Middle East Respiratory Syndrome Coronavirus Intra-Host Populations Are Characterized by Numerous High Frequency Variants

Abstract

Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging human pathogen related to SARS virus. In vitro studies indicate this virus may have a broad host range suggesting an increased pandemic potential. Genetic and epidemiological evidence indicate camels serve as a reservoir for MERS virus but the mechanism of cross species transmission is unclear and many questions remain regarding the susceptibility of humans to infection. Deep sequencing data was obtained from the nasal samples of three camels that had been experimentally infected with a human MERS-CoV isolate. A majority of the genome was covered and average coverage was greater than 12,000x depth. Although only 5 mutations were detected in the consensus sequences, 473 intrahost single nucleotide variants were identified. Many of these variants were present at high frequencies and could potentially influence viral phenotype and the sensitivity of detection assays that target these regions for primer or probe binding.

Fig 1. Coverage Plots.

UDS coverage depth across the genome was plotted for each sample. The X axis shows the genome position and the Y axis shows the depth coverage (log scale).

Fig 2. Histogram of high frequency iSNVs resulting in a nonsynonymous change in the consensus sequence of one or more samples.

The iSNV detected at site t6172, caused a Phe to Ser mutation in nsp 3 residue 1965 and resulted in a consensus change that differentiated the camel genotypes from that of the Seed. An iSNV, g24538, was present at low frequency in the Seed stock but increased in frequency during propagation in camels with a change in consensus sequence occurring in C2D5, resulting in an N1028S mutation. Note, only data from samples with adequate coverage at the relevant iSNV position were included in the histogram.

Fig 3. Heat maps of nonsynonymous iSNV frequencies and nt positions.

Heat maps for each camel (A-C) show the frequencies and positions of iSNVs for each camel and time point, and for Seed inoculum. The number (count) of iSNV for each frequency value is shown along with the heat map color key is shown above each camel heatmap.