Human seasonal influenza under COVID-19 and the potential consequences of influenza lineage elimination

doi:10.21203/rs.3.rs-850533/v1

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Human seasonal influenza under COVID-19 and the potential consequences of influenza lineage elimination

https://doi.org/10.21203/rs.3.rs-850533/v1

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published 31 Mar, 2022

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Annual epidemics of seasonal influenza cause hundreds of thousands of deaths, high levels of morbidity, and substantial economic loss. Yet, global influenza circulation has been heavily suppressed by public health measures and travel restrictions since the onset of the COVID-19 pandemic. Notably, the influenza B/Yamagata lineage has not been conclusively detected since April 2020, and A(H3N2), A(H1N1), and B/Victoria viruses circulate with considerably less genetic diversity. Travel restrictions have largely confined regional outbreaks of A(H3N2) to South and Southeast Asia, B/Victoria epidemics in China, and A(H1N1) in West Africa. Seasonal influenza transmission lineages continue to perish globally, except in select hotspots, which will likely seed future epidemics. Waning population immunity and sporadic case detection will further challenge influenza vaccine strain selection and epidemic control. We offer perspective on the potential short- and long-term evolutionary dynamics of seasonal influenza and discuss potential consequences and mitigation strategies as global travel gradually returns to pre-pandemic levels.

Molecular Epidemiology

Infectious Diseases

Virology

seasonal influenza

short- and long-term evolutionary dynamics

influenza lineage elimination

There is NO Competing Interest.

ExtendedDataFig1.pdf
Extended Data Figure 1 | Evolutionary relationships of the HA genes of A(H3N2) A1b/186D clade. Samples collected since April 2020 are colored. Geographic regions with majority of the samples are labelled alongside the tree. The presented tree is a monophyletic lineage that was extracted from a large-scale analysis comprising all available A(H3N2) virus HA sequences collected since 2018.
ExtendedDataFig2.pdf
Extended Data Figure 2 | Evolutionary relationships of the HA genes of A(H3N2) A1b/94N clade. Samples collected since April 2020 are colored. Geographic regions with majority of the samples are labelled alongside the tree. The presented tree is a monophyletic lineage that was extracted from a large-scale analysis comprising all available A(H3N2) virus HA sequences collected since 2018.
ExtendedDataFig3.pdf
Extended Data Figure 3 | Evolutionary relationships of the HA genes of A(H1N1) 6b1A/187A clade. Samples collected since April 2020 are colored. Geographic regions with majority of the samples are labelled alongside the tree. The presented trees are two closely related monophyletic lineages that were pruned from a large-scale analysis comprising all available A(H1N1) virus HA sequences collected since 2018.
ExtendedDataFig4.pdf
Extended Data Figure 4 | Evolutionary relationships of the HA genes of B/Victoria V1A.3/150K clade. Samples collected since April 2020 are colored. Geographic regions with majority of the samples are labelled alongside the tree. The presented tree is a monophyletic lineage that was pruned from a large-scale analysis comprising all available B/Victoria virus HA sequences collected since 2018.
ExtendedDataFig5.pdf
Extended Data Figure 5 | Internal and international movement restrictions enacted by individual countries against COVID-19. Maps were generated in ourworldindata.org/coronavirus based on the Oxford COVID-19 Government Response Tracker (Hale et al. 2020 Nature Human Behaviour).
ExtendedDataFig6.pdf
Extended Data Figure 6 | Lack of correlation between the stringency of COVID-19 restrictions and seasonal influenza reports for fourteen countries in Africa and Asia. Plots show COVID-19 rate per 100,000, influenza rate per 100,000, stringency index and travel restrictions from May 1st, 2020 to August 1st, 2021. The COVID-19 and influenza rate plots are labelled by country where rates are at least 10% of the maximum rate across all countries. The dotted line in all panels is the median. Influenza activity is only shown for countries with (i) epidemic activity in FluNet supported by sequence in GISAID collected within three weeks of the reported cases; and (ii) to rule out false positive and sporadic cases not indicative of community transmission, a case report rate of at least 0.02 cases per 100,000 population. Stringency measure is an additive of indicators (school and workplace closures, cancellation of public events, restrictions on gatherings, closings of public transport, public information campaigns, stay at home restrictions, restrictions on internal movement, international travel controls, testing policy, contact tracing, face coverings, vaccination policy) rescaled to vary from 0 to 100. International travel restrictions are quantified as, 0 - no measures; 1 - screening; 2 - quarantine of arrivals from high-risk regions; 3 - ban on high-risk regions; and 4 - total border closure. COVID-19 activity was sourced from the WHO COVID-19 Dashboard https://covid19.who.int/ and the multi-sourced Johns Hopkins Coronavirus Resource Center https://coronavirus.jhu.edu/.
ExtendedDataTable1.xlsx
Extended Data Table 1 | Comparison of global confirmed cases of seasonal influenza FluNet data in the 16-month period from December 2018 to March 2020 (before the COVID-19 pandemic) against the 16-month period from April 2020 to July 2021 (during the COVID-19 pandemic).
ExtendedDataTable2.xlsx
Extended Data Table 2 | Circulating clades of seasonal influenza viruses observed from sequences in GISAID from April 2020 to July 2021.
ExtendedDataTable3.xlsx
Extended Data Table 3 | Transmission lineages of seasonal influenza viruses detected during 2020/2021 inferred using large-scale phylogenetic analysis of all HA sequences in GISAID from January 2018 to July 2021.
ExtendedDataTable4.xlsx
Extended Data Table 4 | Acknowledgements for influenza HA sequences downloaded from GISAID.

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Human seasonal influenza under COVID-19 and the potential consequences of influenza lineage elimination

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