Functional comparison of MERS-coronavirus lineages reveals increased replicative fitness of the recombinant lineage 5

Simon Schroeder,Marcel A Müller,Stephan Eggeling,Stefan Pöhlmann,Thorsten Wolff,Ronald Dijkman,Steeve Boulant,Ziad A Memish,Mitra Gultom,Andreas C Hocke ,Anja Richter,Stefan Hippenstiel,Hannah Kleine-Weber,Megan L Stanifer,Diana Fatykhova,Victor M Corman,Volker Thiel,Christin Mache,Doreen Muth,Christian Drosten

doi:10.1038/s41467-021-25519-1

Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels across the Middle East and Africa. Virus-induced pneumonia in humans results from animal contact, with a potential for limited onward transmission. Phenotypic changes have been suspected after a novel recombinant clade (lineage 5) caused large nosocomial outbreaks in Saudi Arabia and South Korea in 2016. However, there has been no functional assessment. Here we perform a comprehensive in vitro and ex vivo comparison of viruses from parental and recombinant virus lineages (lineage 3, n = 7; lineage 4, n = 8; lineage 5, n = 9 viruses) from Saudi Arabia, isolated immediately before and after the shift toward lineage 5. Replication of lineage 5 viruses is significantly increased. Transcriptional profiling finds reduced induction of immune genes IFNB1, CCL5, and IFNL1 in lung cells infected with lineage 5 strains. Phenotypic differences may be determined by IFN antagonism based on experiments using IFN receptor knock out and signaling inhibition. Additionally, lineage 5 is more resilient against IFN pre-treatment of Calu-3 cells (ca. 10-fold difference in replication). This phenotypic change associated with lineage 5 has remained undiscovered by viral sequence surveillance, but may be a relevant indicator of pandemic potential.

Highlights

Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels across the Middle East and Africa
Phylogeny and recombination analysis of MERS-CoV isolates obtained from Saudi Arabian patients
To facilitate a phenotypic comparison of MERS-CoV strains that circulated before and after the 2014 recombination event, we generated 23 virus isolates from patient samples obtained during outbreaks in Saudi Arabia between 2014 and 2015 and one virus isolate obtained from a dromedary camel farm in Dubai in 2017 using a previously established MERS-CoV isolation protocol[25]

Summary

Introduction

Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels across the Middle East and Africa. Phenotypic changes have been suspected after a novel recombinant clade (lineage 5) caused large nosocomial outbreaks in Saudi Arabia and South Korea in 2016. This phenotypic change associated with lineage 5 has remained undiscovered by viral sequence surveillance, but may be a relevant indicator of pandemic potential. Changes of phenotype in association with lineage 5 emergence have been suspected, but phenotypic studies of MERS-CoV strains are generally limited. Mutations in the spike protein positions I529T and D510G observed during the outbreak in Korea were suggested to have contributed to antibody evasion[21] These polymorphisms evolved during and not prior to the Korean MERS-CoV outbreak and cannot explain the dominance of lineage 5 since 201522. One complicating feature of MERS-CoV is that the infection phenotype seen in humans is difficult to reflect in small animal models

Methods

Results

Conclusion