Virus Res . Detection of reassortant influenza B strains from 2004 to 2015 seasons in Barcelona (Catalonia, Spain) by whole genome sequencing

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Virus Res


. 2023 Apr 1;199089.
doi: 10.1016/j.virusres.2023.199089. Online ahead of print.
Detection of reassortant influenza B strains from 2004 to 2015 seasons in Barcelona (Catalonia, Spain) by whole genome sequencing


Cristina Andrés ¹ , Margarita Del Cuerpo ² , Núria Rabella ² , Maria Piñana ¹ , Manuel Jesús Iglesias-Cabezas ¹ , Alejandra González-Sánchez ¹ , Juliana Esperalba ¹ , Ariadna Rando ¹ , Maria Carmen Martín ¹ , Francisco Fuentes ¹ , Susana Rubio ¹ , Narcís Saubi ¹ , Tomàs Pumarola ³ , Andrés Antón ⁴



Affiliations

• PMID: 37011863
• DOI: 10.1016/j.virusres.2023.199089

Abstract

Background: Influenza B viruses (FLUBV) have segmented genomes which enables the virus to evolve by segment reassortment. Since the divergence of both FLUBV lineages, B/Victoria/2/87 (B/VIC) and B/Yamagata/16/88 (B/YAM), PB2, PB1 and HA have kept the same ancestor, while some reassortment events in the other segments have been reported worldwide. The aim of the present study was to find out reassortment episodes in FLUBV strains detected in cases attended at Vall d'hebron University Hospital and Hospital de la Santa Creu i Sant Pau (Barcelona, Spain) from 2004 to 2015 season.
Methods: From October 2004 to May 2015, respiratory tract specimens were received from patients with respiratory tract infection (RTI) suspicion. Influenza detection was carried out by either cell culture isolation, immunofluorescence or PCR-based assays. A RT-PCR was performed to distinguish both lineages by agarose gel electrophoresis. Whole genome amplification was performed using the universal primer set by Zhou et al. in 2012, and subsequently sequenced using Roche 454 GS Junior platform. Bioinformatic analysis was performed to characterise the sequences with B/Malaysia/2506/2007 and B/Florida/4/2006 corresponding sequences as reference of (B/VIC) and (B/YAM), respectively.
Results: A total of 118 FLUBV (75 B/VIC and 43 B/YAM), from 2004-2006, 2008-2011 and 2012-2015 seasons, were studied. The whole genome of fifty-Eight B/VIC and 42 B/YAM viruses was successfully amplified. Based on HA sequences, most B/VIC viruses (37; 64%) belonged to clade 1A (B/Brisbane/60/2008) except to 11 (19%), which fell within clade 1B (B/HongKong/514/2009) and 10 (17%) to B/Malaysia/2506/2004. Nine (20%) B/YAM viruses belonged to clade 2 (B/Massachusetts/02/2012), 18 (42%) to clade 3 (B/Phuket/3073/2013) and 15 (38%) fell within Florida/4/2006. Numerous intra-lineage reassortments in PB2, PB1, NA and NS were found in 2 2010-2011 viruses. An important inter-lineage reassortment event from 2008-2009 (11), 2010-2011 (26) and 2012-2013 (3) FLUBV/VIC (clade 1) strains to FLUBV/YAM (clade 3) was found, in addition to 1 reassortant NS in 2010-2011 B/VIC virus.
Conclusions: Intra- and inter-lineage reassortment episodes were revealed by WGS. While PB2-PB1-HA remained in complex, NP and NS reassortant viruses were found in both lineages. Despite reassorment events are not often, the characterisation only by HA and NA sequences might be underestimating their detection.

Keywords: Influenza B viruses; lineage; molecular epidemiology; reassortment event.