, during one of the twice-yearly WHO-sponsored vaccine consultation meetings. The recommended Northern Hemisphere 2018–19 trivalent influenza vaccine composition included an A/Michigan/45/2015 (H1N1)pdm09-like virus, an A/Singapore/INFIMH-16–0019/2016 (H3N2)-like virus, and a B/Colorado/06/2017-like virus (B/Victoria lineage), with an additional influenza B virus (B/Phuket/3073/2013-like [B/Yamagata lineage]) recommended for quadrivalent vaccines.**** Data obtained from antigenic characterization are important in the assessment of the similarity between reference vaccine viruses and circulating viruses. In vitro antigenic characterization data acquired through hemagglutination inhibition (HI) assays or virus neutralization-based focus reduction assays (FRAs) evaluate whether genetic changes in circulating viruses affect antigenicity; substantial differences could affect vaccine effectiveness. Nearly all influenza viruses received by CDC are genomically characterized using next generation sequencing, and the genomic data are analyzed and submitted to public databases (GenBank: https://www.ncbi.nlm.nih.gov/genbank or EpiFlu: https://www.gisaid.org/). CDC antigenically or genetically characterized 680 influenza viruses collected and submitted by U.S. laboratories and laboratories outside the United States during May 20–October 13, including 351 influenza A(H1N1)pdm09 viruses, 185 influenza A(H3N2) viruses, and 144 influenza B viruses.

Phylogenetic analysis of the A(H1N1)pdm09 hemagglutinin (HA) genes of viruses collected globally since May 20, 2018, identified viruses belonging to HA genetic subgroup 6B.1 (Figure 3). All of the A(H1N1)pdm09 viruses tested (57 in and 87 outside the United States) were antigenically similar (analyzed using HI tests with ferret antisera) to egg and cell-propagated A/Michigan/45/2015 viruses, which are in genetic group 6B.1 and are reference viruses representing the influenza A(H1N1) component of the Northern Hemisphere 2018–19 influenza vaccine.

Figure 3.

Genetic characterization of influenza viruses collected in and outside of the United States during May 20–October 13, 2018

Among 185 influenza A(H3N2) viruses collected and sequenced since May 20, 2018, phylogenetic analyses indicated cocirculation of multiple clades and subgroups of HA genes. The HA genes of the viruses belonged to genetic groups 3C.2a, 3C.2a1, and 3C.3a, with 3C.2a predominating (Figure 3). The majority of genetic group 3C.2a viruses (89% [86/94]) belonged to subclade 3C.2a2. A subset of 111 influenza A(H3N2) viruses was antigenically characterized by HI or FRA (43 in and 68 outside the United States); 102 (91.9%) were well inhibited by ferret antisera raised against cell-propagated A/Singapore/INFIMH-16–0019/2016 (3C.2a1), the reference virus representing the A(H3N2) component of Northern Hemisphere 2018–19 influenza vaccines. However, combined data generated by the WHO GISRS Collaborating Centers demonstrated that ferret antisera raised against egg-propagated A/Singapore/INFIMH-16–0019/2016-like viruses inhibited a smaller proportion of recently circulating viruses. In contrast, ferret antisera raised against egg-propagated A/Switzerland/8060/2017 inhibited the majority of viruses belonging to the globally-predominant subclade 3C.2a2, which was a factor leading to an update of the recommended influenza A(H3N2) component for egg-based vaccines for the 2019 Southern Hemisphere influenza vaccine.††††

Thirty-six influenza B/Victoria-lineage viruses were phylogenetically analyzed. All HA genes belonged to genetic group V1A and 31 (86.1%), belonged to subgroup V1A.1, represented by B/Colorado/06/2017, the reference virus representing the B/Victoria lineage component of Northern Hemisphere 2018–19 influenza vaccines. The V1A.1 subgroup is characterized by a two amino acid deletion in the HA at residues 162–163. One virus belonging to the genetic group V1A-3DEL was identified. This virus had a three amino acid deletion (amino acid residues 162–164) in the HA; similar viruses were identified sporadically in several countries in recent months. Eighteen of 19 antigenically characterized B/Victoria lineage viruses (10 in and nine outside the United States) were well inhibited by ferret antisera raised against cell-propagated B/Colorado/06/2017-like viruses.

Phylogenetic analysis of the influenza B/Yamagata lineage viruses sequenced showed that all HA genes belonged to genetic group Y3 (Figure 3). Among 65 influenza B/Yamagata lineage viruses antigenically characterized (32 in and 33 outside the United States), all were well inhibited by ferret antisera raised against cell-propagated B/Phuket/3073/2013-like viruses, the reference virus representing the influenza B/Yamagata lineage component of the Northern Hemisphere 2018–19 quadrivalent vaccines.

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