Epidemiological and evolutionary dynamics of influenza B virus in coastal Kenya as revealed by genomic analysis of strains sampled over a single season.

Festus M Nyasimi,Joyce U Nyiro,David Collins Owuor,James R Otieno,Charles N Agoti,David James Nokes,Alexander G Mwihuri,Grieven P Otieno,Joyce M Ngoi,George Githinji

doi:10.1093/ve/veaa045

Abstract

The genomic epidemiology of influenza B virus (IBV) remains understudied in Africa despite significance to design of effective local and global control strategies. We undertook surveillance throughout 2016 in coastal Kenya, recruiting individuals presenting with acute respiratory illness at nine outpatient health facilities (any age) or admitted to the Kilifi County Hospital (<5 years old). Whole genomes were sequenced for a selected 111 positives; 94 (84.7%) of B/Victoria lineage and 17 (15.3%) of B/Yamagata lineage. Inter-lineage reassortment was detected in ten viruses; nine with B/Yamagata backbone but B/Victoria NA and NP segments and one with a B/Victoria backbone but B/Yamagata PB2, PB1, PA, and MP segments. Five phylogenomic clusters were identified among the sequenced viruses; (i), pure B/Victoria clade 1A (n = 93, 83.8%), (ii), reassortant B/Victoria clade 1A (n = 1, 0.9%), (iii), pure B/Yamagata clade 2 (n = 2, 1.8%), (iv), pure B/Yamagata clade 3 (n = 6, 5.4%), and (v), reassortant B/Yamagata clade 3 (n = 9, 8.1%). Using divergence dates and clustering patterns in the presence of global background sequences, we counted up to twenty-nine independent IBV strain introductions into the study area (∼900 km2) in 2016. Local viruses, including the reassortant B/Yamagata strains, clustered closely with viruses from neighbouring Tanzania and Uganda. Our study demonstrated that genomic analysis provides a clearer picture of locally circulating IBV diversity. The high number of IBV introductions highlights the challenge in controlling local influenza epidemics by targeted approaches, for example, sub-population vaccination or patient quarantine. The finding of divergent IBV strains co-circulating within a single season emphasises why broad immunity vaccines are the most ideal for influenza control in Kenya.

Highlights

MAIN TEXT (Word count 5284) Human influenza B virus (IBV) is responsible for about 30% of the influenza virus morbidity and mortality during seasonal influenza epidemics (Caini et al 2018a; Paul Glezen et al 2013; Seleka et al 2017)
It was observed that the two IBV lineages alternated in predominance; B/Victoria lineage predominated in the years 2012 and 2016 while B/Yamagata predominated in year 2013, 2014 and 2015 (Emukule et al 2019)
NP swabs were collected from the nine Kilifi Health and Demographic Surveillance System (KHDSS) outpatient facilities and 574 NP/OP swabs from inpatients at Kilifi County Hospital (KCH), Figure 1, panel (b)

Summary

Introduction

MAIN TEXT (Word count 5284) Human influenza B virus (IBV) is responsible for about 30% of the influenza virus morbidity and mortality during seasonal influenza epidemics (Caini et al 2018a; Paul Glezen et al 2013; Seleka et al 2017). The B/Victoria lineage viruses display a clear antigenic drift of a single clade in successive years with strong seasonal fluctuations in their incidence, while the B/Yamagata lineage viruses exhibit continuous cocirculation of multiple genetic clades which alternate in their dominance over years (Langat et al 2017). 3 https://mc.manuscriptcentral.com/vevolu a key consideration during selection of influenza strains to include in vaccines for upcoming seasons and for understanding observed vaccine effectiveness (Rajao and Perez 2018). Such information is frequently unavailable for majority of developing countries (Caini et al 2015; Caini et al 2018a). It was observed that the two IBV lineages alternated in predominance; B/Victoria lineage predominated in the years 2012 and 2016 while B/Yamagata predominated in year 2013, 2014 and 2015 (Emukule et al 2019)

Methods

Results

Conclusion