Noronet report, April 2013

Transcription

1 Noronet report, April 2013 Janko van Beek, Annelies Kroneman, Harry Vennema, Marion Koopmans National Institute for Public Health and the Environment, Bilthoven, The Netherlands The major aim of Noronet is to share epidemiological and molecular data of norovirus outbreaks in order to detect trends and identify possible (foodborne) outbreaks. This report focus on new norovirus nomenclature, distribution and variation of GII.4 Sydney_2012, and shellfish outbreaks. All submitted data between and and with a sample date in was used for this report. Results are shown based on sample date and the shown typing results are according to the norovirus typing tool (Kroneman, Vennema et al. 2011). Update norovirus nomenclature At the 4 th international meeting on caliciviruses in Chile in 2010 the need for common classification standards was discussed and an international norovirus working group of virologists was assembled to develop a consensus on the norovirus nomenclature and typing system. After a long period of discussions this has now resulted in a paper in Archives of Virology, which will be published soon. Authors are from RIVM (Annelies Kroneman, Harry Vennema and Marion Koopmans, Centers for Disease Control and Prevention, Atlanta, USA (Everardo Vega and Jan Vinjé), University of New South Wales, Sydney, Australia (Peter White), University of Heidelberg, Germany (Grant Hansman), Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, USA (Kim Green), University of Bari Aldo Moro, Valenzano, Italy (Vito Martella), National Institute of Infectious Diseases, Tokyo, Japan (Kazuhiko Katayama). In this paper, we outline a phylogenetic approach to classify noroviruses. Furthermore, the dual nomenclature using both polymerase and capsid sequences, which we already applied in the NoroNet database, has been formalized and described in the paper. This new consensus has several consequences for the norovirus typing tool and for the nomenclature of the sequences in the Noronet database. The new names and some new reference sequences have been implemented in the typing tool, and all sequences in the NoroNet database have been re-typed accordingly. Capsid/ORF2/VP1: A new genotype has been added: GI.9 (prototype: HQ637267, Norovirus Hu/GI/Vancouver730/2004/CAN) Polymerase/ORF1: Polymerase based genotypes are now written with a P : GII.P4 Three former orphan polymerase types GI.e, GII.b and GII.d, have been associated with a new capsid sequence and are re-named GI.P9, GII.P21 and GII.P22 respectively GII.4 Variants:

2 The variant names have been adapted: a variant is now identified by year and location of the first full length capsid sequence in the public domain, instead of the first year in which it became epidemic: e.g. GII is now GII.4 New Orleans For some older variants, reference viruses that have been used extensively in publications do not comply with this rule. For example, Farmington Hills and Hunter are not the first complete capsid sequences in GenBank, but as these names are broadly used, they have not been altered. The new variant GII.4 Sydney 2012 has been added, resulting in variant assignment of a set of previously un-typed variants. A short description of the new nomenclature and the changes in the typingtool can be found on the noronet website: and tool. Outbreak / sporadic case reporting Since the last NoroNet report in September 2012, 7 countries (Australia, Chile, Hong Kong, New Zealand, Russia, Slovenia and South Africa) have started uploading data. We welcome these new countries and are happy to see that the NoroNet world coverage increases. We welcome back Slovenia, which has been a participant in the FBVE network from the start, but has not been able to contribute in the past years. Now that countries at the southern hemisphere are uploading data, we will have to interpret seasonal trends more carefully. Besides norovirus GI and GII outbreaks / sporadic cases, Sweden and Germany both reported a GIV outbreak in respectively Feb 2010 and In Sweden 3 out of 4 samples were positive for NoV GIV, the suspected mode of transmission was foodborne (food item not specified) and the outbreak occurred during a conference in a hotel. For the German GIV outbreak no epi data was reported.

3 Table 1 Number of reported norovirus outbreaks / sporadic cases by sample year Country Total AUSTRALIA 2 2 AUSTRIA BELGIUM CHILE 4 4 CHINA DENMARK FINLAND FRANCE GERMANY HONG KONG HUNGARY IRELAND ITALY 1 1 JAPAN NETHERLANDS NEW ZEALAND RUSSIAN FEDERATION SLOVENIA 1 1 SOUTH AFRICA SPAIN SWEDEN UNITED KINGDOM Total Genogroup I diversity and trends 8% of the total submitted sequences belongs to norovirus GI. Table 2A & 2B show the norovirus GI polymerase and capsid diversity from 2010 until GI.Pb, GI.P4, and GI.P7 (pol) and GI.4, GI.3, and GI.6 (cap) were the most frequently detected GI genotypes.

4 Table 2A Genogroup I polymerase diversity and trends by sample year Genotype Total Could not assign GI.P GI.P GI.P GI.P GI.P5 1 1 GI.P GI.P9 1 1 GI.Pa GI.Pb GI.Pd 1 1 GI.Pf 6 6 Total Table 2B Genogroup I capsid diversity and trends by sample year Genotype Total GI GI GI GI GI GI GI GI Total Norovirus GII diversity and trends The majority (92%) of reported norovirus sequences belongs to GII. Table 3A & 3B show the norovirus GII diversity and trends with sample date in 2010 until Besides GII.(P)4, the most frequently reported genotypes were GII.Pe, GII.Pg, and GII.P7 (pol) and GII.6, GII.1, GII.3 (cap). The increase of GII.Pe in 2012 was most likely caused by the emergence of the new GII.4 variant Sydney_2012. As far as we know, this new capsid variant has only been found in combination with polymerase GII.Pe. Figure 1 shows the distribution over time of GI, GII non GII.4 or GII.Pe, and GII sequences. All indicated norovirus groups are present throughout the year. Winter peaks (Northern Hemisphere) are mainly caused by GII.4 and in winter 2012/2013 supplemented by GII.Pe, but other GII and to a lesser extent GI, are elevated in the winter season as well. The GII.(P)4 variant Den_Haag_2006b almost disappeared in 2012 (table 4A & B). New_Orleans_2009 and Sydney_2012 were detected most frequently in In figure 2A & 2B all GII.4 variants + GII.Pe are shown over time. The majority of capsid sequences belong to variant Sydney_2012,

5 while on polymerase level approximately 50% of sequences belong to GII.Pe and approximately 50% belong to the variant New_Orleans_2009. Surprisingly, almost all winter season 2012/2013 GII.P4 New_Orleans_2009 sequences originated from The Netherlands (data not shown), indicating that in other reporting countries GII.Pe and GII.4 Sydney_2012 were dominant. Figure 3A & 3B show the number of reported GII.Pe and GII.4 Sydney_2012 sequences by country and time. The majority of GII.Pe sequences were reported by New Zealand, The Netherlands, and France. The majority of GII.4 Sydney_2012 capsid sequence were reported by New Zealand, Japan and France. Sydney_2012 peaked approximately 2 months earlier compared to previous GII.4 seasons. For New Zealand (Southern Hemisphere) the peak coincided with other countries in the Northern Hemisphere and was one month delayed compared to earlier seasons. The NoV seasonality in New Zealand follows a distinct pattern compared to other countries. For the period , the NoV incidence peaked on average in October (spring), but this was not seen each year (Greening, Hewitt et al. 2012). Table 3A Genogroup II polymerase diversity and trends by sample year Genotype Total Could not assign GII.P GII.P GII.P GII.P GII.P GII.P GII.P GII.P GII.P GII.P GII.Pe GII.Pg Total

6 Table 3B Genogroup II capsid diversity and trends by sample year Genotype Total Could not assign 1 1 GII GII GII GII GII GII GII GII GII GII GII GII GII GII GII Total Figure 1 GI, GII non GII.P4 or GII.Pe, and GII distribution by sample month and year based on polymerase sequences (stacked plot).

7 Table 4A GII.4 variant polymerase diversity and trends GII.P4 variant Total Could not assign Yerseke_2006a Den_Haag_2006b Apeldoorn_ New_Orleans_ Total Table 4B GII.4 variant capsid diversity and trends GII.4 variant Total Could not assign Yerseke_2006a 1 1 Den_Haag_2006b Apeldoorn_ Osaka_ New_Orleans_ Sydney_ Total Figure 2A GII.P4 variant distribution by sample month and year based on polymerase sequences (stacked plot).

8 Figure 2B GII.4 variant distribution by sample month and year based on capsid sequences (stacked plot). Figure 3A Number of reported GII.Pe sequences by sample month, year and origin based on polymerase sequences (stacked plot).

9 Figure 3B Number of reported GII.4 Sydney_2012 sequences by sample month, year and origin based on capsid sequences (stacked plot). GII.4 Sydney_2012 variation All GII.4 Sydney_2012 region C sequences with a minimum overlapping length of 275 nucleotides were selected and aligned with ClustalW and a Neighborjoining tree was computed with BioEdit (figure 4). Most sequences originate from France, Japan and New Zealand. Clusters of identical sequences are represented by one sequence, indicated in red, with cluster size and country of origin. Mutations compared to the reference strain (Genbank: JX459908) are indicated in the figure in red. None of these nucleotide mutations results in amino-acid mutations. A large cluster of closely related sequences (indicated as Cluster New Zealand) has only been found in New Zealand and these sequences have 5 mutations compared to the reference sequence (genbank: JX459908).

10 Figure 4 Neighbor-joining tree of GII.4 Sydney_2012 (capsid) sequences + GII.4 variant reference sequences used in the typing tool (blue). Labels indicate reported outbreak numbers and the corresponding sequences can be found in the Noronet database. Red lines indicate clusters of identical sequences with one sequence arbitrarily chosen as representative for that cluster.

11 Shellfish outbreaks Sixty foodborne outbreaks in the set with sample date reported shellfish as the suspected food item (figure 5). Many of these outbreaks were reported with more than one sequence and often from different genotypes. In total 122 sequences were reported by seven countries, with France reporting over 50%. The fraction of GII.(P)4 was much lower and the fraction of GI much higher compared to the complete set. Of the 89 GII sequences, 52 had an overlap of at least 100 nt (region c). These sequences were aligned and a NJ tree was computed with the Noronet phylo tool. A small international cluster is present (OB: 85PO0112, RCC07/12, 12L , 12L , 67DA0310) of 5 identical GII.1 sequences involving France, Spain, and Denmark (figure 6). Figure 5 Number of reported outbreaks related to shellfish from 2010 until early 2013.

12 Figure 6 Neighbor-joining tree of shellfish related outbreaks. References Greening, G. E., J. Hewitt, et al. (2012). "Molecular epidemiology of norovirus gastroenteritis outbreaks in New Zealand from " J Med Virol 84(9): Kroneman, A., H. Vennema, et al. (2011). "An automated genotyping tool for enteroviruses and noroviruses." J Clin Virol 51(2): Kroneman, A, E. Vega, et al. (2013). Proposal for a Unified Norovirus Genotyping and Strain Nomenclature. Arch Virol in press