Report on influenza viruses received and tested by the Melbourne WHO Collaborating Centre for Reference and Research on Influenza in 2019 - Report ...
←
→
Page content transcription
If your browser does not render page correctly, please read the page content below
2021 Volume 45 https://doi.org/10.33321/cdi.2021.45.43 Report on influenza viruses received and tested by the Melbourne WHO Collaborating Centre for Reference and Research on Influenza in 2019 Heidi Peck, Jean Moselen, Sook Kwan Brown, Megan Triantafilou, Hilda Lau, Miguel Grau, Ian G Barr, Vivian KY Leung
Communicable Diseases Intelligence Communicable Diseases Intelligence
ISSN: 2209-6051 Online (CDI) is a peer-reviewed scientific journal
published by the Office of Health Protection
and Response, Department of Health. The
This journal is indexed by Index Medicus and Medline.
journal aims to disseminate information on
the epidemiology, surveillance, prevention
Creative Commons Licence - Attribution-NonCommercial-
and control of communicable diseases of
NoDerivatives CC BY-NC-ND
relevance to Australia.
© 2021 Commonwealth of Australia as represented by the
Editor
Department of Health
Jennie Hood
This publication is licensed under a Creative Commons Attribution-
Deputy Editor
Non-Commercial NoDerivatives 4.0 International Licence from
Simon Petrie
https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
(Licence). You must read and understand the Licence before using
Design and Production
any material from this publication.
Kasra Yousefi
Restrictions
Editorial Advisory Board
The Licence does not cover, and there is no permission given for, use
David Durrheim,
of any of the following material found in this publication (if any):
Mark Ferson, John Kaldor,
Martyn Kirk and Linda Selvey
• the Commonwealth Coat of Arms (by way of information, the
terms under which the Coat of Arms may be used can be found at
Website
www.itsanhonour.gov.au);
http://www.health.gov.au/cdi
• any logos (including the Department of Health’s logo) and
Contacts
trademarks;
CDI is produced by the
Office of Health Protection
• any photographs and images;
and Response, Australian
• any signatures; and Government Department of
Health, GPO Box 9848, (MDP 6)
• any material belonging to third parties. CANBERRA ACT 2601
Disclaimer Email:
Opinions expressed in Communicable Diseases Intelligence are cdi.editor@health.gov.au
those of the authors and not necessarily those of the Australian
Government Department of Health or the Communicable Diseases Submit an Article
Network Australia. Data may be subject to revision. You are invited to submit
your next communicable
Enquiries disease related article
Enquiries regarding any other use of this publication should be to the Communicable
addressed to the Communication Branch, Department of Health, Diseases Intelligence (CDI)
GPO Box 9848, Canberra ACT 2601, or via e-mail to: for consideration. More
copyright@health.gov.au information regarding CDI can
be found at:
Communicable Diseases Network Australia http://health.gov.au/cdi.
Communicable Diseases Intelligence contributes to the work of the
Communicable Diseases Network Australia. Further enquiries should be
http://www.health.gov.au/cdna directed to:
cdi.editor@health.gov.au.Annual report
Report on influenza viruses received and tested
by the Melbourne WHO Collaborating Centre for
Reference and Research on Influenza in 2019
Heidi Peck, Jean Moselen, Sook Kwan Brown, Megan Triantafilou, Hilda Lau, Miguel Grau, Ian G Barr, Vivian KY Leung
Abstract
As part of its role in the World Health Organization’s (WHO) Global Influenza Surveillance and
Response System (GISRS), the WHO Collaborating Centre for Reference and Research on Influenza
in Melbourne received a record total of 9,266 human influenza positive samples during 2019. Viruses
were analysed for their antigenic, genetic and antiviral susceptibility properties. Selected viruses
were propagated in qualified cells or embryonated hen’s eggs for potential use in seasonal influenza
virus vaccines. In 2019, influenza A(H3N2) viruses predominated over influenza A(H1N1)pdm09
and B viruses, accounting for a total of 51% of all viruses analysed. The majority of A(H1N1)pdm09,
A(H3N2) and influenza B viruses analysed at the Centre were found to be antigenically similar to the
respective WHO recommended vaccine strains for the Southern Hemisphere in 2019. However, phy-
logenetic analysis indicated that a significant proportion of circulating A(H3N2) viruses had under-
gone genetic drift relative to the WHO recommended vaccine strain for 2019. Of 5,301 samples tested
for susceptibility to the neuraminidase inhibitors oseltamivir and zanamivir, four A(H1N1)pdm09
viruses showed highly reduced inhibition with oseltamivir, one A(H1N1)pdm09 virus showed highly
reduced inhibition with zanamivir and three B/Victoria viruses showed highly reduced inhibition
with zanamivir.
Keywords: influenza, vaccines, GISRS, surveillance, laboratory, annual report, WHO
Introduction recommendations on which influenza strains
should be included in the influenza vaccine for
The World Health Organization (WHO) the upcoming influenza season in either the
Collaborating Centre for Reference and Research northern or southern hemisphere. This report
on Influenza in Melbourne (the Centre) is summarises the results of virological surveil-
part of the World Health Organization Global lance activities undertaken at the Centre in
Influenza Surveillance and Response System Melbourne during 2019.
(WHO GISRS). GISRS is a worldwide network
of laboratories that was established in 1952 to Two types of influenza viruses (A and B) cause
monitor changes in influenza viruses circulat- significant disease in humans. Influenza A
ing in the human population, with the aim of viruses are further classified into subtypes,
reducing influenza’s impact through the use based on their haemagglutinin (HA) and neu-
of vaccines and antiviral drugs.1,2 The Centre raminidase (NA) surface proteins. Globally,
in Melbourne is one of five such Collaborating there are currently two influenza A subtypes
Centres (others are in Atlanta, Beijing, London circulating in the human population – A(H1N1)
and Tokyo) that monitor antigenic and genetic pdm09 and A(H3N2). Influenza B viruses are
changes in circulating human influenza viruses; not classified into subtypes; however, there are
the Centre participates in making twice-yearly two distinct co-circulating lineages of influenza
health.gov.au/cdi Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 1 of 16B viruses – B/Victoria/2/87 (B/Victoria lineage) B/Colorado/06/2017-like (Victoria lineage), and
and B/Yamagata/16/88 (B/Yamagata lineage). B/Phuket/3073/2013-like (Yamagata lineage)
Influenza C viruses are also detected each year viruses that were recommended for inclusion
from humans, but these viruses do not cause in the southern hemisphere 2019 influenza
severe disease and are not a major focus of vaccine. In recent years (including 2019), HI
influenza surveillance. assays involving A(H3N2) viruses have been
performed in the presence of 20 nM oseltamivir
Methods carboxylate (OC) to reduce non-specific bind-
ing of the NA protein.5 The addition of OC
Virus isolation reduces the number of influenza virus isolates
that can be tested by HI because around 11% of
All A(H1N1)pdm09 and influenza B viral iso- viruses lose the ability to bind RBC and there-
lates received at the Centre were re-passaged in fore cannot be assayed by HI. To test a subset
cell culture using Madin-Darby Canine Kidney of these viruses, the Centre has employed the
(MDCK) cells, whilst all A(H3N2) viral isolates Focus Reduction Assay (FRA), a microneutrali-
were re-passaged in MDCK-SIAT-1 cells.3 Virus sation assay which is more specific and sensitive
isolation in cell culture was also attempted than the HI assay and does not require bind-
from a selection of original clinical specimens ing to RBCs.6 The FRA utilised the same ferret
received using the same cell types as described antisera as did the HI assay and was performed
above when the type/subtype was known. A as previously described,7 but with 1.2% Avicell
smaller subset of influenza-positive original RC591 (IMCD Mulgrave, Australia) replacing
clinical samples was directly inoculated into the carboxymethyl cellulose.
eggs and a qualified cell line to generate poten-
tial candidate vaccine viruses (CVV). Genetic analysis
Antigenic analysis For influenza-positive samples that failed to
grow in MDCK cells, real-time reverse tran-
The antigenic properties of influenza viral iso- scription polymerase chain reaction (RT-PCR)
lates were analysed using the haemagglutination was performed to determine the influenza type/
inhibition (HI) assay as previously described4 subtype/lineage using the CDC Influenza Virus
and by the Focus Reduction Assay (FRA) for a Real-Time RT-PCR kit.i
subset of A(H3N2) viruses. The majority of the
HI assays were performed using the TECAN A substantial subset of influenza viruses ana-
Freedom EVO200 robot platform which incor- lysed at the Centre underwent genetic analysis
porates a camera (SciRobotics, Kfar Saba, by sequencing of viral RNA genes – usually
Israel) and imaging software (FluHemaTM) for HA and NA genes as well as the matrix gene
automated analysis. In HI assays, viruses were for influenza A viruses and non-structural pro-
tested for their ability to agglutinate turkey tein gene (NS) for influenza B viruses. Whole
(A(H1N1)pdm09 and B viruses) or guinea pig genome sequencing (WGS) of a smaller subset
(A(H3N2)) red blood cells (RBC) in the pres- of viruses was also performed.
ence of post-infection ferret antisera raised
against several reference viruses. Isolates were
identified as antigenically similar to the refer- i The CDC Influenza Virus Real-Time RT-PCR Influenza A/B
ence strain if the test samples had a titre that Typing Panel (RUO) (Catalog No. FluRUO-01), FR-198, was
was no more than 4-fold higher than the titre obtained through the International Reagent Resource,
of the homologous reference strain. During Influenza Division, WHO Collaborating Center for Surveillance,
2019, results were reported with reference Epidemiology and Control of Influenza, Centers for Disease
to the A/Michigan/45/2009 (H1N1pdm09)- Control and Prevention, Atlanta, GA, USA. https://www.
like, A/Switzerland/8060/2017 (H3N2)-like, internationalreagentresource.org/.
2 of 16 Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 health.gov.au/cdiFor sequencing, RNA was extracted from iso- Australia). For reporting purposes, ‘highly
lates or original clinical specimens using either reduced inhibition’ of influenza A viruses has
a manual QIAGEN QIAamp Viral RNA kit been defined by WHO as a ≥ 100-fold increase
or the automated QIAGEN QIAXtractor plat- in IC50 in a NAI assay. For influenza B viruses,
form, followed by RT-PCR using the BIOLINE this figure was a ≥ 50-fold increase. However, it
MyTaq one step RT-PCR kit according to the should be noted that the relationship between
manufacturer’s recommendations, with gene- the IC50 value and the clinical effectiveness
specific primers (primer sequences available on of a neuraminidase inhibitor is not yet well
request). Conventional Sanger sequencing was understood and a small or medium reduction
carried out on PCR products using an Applied in inhibition may not be clinically significant.
Biosystems 3500XL Genetic Analyzer (Applied
Biosystems, Foster City, CA, USA). Sequence Viruses found to have highly reduced inhibition
assembly was performed using the Geneious by either oseltamivir or zanamivir underwent
Prime software version 9.0.4 (Biomatters Ltd, genetic analysis using pyrosequencing, Sanger
Auckland, New Zealand). sequencing or WGS to determine the presence
of amino acid substitutions in the NA protein
WGS was performed on a selection of viruses that were associated with the reduction of inhi-
using the SuperScript-III One-Step Platinum bition by neuraminidase inhibitors. For exam-
Hi-Fi PCR kit according to the manufacturer’s ple, a change from histidine to tyrosine at posi-
recommendations, with universal primers tion 275 (H275Y) of the NA protein of A(H1N1)
(primer sequences available on request). WGS pdm09 viruses is known to reduce inhibition by
was conducted using an Applied Biosystems oseltamivir, as does the H273Y NA mutation in
Ion TorrentTM Personal Genome MachineTM B viruses.9 Pyrosequencing was also performed
(PGM) System according to the manufacturer’s on original clinical specimens of selected
recommendations. These sequences were ana- viruses which may have contained a known
lysed using a proprietary pipeline, FluLINE.8 mutation such as H275Y if no isolate was avail-
Phylogenetic analysis was performed using able for phenotypic testing. Pyrosequencing
Geneious 9.0.4 and FigTree v1.3.1 software. was performed as previously described10 using
the MyTaq One-Step RT-PCR Kit (QIAGEN,
Antiviral drug resistance testing Hilden, Germany) for virus amplification, with
pyrosequencing reactions performed using
Circulating viruses were tested for their the PyroMark instrument (QIAGEN, Hilden,
sensitivity to the currently-used neurami- Germany).
nidase inhibitors oseltamivir (Tamiflu) and
zanamivir (Relenza). The neuraminidase Candidate vaccine strains
inhibition (NAI) assay used was a func-
tional fluorescence-based assay using the The viruses used in production of human influ-
substrate 2’-(4-methylumbelliferyl)-α-D-N- enza vaccines are required by regulatory author-
acetylneuraminic acid (MUNANA), in which ities to be isolated and passaged in embryonated
the susceptibility of test viruses to the antiviral hen’s eggs or qualified cell lines11–13 directly from
drugs was measured in terms of the drug con- human clinical respiratory samples. The Centre
centration needed to reduce the influenza neu- has undertaken primary isolation of selected
raminidase enzymatic activity by 50% (IC50), viruses from clinical samples directly into eggs,
and compared to values obtained with sensitive using previously described methods.14 Briefly,
reference viruses of the same subtype or line- the viruses were inoculated into the amniotic
age. NAI assays were performed as previously cavity of embryonated eggs and, once virus
described,9 with the incorporation of a robotic growth was established, isolates were passaged
platform by Tecan EVO 200 and Infinite 200Pro in the allantoic cavity until a sufficient titre was
for liquid handling and plate reading (Tecan obtained. Egg incubation conditions differed
health.gov.au/cdi Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 3 of 16slightly, with A(H1N1)pdm09 and A(H3N2) A(H1N1)pdm09 and B. For samples received
viruses incubated at 35 oC for three days, and from Australia where the lineage was con-
influenza B viruses incubated at 33 oC for three firmed, B/Victoria viruses predominated sig-
days. In addition, selected clinical samples were nificantly over B/Yamagata viruses (93% and
inoculated into the qualified cell line MDCK 7% of B viruses respectively). Overall, isolation
33016PF (Seqirus Limited, Holly Springs, NC, and re-passaging was attempted for 9,146 (99%)
USA)15 and incubated at 35 oC for three days, of the samples received and this yielded 6,101
with viral growth monitored by haemagglu- isolates (overall isolation rate of 67%). Isolation
tination of turkey or guinea pig RBC. These rates were lower for clinical specimens (60.5%)
isolates were then analysed by HI assay, real than for virus isolates received (94.9%). Of the
time RT-PCR and genetic sequencing using the viruses for which type and subtype could be
methods described above. confirmed, isolation rates by cell propagation
were 75% (1,767/2,350) for A(H1N1)pdm09;
Results 81% (3,150/3,911) for A(H3N2); and 81%
(1,142/1,407) for influenza B. However, amongst
During 2019, the Centre received 9,266 samples these viruses, 15% (464/3,150) of A(H3N2) iso-
(including 7,687 clinical specimens, 1,014 virus lates did not reach sufficient titres for antigenic
isolates and 569 paired specimens and isolates) analysis. A total of 4,445 viral isolates were
from 40 laboratories in 17 countries (Figure successfully characterised by HI assay, and
1). As in previous years, most samples were were compared to the 2019 reference viruses
submitted by laboratories in the Asia-Pacific (Table 1). In addition, 991 samples were charac-
region,16–19 with the majority received from terised by real-time RT-PCR to determine their
Australia (7,410 samples; 80%). However, unlike type/subtype or lineage. Sanger sequencing and
previous years, a large number of samples were WGS techniques were used to sequence the HA
received between January and April, which is genes of 2,487 viruses. The full genomes of 415
before the typical Southern Hemisphere tem- viruses were also sequenced using either Sanger
perate regions influenza season. Figure 2 shows sequencing or WGS. Of the samples for which
the weekly temporal distribution of samples results could be obtained by antigenic or genetic
sent to the Centre by type and subtype/line- analysis (n = 6,368), influenza A(H3N2) viruses
age. During 2019, influenza A(H3N2) was the predominated, comprising 49% (n = 3,133) of
predominant circulating strain, followed by viruses received and analysed.
Figure 1: Geographic spread of influenza laboratories sending viruses to the Centre during 2019
4 of 16 Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 health.gov.au/cdiTable 1: Antigenic analysis of viruses received by the Centre in 2019, by geographic region of origin
A(H1N1)pdm09 reference strain: A(H3N2)a reference strain: B/Victoria reference strain: B/Yamagata reference strain:
health.gov.au/cdi
A/Michigan/45/2015 (cell) A/Switzerland/8060/2017 (cell) B/Colorado/06/2017 (cell) B/Phuket/3073/2013 (cell)
Low reactor Low reactor Low reactor Low reactor
Region Like Like Like Like
(%) (%) (%) (%)
Australasia 1,136 31 (2.7%) 1,214 347 (22.2%) 503 64 (11.3%) 41 1 (2.4%)
South East Asia 298 26 (8%) 58 96 (62.3%) 118 48 (28.9%) 79 0
Pacific 80 34 (29.8%) 25 5 (16.7%) 99 22 (18.2%) 2 0
Africa 3 0 4 11 (73.3%) 0 0 0 0
South Asia 13 0 0 5 (100%) 18 0 4 0
East Asia 31 3 (8.8%) 4 1 (20%) 11 9 (45%) 1 0
Total 1,561 94 (5.7%) 1,305 465 (26.3%) 749 143 (16%) 127 1 (0.8%)
a Note that a small number of A(H3N2) virus isolates that were obtained could not be analysed by HI assay due to low haemagglutination assay (HA) titre in the presence of oseltamivir.
Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021
5 of 16Figure 2: Number of samples received at the Centre by week of sample collection 2019
300
A(H1N1)pdm09
A(H3N2)
250
B/Victoria
B/Yamagata
200
Number of samples received
150
100
50
0
1 2 3 4 5 6 7 8 9 10 11 12 13 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
Week of sample collection
A(H1N1)pdm09 Of 1,701 A(H1N1)pdm09 viruses tested, three
viruses exhibited highly reduced inhibition
Of the 1,655 A(H1N1)pdm09 isolates analysed by oseltamivir and one virus exhibited highly
by HI assay using ferret antisera in 2019, a reduced inhibition by zanamivir. The viruses
majority (94%) were antigenically similar to the showing highly reduced inhibition by oseltami-
vaccine reference strain A/Michigan/45/2015 vir (two from Australia and one from Malaysia)
(Table 1). were confirmed to contain the H275Y substitu-
tion in their NA genes, a known mutation that
Sequencing and phylogenetic analysis of HA is associated with highly reduced inhibition by
genes from 644 viruses showed that all A(H1N1) oseltamivir. Another NA substitution linked
pdm09 viruses sent to the Centre during 2019 to the reduction in inhibition by zanamivir
fell into the 6B.1 clade (Figure 3). The majority was also identified in one of the viruses from
of these viruses reacted in a similar manner to Australia.20 This virus was confirmed to contain
the 2019 vaccine virus A/Michigan/45/2015 in the E119G substitution in its NA gene.
HI assays using ferret antisera.
Eighteen A(H1N1)pdm09 viruses were inocu-
lated into eggs for isolation of candidate vaccine
strains with 16 (89%) successfully isolated; all
fell into the genetic subclade 6B.1A. Thirty-nine
viruses were inoculated into the qualified cell
line MDCK 33016PF, of which 25 (64%) grew
successfully and all also fell into the genetic
subclade 6B.1A.
6 of 16 Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 health.gov.au/cdiFigure 3: Phylogenetic tree of haemagglutinin genes of A(H1N1)pdm09 viruses received by the
Centre during 2019
A/Victoria/265/2019 oct
A/Ratchaburi/435/2019 nov
A/Lopburi/4448/2019 dec
Legend A/Perth/182/2019 dec
niidA/Okinawa/93/2019 aug
A/Perth/1156/2019 dec
#2019 SOUTHERN HEMISPHERE VACCINE STRAIN A/South Australia/476/2019 dec
A/Sydney/1237/2019 nov
A/Brisbane/146/2019 oct
e: egg isolate A/Canberra/411/2019 nov
A/Perth/1154/2019 oct
A/Victoria/2569/2019 nov
^REFERENCE VIRUS A/Philippines/39/2019 oct
A/Chanthaburi/443/2019 nov
A/Malaysia/RP2260/2019 oct
│Braces indicate clades R45K
A/Philippines/34/2019 oct
T120I
A/Sydney/454/2019 oct
(+/-) Indicates gain/loss of a potential glycosylation site. A/Brisbane/149/2019 oct
A/Brisbane/144/2019 oct
A/Philippines/37/2019 oct
Scale bar represents 0.3% nucleotide sequence difference A/Canberra/415/2019 nov
A/South Australia/1128/2019 dec
between viruses. Amino acid changes relative to the outgroup D187A A/Perth/178/2019 nov
sequence (A/CALIFORNIA/07/2009e) are shown. Q189E A/Brisbane/142/2019 oct
A/Malaysia/UM015/2019 oct
A/Sydney/1235/2019 nov
D187V A/Guangdong-Maonan/SWL1536/2019e jun
A/Victoria/2455/2019e aug
A/Victoria/2454/2019e aug
A/Malaysia/RP2253/2019 oct
A/Lopburi/440/2019 nov
A/Sydney/451/2019 oct
A/Malaysia/RP2255/2019 oct 183P-5A
A/Chiang Rai/1391/2019 dec
A186T A/Victoria/267/2019 oct
A/Darwin/739/2019 oct
A/Malaysia/RP2261/2019 oct
A/Nakhonphanom/487/2019 dec
A/Bangkok/426/2019 oct
A/Nakhonsithammarat/425/2019 oct
A/South Australia/466/2019 nov
A/South Africa/R05624/2019 may
A/South Australia/451/2019 oct
A/Victoria/2568/2019 nov 6B.1A/183P-5
A/Cambodia/D1216368/2019 nov
mohA/Singapore/GP2220/2019 nov
A/Victoria/2570/2019 nov
K504R A/Philippines/31/2019 oct
A/Sri Lanka/15/2019 apr
A/Darwin/764/2019 nov
A/Brunei/8/2019 mar
A/Macau/600148/2019 jan
A/Cambodia/d0619361/2019 may
A/New Caledonia/87/2019 may
A/South Australia/477/2019 dec
A/Timor Leste/41/2019 apr
A/New Caledonia/67/2019 jun
A/New Caledonia/95/2019 jun
A/Sri Lanka/40/2019 aug
A/Victoria/214/2019e aug
N129D A/Darwin/639/2019e aug
T185I A/Victoria/255/2019 sep
A/Victoria/212/2019e aug
^A/DARWIN/6/2018e
A/Darwin/123/2018e
A/Darwin/122/2018e
A/Darwin/125/2018e
A/Darwin/1024/2019 nov
A/Perth/193/2019 nov
A/Canberra/417/2019 nov
K520A
N260D A/Darwin/738/2019 oct
A/CANBERRA/337/2019e aug
A/Canberra/394/2019 oct
A/Canberra/400/2019 oct
A/South Australia/456/2019 oct
A/Darwin/784/2019 dec
K130N, K160M A/South Australia/471/2019 nov 183P-5B
T216K, H296M A/Philippines/27/2019 sep
A/Wellington/36/2019 jun
A/Brisbane/147/2019 oct
A/Iowa/12/2019e jun
^crickA/SWITZERLAND/3330/2017e
E235D A/Fiji/54/2018e
V520A A/South Australia/49/2018e sep
A/Darwin/4/2018e oct
A/Brisbane/59/2018e
P183S ^A/SOUTH AUSTRALIA/272/2017e
T120A A/Fujian Gulou/SWL1884/2018e 183P-6
A/Newcastle/31/2019 mar
A/South Africa/R03973/2019 apr
^A/BRISBANE/157/2018
A/Canberra/13/2019e jan
A/Darwin/102/2019e mar
A/Newcastle/46/2019e mar
A/Brunei/5/2019e feb
A/Brunei/54/2019 apr
A/Fiji/26/2019 mar
A/Fiji/51/2019 mar 183P-2
L233I A/Brisbane/70/2018e
V520A A/Brisbane/72/2018e
A/Brisbane/68/2018e 6B.1A
^A/CHRISTCHURCH/506/2018e
A/Cambodia/FSS40727/2019 jun
R45G, P282A ^A/TOWNSVILLE/21/2018
I298V
A/Christchurch/515/2018e
^A/PERTH/183/2018 nov 183P-4
^A/BRISBANE/02/2018e
A/Newcastle/45/2018e
A/BeijingXicheng/SWL1633/2018e
183P-1
A/Timor-Leste/94/2019 apr
K302T, I404M A/Timor Leste/34/2019 mar
S74R, S164T, S183P N496S, E506D A/Victoria/700/2019 mar 183P-7
P83S, S84N, D97N, S162N (+) R223Q, I295V ^A/INDIANA/30/2019
K163Q, S185T, S203T, I216T A/Macau/600080/2019 jan
A256T, K283E, I321V, E374K ^cdcA/MEXICO/2549/2018 183P-3
S451N, E499K A/MICHIGAN/45/2015e ^A/BRISBANE/37/2017
^A/CALIFORNIA/07/2009e
0.003
health.gov.au/cdi Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 7 of 16A(H3N2) None of the 2,323 A(H3N2) viruses tested by
NAI assay showed highly reduced inhibition by
Antigenic analysis of 2,104 A(H3N2) subtype oseltamivir or zanamivir.
isolates using the HI assay showed that 26%
were low reactors to the ferret antisera prepared Influenza B
against the cell-propagated reference strain A/
Switzerland/8060/2017/2017 (Table 1). However, Amongst influenza B viruses received at the
99% of viruses were low reactors to the ferret Centre during 2019, B/Victoria-lineage viruses
antisera prepared against the egg-propagated were predominant over B/Yamagata-lineage
strain A/Switzerland/8060/2017 (data not viruses (Figure 2). A total of 1,020 influenza B
shown). An additional 464 A(H3N2) viruses viruses were characterised by HI assay. Almost
were inoculated and isolated by cell culture all B/Yamagata-lineage viruses were antigeni-
but did not reach sufficient titres for antigenic cally similar to the B/Phuket/3073/2013-like
analysis, whilst a further 334 were successfully vaccine virus, while 84% of B/Victoria-lineage
isolated but did not reach sufficient titres when viruses were antigenically similar to the
tested by HI assay in the presence of oseltamivir B/Colorado/06/2017 vaccine virus (Table 1).
carboxylate.
Sequencing was performed on HA genes from 367
A total of 75 A(H3N2) viruses that could not be B/Victoria viruses and 88 B/Yamagata viruses. A
characterised by HI assay were analysed using the small number of B viruses (51/367; 14%) were
FRA assay. The FRA assay indicated that 16% of genetically similar to the B/Colorado/06/2017
these viruses showed greater than four-fold dif- reference virus, with a two-amino-acid deletion
ference in titre compared to the cell-propagated in the HA protein (positions 162–163) (Figure 5);
reference strain A/Switzerland/8060/2017; how- however, the majority of viruses (272/367; 74%)
ever, the majority of viruses (93%) had a greater had a three-amino-acid deletion in the HA pro-
than four-fold difference in titre compared to tein at positions 162–164 and formed a separate
the egg-propagated strain (data not shown). phylogenetic clade from the B/Colorado/06/2017
clade. All B/Yamagata-lineage viruses belonged
The HA genes of 1,309 A(H3N2) viruses to genetic clade 3 (or Y3), which is the same
were sequenced. Phylogenetic analysis indi- genetic clade as the 2019 vaccine virus B/
cated that the majority of circulating viruses Phuket/3073/2013 (Figure 6).
fell into subclade 3C.2a1b based on their
HA genes, whereas the 2019 vaccine strain, Egg isolation was attempted for 15 B/Victoria
A/Switzerland/8060/2017 fell into subclade and eight B/Yamagata-lineage viruses, result-
3C.2a2 (Figure 4). A small number of A(H3N2) ing in the successful isolation of 11 (73%)
viruses fell into the 3C.3a and 3C.2a3 clades. B/Victoria-lineage viruses and four (50%) B/
Yamagata-lineage viruses. All B/Victoria-lineage
Forty-seven viruses were inoculated into viruses isolated were from genetic subclade V1A,
eggs, of which 27 (57%) grew successfully and two of which were further grouped into V1A.1
consisted of 21 viruses from genetic subclades and eight others in V1A.3. All B/Yamagata-
3C.2a1b+131K and two from 3C.2a1b+135K. lineage viruses isolated were from genetic clade
Additionally, four subclade 3C.3a viruses were Y3. For viruses inoculated into the qualified
isolated. Fifty-seven viruses were inoculated into cell line MDCK 33016PF, nine of 16 (56%) B/
the qualified cell line MDCK 33016PF, of which Victoria-lineage viruses and four (80%) of five B/
38 (67%) grew successfully, with 23 viruses from Yamagata-lineage viruses were isolated. At least
genetic subclades 3C.2a1b+131K, four from one representative from the major clades of each
3C.2a1b+135K and 11 from 3C.3a. B lineage was isolated. A total of 21 viruses were
inoculated into the qualified cell line MDCK
33016PF, of which 13 (62%) grew successfully.
8 of 16 Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 health.gov.au/cdiFigure 4: Phylogenetic tree of haemagglutinin genes of A(H3N2) viruses received by the Centre
during 2019
Legend A/South Australia/464/2019 nov
A/South Australia/457/2019 oct
#2019 SOUTHERN HEMISPHERE VACCINE STRAIN A/Victoria/2542/2019 oct
A/South Australia/467/2019 nov
A/Victoria/2854/2019 oct
e: egg isolate A/Victoria/2540/2019 oct
A/Victoria/2490/2019 sep
A/South Australia/468/2019 nov
^REFERENCE VIRUS A/Shanghai-Jiading/197/2019 dec
A/Victoria/2580/2019 nov
│Braces indicate clades A/Sydney/1228/2019 sep
A/Tasmania/1038/2019 oct +197R
A/Victoria/2565/2019 oct
(+/-) Indicates gain/loss of a potential glycosylation site. Q197R A/Perth/1051/2019 jun
E484G A/Victoria/2479/2019 sep
A/Darwin/727/2019 oct
Scale bar represents 0.3% nucleotide sequence difference A/South Australia/439/2019 oct
between viruses. Amino acid changes relative to the outgroup A/Victoria/169/2019e jul
sequence (A/TEXAS/50/2012) are shown. A/Tasmania/1037/2019 sep
A/Tasmania/557/2019 may
A/South Australia/447/2019 oct
A/Canberra/398/2019 oct
A/Tasmania/1025/2019 jul
A/Sydney/478/2019 sep
A/Canberra/412/2019 nov
A/Darwin/402/2019e may
A/Darwin/384/2019e may
A/Victoria/718/2019e may
A/South Australia/36/2019e feb
A/Nonthaburi/424/2019 oct
A/Ayutthaya/458/2019 nov
A/South Africa/R05117/2019 may
A/New Caledonia/59/2019e mar
A/Christchurch/516/2019e apr
A/New Caledonia/99/2019 jul
A/Victoria/2539/2019 oct
A/Brisbane/1137/2019 sep
A/Christchurch/514/2019e apr 3C.2a1b+131K
A/Sri Lanka/41/2019 aug
A/Victoria/2534/2019 sep
A/South Africa//R06415/2019 jun
A/Sri Lanka/35/2019 jul
A/Cambodia/FSS40728/2019 jun
A/South Australia/82/2019e feb
A/Newcastle/42/2019e mar
^A/SOUTH AUSTRALIA/34/2019e feb
^A/NEWCASTLE/82/2018e
A/Sydney/53/2019e mar
V347M A/Hawkes Bay/1/2019 mar
V505I A/Bangkok/454/2019 nov
A/Victoria/2573/2019 nov
A/South Australia/39/2019e feb
A/Newcastle/83/2018e
A/ChiangRai/449/2019 nov
T131K A/South Australia/469/2019 nov
V529I A/Canberra/407/2019 oct
A/Victoria/2566/2019 nov
A/South Australia/474/2019 nov
A/Malaysia/RP2256/2019 oct
A/Sydney/1234/2019 oct
crickA/Qatar/16-VI-19-0049409/2019 aug
K83E A/Victoria/2845/2019 oct
A/Sri Lanka/23/2019 jul
A/Sri Lanka/27/2019 jul
mohA/Singapore/EN0894/2019 nov
A/Victoria/213/2019 aug
A/Philippines/46/2019 sep
E62G, K92R, N121K, R142G A/Victoria/268/2019 oct
K160T(+), N171K, H311Q A/Victoria/2833/2019 sep
I406V, G484E A/Darwin/730/2019 oct
E50K A/Philippines/40/2019 oct
A/Philippines/51/2019 nov
+137F
cdcA/Hong Kong/2671/2019 jun
A/Macau/603415/2019may
S137F A/Hong Kong/45/2019
mohA/Singapore/TT0882/2019 nov
A/South Australia/2/2019e jan
3C.2a1b+135K
A/South Australia/4/2019e jan
A/Brisbane/148/2019e oct
A/Victoria/2574/2019 nov
A/Hong Kong/681/2018e
A/Timor Leste/5/2019 mar
A/South Africa/R03989/2019 apr
^A/FIJI/71/2017
T135K(-) G62E ^A/SYDNEY/22/2018e
K135N ^A/PHILIPPINES/13/2017 3C.2a1b+135N
T131K, R142K, L194P, R261Q A/SWITZERLAND/8060/2017e
A/South Australia/10/2018e
3C.2a2
A/Timor Leste/3/2019 mar
T30A, T128A(-), T135K(-) A/TimorLeste/43/2019 mar
L3I, N144S(-) S144K R142G, R261Q
A/Malaysia/RP0118/2019 3C.2a3
S159Y, V186G ^A/SINGAPORE/TT1374/2016e
Q311H, D489N
^A/MICHIGAN/15/2014
^A/HONG KONG/4801/2014e 3C.2a
A/Townsville/60/2019 oct
A/Brisbane/141/2019 oct
A/Darwin/725/2019 oct
A/Brisbane/145/2019 oct
A/Brisbane/1024/2019 jul
A/Darwin/721/2019 sep
A/Townsville/59/2019 oct
A/Sydney/475/2019 sep
A/Victoria/2482/2019 sep
K82R A/South Australia/458/2019 oct
A/Wellington/53/2019 sep
H56Y, N121D A/Canberra/23/2019 feb
A/Perth/1113/2019 jul 3C.3a
A/South Australia/218/2019e mar
^A/KANSAS/14/2017e
I478M A/Victoria/703/2019e apr
A/Newcastle/623/2019e feb
A/South Australia/470/2019 nov
L3I, S91N, N144K(-) A/South Africa/R06423/2019 jun
V186G, F193S, D489N A/South Africa/R06864/2019 jun
T128A,(-) A138S A/Beijing/2019 15554/2018e
R142G, K326R
A/Brisbane/34/2018e
^A/SWITZERLAND/9715293/2013e
^A/TEXAS/50/2012e
0.003
health.gov.au/cdi Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 9 of 16Figure 5: Phylogenetic tree of haemagglutinin genes of B/Victoria-lineage viruses received by the
Centre during 2019
Legend N197K(-)
B/South Australia/1022/2019 sep
B/South Australia/125/2019 oct***
#2019 SOUTHERN HEMISPHERE VACCINE STRAIN B/Chiang Rai/431/2019 oct*
B/Cambodia/FSS42434/2019 nov
B/Chiang Rai/1387/2019 dec*
e: egg isolate B/Yasothon/381/2019 aug
E128K B/Cambodia/D1225364/2019 dec
^REFERENCE VIRUS B/Brunei/17/2019 sep
B/Victoria/2546/2019 nov
B/Canberra/84/2019 oct V1A.3 +128K
│Braces indicate clades B/Darwin/189/2019 dec
B/Philippines/31/2019 oct
B/Darwin/151/2019 oct*
Scale bar represents 0.3% nucleotide sequence difference B/Chiang Rai/452/2019 nov
between viruses. Amino acid changes relative to the outgroup B/Newcastle/1000/2019 jul
sequence (B/BRISBANE/60/2008e) are shown. B/Malaysia/RP2142/2019 oct
B/Cambodia/FSS41540/2019 dec*
B/Darwin/161/2019 oct
(+/-) Indicates gain/loss of a potential glycosylation site. B/Brunei/13/2019 aug
B/Sri Lanka/29/2019 dec*
B/Nakhonphanom/412/2019 nov
2 DEL and 3 DEL indicate subclades containing 2 or 3 amino B/Cambodia/D1216371/2019 nov
acid deletions at the positions162/163 and 162-164 respectively. B/Victoria/46/2019 sep
Deletions are also noted in: B/TimorLeste/3/2019 mar
B/Malaysia/UM008/2019 aug
* = N197X B/Cambodia/D1216360/2019 nov
** = N199X B/Perth/33/2019 jun
*** =N197X & N199X B/Nakhonphanom/460/2019 nov
B/Trang/437/2019 nov
^B/WASHINGTON/02/2019 jan
B/Cambodia/D1016373/2019 oct
B/Macau/602915/2019 apr
B/Victoria/6/2019 jun
B/Ratchaburi/415/2019 oct
A202T B/Victoria/2071/2019 sep
B/Ayutthaya/362/2019 aug
B/Philippines/4/2019 jan
B/Victoria/48/2019 oct**
B/Sydney/52/2019 nov
B/Wellington/15/2019 may
B/Sydney/507/2019 aug V1A.3
T199A(-) B/Darwin/20/2019e mar 3 DEL
B/Darwin/7/2019e mar**
B/Darwin/8/2019e mar**
B/Malaysia/RP2138/2019 jul
B/Townsville/8/2019 sep V1A
B/South Australia/40/2019 apr
B/New Caledonia/10/2019 jul
B/Vanuatu/2/2019 may
G133R B/WallisFutuna/7/2019 jul
B/Victoria/2111/2019 nov
B/Canberra/76/2019 sep**
A127T, N150K B/Newcastle/8/2019 aug
G184E, N197D B/Sri Lanka/26/2019 dec
R279K B/Canberra/87/2019 oct
B/Brisbane/35/2018e
K136E B/Victoria/705/2018e
B/Philippines/28/2019 oct
B/Philippines/27/2019 oct
B/Victoria/2113/2019 dec V1A.3 +150K
B/Victoria/2110/2019 nov
cdcB/Florida/39/2018
I180T, K209N B/Victoria/905/2019 V1A.2
^B/HONG KONG/269/2017e 3 DEL
^B/BRISBANE/46/2015e
B/Sydney/1/2019 jan
B/Fiji/2/2019 apr
B/Brunei/1/2019 jan
B/Perth/1031/2019 jun
^B/TOWNSVILLE/8/2016
B/TimorLeste/5/2019 feb
B/Victoria/25/2019 aug
I180V
B/Perth/32/2019 jun
R498K
N197S(-) B/Perth/1035/2019 jun V1A.1
B/Darwin/69/2019 jun 2 DEL
I117V, V146I B/Townsville/13/2019 nov
D129G
B/Philippines/1/2019 jan
K165N # B/COLORADO/6/2017e
N129D N197S(-)
B/Maryland/15/2016
T221I
B/ZhejiangWuxin/113/2018e
cdcB/CHONGQINGBANAN/1840/2017
^cdcB/TEXAS/02/2013e**
^B/DARWIN/40/2012*
^B/SOUTH AUSTRALIA/81/2012e
^B/BRISBANE/18/2013e*
^B/VICTORIA/502/2015e
^B/BRISBANE/60/2008e
^B/SYDNEY/508/2010e V1B
0.003
10 of 16 Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 health.gov.au/cdiFigure 6: Phylogenetic tree of haemagglutinin genes of B/Yamagata-lineage viruses received by
the Centre during 2019
B/Cambodia/d0503379/2019 apr
B/Cambodia/d0528380/2019 may
B/Mukdahan/17/2019 jan
Legend B/NakhonSiThammarat/2950/2018
B/PrachuapKhiriKhan/352/2018
B/Cambodia/FSS38583/2018
#2019 SOUTHERN HEMISPHERE VACCINE STRAIN B/Chanthaburi/349/2018
B/Sydney/703/2019 mar
B/Newcastle/1/2019 jan
e: egg isolate B/Cambodia/c1217372/2018
B/Darwin/1/2019 jan
^REFERENCE VIRUS B/Canberra/2/2019 jan
S120T nihwB/Finland/164/2019 dec
B/Brunei/5/2019 feb
│Braces indicate clades B/Victoria/33/2019 aug
nicrfB/Saint Petersburg/RII 346/2019 dec
B/South Australia/6/2019e feb
(+/-) Indicates gain/loss of a potential glycosylation site. V177I B/South Australia/7/2019 feb
B/Sydney/44/2018
D230N B/South Australia/8/2019 feb
Scale bar represents 0.4% nucleotide sequence difference N164K
B/South Australia/11/2019 feb
between viruses. Amino acid changes relative to the outgroup B/South Australia/13/2019 feb
sequence (B/FLORIDA/4/2006) are shown. crickB/Norway/2992/2019 dec
B/Malaysia/RP1205/2019 feb
B/Malaysia/RP2125/2019 jun
G141R
B/Darwin/58/2019e may
B/Brunei/3/2019 jan
D233N(+) B/Malaysia/RP1248/2019 apr
B/Philippines/19/2019 jan
B/Malaysia/RP0882/2019 feb
B/Malaysia/RP4022/2018
B/Brunei/10/2019e mar
V177I
B/Brunei/2/2019 jan
B/Malaysia/RP0778/2019 jan
B/South Australia/82/2018
B/South Australia/86/2018
cdcB/Colombia/7437/2019 dec
B/South Australia/67/2018
B/Bangkok/332/2018 Y3
B/Victoria/15/2018
B/South Australia/57/2018
B/Darwin/25/2018
N218D B/Victoria/2042/2018
B/Christchurch/500/2018e
D233N(+) B/Sri Lanka/1/2019 jan
B/Perth/2/2019 jan
B/South Australia/53/2018
B/Sydney/2/2019 jan
B/Perth/18/2019 apr
cdcB/Chile/8423/2019 nov
B/Newcastle/602/2019 jan
B/Macau/601172/2019 feb
B/Philippines/8/2019 jan
B/South Australia/3/2019 jan
B/WallisFutuna/4/2019 may
B/Wallis Futuna/2/2019 may
B/Brisbane/1/2019 jan
B/Tauranga/1/2018 jun
ipB/Bretagne/2404/2019 nov
afcamB/Nevada/9922/2019 nov
B/South Australia/4/2019 jan
B/Tasmania/503/2019 jul
B/Cambodia/d0131375/2019 jan
B/JilinChaoyang/11723/2018e
B/BeijingChaoyang/12977/2017e
B/South Australia/34/2018
B/Newcastle/56/2018
D230N B/Victoria/2002/2019 jan
B/Malaysia/RP0776/2019 jan
L173Q
^B/PERTH/4/2017
N116K, D197N(+) M252V
K299E, E313K
^B/WELLINGTON/40/2017
^B/CANTERBURY/5/2017
B/ShanghaiPudongxin/114/2018e
^B/SYDNEY/10/2016 feb
S150I, N165Y #B/PHUKET/3073/2013e
K88R, S230G, E479D N203S, G230D ^B/WISCONSIN/01/2010e
^cdcB/HUBEIWUJIAGANG/20158/2009e
^B/MASSACHUSETTS/02/2012e Y2
^B/FLORIDA/4/2006 Y1
0.004
health.gov.au/cdi Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 11 of 16Of 54 B/Yamagata-lineage viruses tested, none The predominant circulating virus in January
displayed highly reduced inhibition by oseltami- and February 2019 across Australia was
vir or zanamivir. However, three of the 1,223 A(H1N1)pdm09, while influenza A(H3N2)
B/Victoria-lineage viruses tested showed highly virus submissions began to increase rapidly in
reduced inhibition by zanamivir. Two of the March 2019, subsequently becoming the pre-
viruses, one each from Malaysia and Australia, dominant circulating strain in 2019. Influenza
contained an E105K substitution in their NA A(H3N2) viruses accounted overall for 51%
genes, which has been shown to reduce sus- of samples submitted to the Centre, followed
ceptibility to neuraminidase inhibitor drugs.16 by A(H1N1)pdm09 (30%), while influenza B
A B/Victoria-lineage virus from Malaysia was viruses comprised 18% of samples received.
found to contain gene sequence coding for a Globally, influenza A viruses were predomi-
novel dual-amino-acid substitution, T146P + nant in 2019, with co-circulation of A(H1N1)
N169S, in its NA gene. pdm09 and A(H3N2). In the southern hemi-
sphere, A(H1N1)pdm09 predominated in South
Discussion America, followed by A(H3N2). By contrast,
A(H3N2) predominated in South Africa with
During 2019 the Centre received a larger very few detections of A(H1N1)pdm09, while
number of samples than in any previous single in tropical Asia, A(H1N1)pdm09 was the domi-
year,17–19,21,22 with the majority of viruses received nant circulating strain followed by B/Victoria
(80%) from Australia. The high volume of sam- viruses.26
ples received correlated with a record number
of laboratory-confirmed influenza notifications Older adults are typically more affected in years
in Australia (313,365 cases) during the 2019 when A(H3N2) viruses predominate, while
Australian influenza season.23 There was a con- younger populations are usually more affected
tinuation of intense inter-seasonal activity, with by A(H1N1)pdm09.27 Consistent with this
notifications of laboratory-confirmed influenza observation, high notification rates occurred in
at the end of May twelve times higher than dur- 2019 among children aged 5–9 years (2,646 per
ing the same time period in the previous three 100,000 population) and adults aged ≥ 85 years
years.24 The 2019 Australian season was charac- (2,370 per 100,000 population) in Australia.23
terised by an early peak and extended activity, Deaths associated with influenza and pneu-
with jurisdictions such as the Australian Capital monia were the ninth leading cause of death in
Territory and Tasmania displaying multiple 2019, with 4,124 deaths recorded.28
peaks of activity.25 Unlike previous seasons,
where influenza samples received at the Centre Most of the influenza A(H1N1)pdm09 viruses
typically peaked in August, the Centre saw a received were antigenically and genetically sim-
dramatic increase in samples received early in ilar to the vaccine strain, A/Brisbane/02/2018,
the year, peaking in July 2019, with over 1,500 which is in the 6B.1A/183P-1 genetic clade. A
samples received in that month alone. number of A(H1N1)pdm09 viruses had amino
acid changes in the HA gene, most significantly
The geographic spread of influenza around at residues 156 and 250; the former mutation
Australia began with a large epidemic of has been previously associated with significant
A(H1N1)pdm09 in the Northern Territory, antigenic changes in the haemagglutination
in December 2018. This was followed by large inhibition (HI) assay. These viruses were first
and sustained outbreaks of influenza in east- detected in Fiji and Brunei in early 2019 and
ern Australian jurisdictions, most notably were subsequently seen in some returned trav-
South Australia, in the first quarter of 2019. ellers from these regions to Australia. These
The Australian Capital Territory and Western antigenically-distinct viruses comprised 5.7%
Australia had comparatively lower levels of of the A(H1N1)pdm09 viruses tested and were
influenza notification but even these both had in the 6B.1A/183-P2 genetic clade. Mid-season
record notifications in 2019.25 vaccine effectiveness (VE) estimates suggest
12 of 16 Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 health.gov.au/cdithat vaccine protection in Australia for all age HA positions 162–164, and made up 64% of
groups was highest against A(H1N1)pdm09 viruses genetically analysed at the Centre. The
viruses among both primary care (62%, 95% increase in circulation of this deletion variant
CI: 39,78) and hospitalised patients (70%, 95% also contributed to an increase in low-reacting
CI: 49, 82).29 viruses in the HI assay, indicating a corre-
sponding antigenic change compared to the
Antigenic analysis of A(H3N2) viruses showed vaccine virus. This led to the subsequent change
that the majority of viruses displayed similar in the recommendation for the 2020 Southern
antigenic characteristics to the cell-propagated Hemisphere B/Victoria-lineage vaccine compo-
vaccine strain, A/Switzerland/8060/2017. As nent to a B/Washington/02/2019-like triple HA
in previous years, there have been ongoing deletion virus.31 B/Yamagata viruses comprised
difficulties in the antigenic characterisation of only 10% of influenza B viruses analysed at the
A(H3N2) viruses. Evolutionary changes in this Centre, and all these viruses were antigenically
subtype continue to pose challenges in detect- and genetically similar to the vaccine strain,
ing antigenic changes using the HI assay.5,30 B/Phuket/3073/2013.
Oseltamivir carboxylate was used in the HI
assay to prevent binding of the NA protein to red With the ongoing evolution of influenza viruses
blood cells, which resulted in a small number of and the absence of an effective universal vaccine,
A(H3N2) viruses having insufficient titre to be there remains a need for continuous influenza
tested in the HI assay (16% of A(H3N2) viruses surveillance and regular updating of influenza
isolated). The FRA continued to be used as com- vaccines. The work performed by the Centre in
plementary antigenic assay but remains time- Melbourne is part of the ongoing efforts of the
and labour-intensive. Of the viruses analysed WHO GISRS to perform these tasks in an effort
by FRA, 75% and 7%, respectively, were anti- to better control the disease burden of influenza.
genically similar to the cell- and egg-propagated
reference strain (A/Switzerland/8060/2017).
There were several distinct genetic clades
amongst circulating A(H3N2) viruses,
with the majority of viruses belonging to
the 3C.2a1b+131K HA clade, followed by
the 3C.2a1b+135K HA clade. Interestingly,
3C.2a2 viruses, which were represented by
the 2019 Southern Hemisphere vaccine strain
A/Switzerland/8060/2018, only accounted for
a very small proportion of circulating viruses
during 2019 and also led to a change in the
2020 Southern Hemisphere A(H3N2) vaccine
component to an A/South Australia/34/2019-
like virus.31
The majority of influenza B isolates analysed at
the Centre belonged to the B/Victoria-lineage
(86%). These B/Victoria-lineage viruses were
mostly antigenically similar to the vaccine
strain B/Colorado/6/2017; however, the major-
ity were phylogenetically similar to a new
variant that had previously emerged in the
Northern Hemisphere. This variant contained a
three-amino-acid deletion in the HA gene, from
health.gov.au/cdi Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 13 of 16Acknowledgements References
The authors would like to thank all the National 1. Hay AJ, McCauley JW. The WHO global
Influenza Centres and other contributing labo- influenza surveillance and response system
ratories who sent influenza-positive samples (GISRS)—a future perspective. Influenza
to the Centre during 2019. We thank Ms Leah Other Respir Viruses. 2018;12(5):551–7.
Gillespie for technical advice and thank Dr Kanta
Subbarao for her comments and input to this 2. Monto AS. Reflections on the Global In-
report. The FluLINE was developed by October fluenza Surveillance and Response System
Sessions and Uma Kamaraj from Duke-NUS (GISRS) at 65 years: an expanding frame-
Medical School, Singapore. The Melbourne work for influenza detection, prevention
WHO Collaborating Centre for Reference and and control. Influenza Other Respir Viruses.
Research on Influenza is supported by the 2018;12(1):10–2.
Australian Government Department of Health.
3. Oh DY, Barr IG, Mosse JA, Laurie KL.
Author details MDCK-SIAT1 cells show improved isola-
tion rates for recent human influenza viruses
Ms Heidi Peck, Head – Serology1 compared to conventional MDCK cells. J
Ms Jean Moselen, Medical Scientist1 Clin Microbiol. 2008;46(7):2189–94.
Mrs Sook Kwan Brown, Medical Scientist1
Ms Megan Triantafilou, Medical Scientist1 4. Hobson D, Curry RL, Beare AS, Ward-Gard-
Ms Hilda Lau, Medical Scientist1 ner A. The role of serum haemagglutination-
Mr Miguel Grau, Bioinformatician1 inhibiting antibody in protection against
Prof. Ian G Barr, Deputy Director1 challenge infection with influenza A2 and B
Ms Vivian KY Leung, Epidemiologist1 viruses. J Hyg (Lond). 1972;70(4):767–77.
1. WHO Collaborating Centre for Reference 5. Lin YP, Gregory V, Collins P, Kloess J,
and Research on Influenza Wharton S, Cattle N et al. Neuraminidase
receptor binding variants of human influ-
Corresponding author enza A(H3N2) viruses resulting from sub-
stitution of aspartic acid 151 in the cata-
Ms Vivian Leung lytic site: a role in virus attachment? J Virol.
2010;84(13):6769–81.
WHO Collaborating Centre for Reference and
Research on Influenza, Peter Doherty Institute 6. Okuno Y, Tanaka K, Baba K, Maeda A,
for Infection and Immunity, 792 Elizabeth St, Kunita N, Ueda S. Rapid focus reduction
Melbourne VIC 3000 AUSTRALIA. neutralization test of influenza A and B
viruses in microtiter system. J Clin Microbiol.
Email: vivian.leung@influenzacentre.org 1990;28(6):1308–13.
7. Tilmanis D, van Baalen C, Oh DY, Rossignol
JF, Hurt AC. The susceptibility of circulating
human influenza viruses to tizoxanide, the
active metabolite of nitazoxanide. Antiviral
Res. 2017;147:142–8.
8. Zhou B, Deng YM, Barnes JR, Sessions OM,
Chou TW, Wilson M et al. Multiplex reverse
transcription-PCR for simultaneous surveil-
14 of 16 Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 health.gov.au/cdilance of influenza A and B viruses. J Clin 17. Leung VK, Spirason N, Lau H, Buettner
Microbiol. 2017;55(12):3492–501. I, Leang SK, Chow MK. Influenza viruses
received and tested by the Melbourne WHO
9. Hurt AC, Besselaar TG, Daniels RS, Ermetal Collaborating Centre for Reference and
B, Fry A, Gubareva L et al. Global update on Research on Influenza annual report, 2015.
the susceptibility of human influenza viruses Commun Dis Intell Q Rep. 2017;41(2):E150–
to neuraminidase inhibitors, 2014–2015. 60.
Antiviral Res. 2016;132:178–85.
18. Roe M, Kaye M, Iannello P, Lau H, Buettner
10. Deng YM, Caldwell N, Barr IG. Rapid de- I, Tolosa MX et al. Report on influenza vi-
tection and subtyping of human influenza A ruses received and tested by the Melbourne
viruses and reassortants by pyrosequencing. WHO Collaborating Centre for Reference
PLoS One. 2011;6(8):e23400. doi: https://doi. and Research on Influenza in 2017. Commun
org/10.1371/journal.pone.0023400. Dis Intell (2018). 2019;43. doi: https://doi.
org/10.33321/cdi.2019.43.25.
11. Gerdil C. The annual production cy-
cle for influenza vaccine. Vaccine. 19. Leung VK, Deng YM, Kaye M, Buettner
2003;21(16):1776–9. I, Lau H, Leang SK et al. Annual report on
influenza viruses received and tested by the
12. Stohr K, Bucher D, Colgate T, Wood J. Melbourne WHO Collaborating Centre for
Influenza virus surveillance, vaccine strain Reference and Research on Influenza in 2016.
selection, and manufacture. Meth Mol Biol. Commun Dis Intell (2018). 2019;43. doi:
2012;865:147–62. https://doi.org/10.33321/cdi.2019.43.3.
13. Weir JP, Gruber MF. An overview of the 20. Tamura D, DeBiasi RL, Okomo-Adhiambo
regulation of influenza vaccines in the M, Mishin VP, Campbell AP, Loechelt B
United States. Influenza Other Respir Viruses. et al. Emergence of multidrug-resistant
2016;10(5):354–60. influenza A(H1N1)pdm09 virus variants
in an immunocompromised child treated
14. WHO Global Influenza Surveillance Net- with oseltamivir and zanamivir. J Infect Dis.
work. Manual for the laboratory diagnosis 2015;212(8):1209–13.
and virological surveillance of influenza.
Geneva: World Health Organization; 2011. 21. Sullivan SG, Chow MK, Barr IG, Kelso A.
Available from: https://www.who.int/influen- Influenza viruses received and tested by the
za/gisrs_laboratory/manual_diagnosis_sur- Melbourne WHO Collaborating Centre for
veillance_influenza/en/. Reference and Research on Influenza an-
nual report, 2014. Commun Dis Intell Q Rep.
15. Roth B, Mohr H, Enders M, Garten W, 2015;39(4):E602–11.
Gregersen JP. Isolation of influenza viruses
in MDCK 33016PF cells and clearance of 22. Price OH, Spirason N, Rynehart C, Brown
contaminating respiratory viruses. Vaccine. SK, Todd A, Peck H et al. Report on in-
2012;30(3):517–22. fluenza viruses received and tested by the
Melbourne WHO Collaborating Centre for
16. Farrukee R, Leang SK, Butler J, Lee RTC, Reference and Research on Influenza in 2018.
Maurer-Stroh S, Tilmanis D et al. Influenza Commun Dis Intell (2018). 2020;44. doi:
viruses with B/Yamagata- and B/Victoria-like https://doi.org//10.33321/cdi.2020.44.16.
neuraminidases are differentially affected by
mutations that alter antiviral susceptibility. J 23. Australian Government Department of
Antimicrob Chemother. 2015;70(7):2004–12. Health. National Notifiable Diseases Surveil-
health.gov.au/cdi Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 15 of 16lance System. [Internet.] Canberra: Australi- doi: https://doi.org/10.2807/1560-7917.
an Government Department of Health; 2021. ES.2019.24.45.1900645.
Available from: http://www9.health.gov.au/
cda/source/cda-index.cfm. 30. Barr IG, Russell C, Besselaar TG, Cox NJ,
Daniels RS, Donis R et al. WHO recommen-
24. Barr IG, Deng YM, Grau ML, Han AX, dations for the viruses used in the 2013–2014
Gilmour R, Irwin M et al. Intense inter- Northern Hemisphere influenza vaccine:
seasonal influenza outbreaks, Australia, epidemiology, antigenic and genetic char-
2018/19. Euro Surveill. 2019;24(33):1900421. acteristics of influenza A(H1N1)pdm09,
doi: https://doi.org/10.2807/1560-7917. A(H3N2) and B influenza viruses collected
ES.2019.24.33.1900421. from October 2012 to January 2013. Vaccine.
2014;32(37):4713–25.
25. Australian Government Department of
Health. Australian Influenza Surveillance 31. WHO. Recommended composition of influ-
Report – No 12 – 2019. [Internet.] Can- enza virus vaccines for use in the 2020 south-
berra; Australian Government Depart- ern hemisphere influenza season. [Internet.]
ment of Health; 10 October 2019. Available Geneva: WHO; 27 September 2019. Available
from: https://www1.health.gov.au/internet/ from: https://www.who.int/influenza/vac-
main/publishing.nsf/Content/ozflu-surveil- cines/virus/recommendations/2020_south/
no12-19.htm. en/.
26. World Health Organization (WHO). Rec-
ommended composition of influenza virus
vaccines for use in the 2019 southern hemi-
sphere influenza season. Geneva: WHO; 27
September 2018. Available from: https://
www.who.int/influenza/vaccines/virus/rec-
ommendations/2019_south/en/.
27. Thompson WW, Shay DK, Weintraub
E, Brammer L, Bridges CB, Cox NJ et al.
Influenza-associated hospitalizations in the
United States. JAMA. 2004;292(11):1333–40.
28. Australian Bureau of Statistics. 3303.0 Caus-
es of death, Australia, 2019. Table 1.1. Un-
derlying cause of death, All causes, Australia,
2019. [Downloadable dataset.] Canberra:
Australian Bureau of Statistics; 23 October
2020. Available from: https://www.abs.gov.
au/statistics/health/causes-death/causes-
death-australia/2019#data-download.
29. Sullivan SG, Arriola CS, Bocacao J, Burgos
P, Bustos P, Carville KS et al. Heterogeneity
in influenza seasonality and vaccine effec-
tiveness in Australia, Chile, New Zealand
and South Africa: early estimates of the 2019
influenza season. Euro Surveill. 2019;24(45).
16 of 16 Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021 health.gov.au/cdiYou can also read
