Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection

Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has infected almost 200 million people worldwide by July 2021 and the pandemic has been characterized by infection waves of viral lineages showing distinct fitness profiles. The simultaneous infection of a single individual by two distinct SARS-CoV-2 lineages may impact COVID-19 disease progression and provides a window of opportunity for viral recombination and the emergence of new lineages with differential phenotype. Several hundred SARS-CoV-2 lineages are currently well phylogenetically defined, but two main factors have precluded major coinfection/codetection and recombination analysis thus far: (i) the low diversity of SARS-CoV-2 lineages during the first year of the pandemic, which limited the identification of lineage defining mutations necessary to distinguish coinfecting/recombining viral lineages; and the (ii) limited availability of raw sequencing data where abundance and distribution of intrasample/intrahost variability can be accessed. Here, we assembled a large sequencing dataset from Brazilian samples covering a period of 18 May 2020 to 30 April 2021 and probed it for unexpected patterns of high intrasample/intrahost variability. This approach enabled us to detect nine cases of SARS-CoV-2 coinfection with well characterized lineage-defining mutations, representing 0.61 % of all samples investigated. In addition, we matched these SARS-CoV-2 coinfections with spatio-temporal epidemiological data confirming its plausibility with the cocirculating lineages at the timeframe investigated. Our data suggests that coinfection with distinct SARS-CoV-2 lineages is a rare phenomenon, although it is certainly a lower bound estimate considering the difficulty to detect coinfections with very similar SARS-CoV-2 lineages and the low number of samples sequenced from the total number of infections.

Keywords: COVID-19; codetection; coinfection; genomics.

Fig. 1.

Number of intrahost variant sites from 1150 SARS-CoV-2 samples and phylogenetic analysis of alternative MajV and MinV consensus genomes recovered from the same sample. (a) Dot plot with number of iSNVs per sample; (b) maximum-likelihood phylogenetic tree. Others: R, S, U, L, D, C lineages. Red arrows represent samples with alternative genomes showing lineage change while black arrows indicate alternative samples with no lineage change.

Fig. 2.

MajV and MinV of samples with codetection of different SARS-CoV-2 lineages. (a) Karyoploter with iSNV sites across the SARS-CoV-2 genome. (b) iSNV sites with read-depth frequency supporting MajV and MinV. Defining SNPs based on data of outbreak.info update on 24 July 2021, are indicated with a circle. Karyoplots depicting iSNV-site sequencing depth can be accessed in File S1, and raw depth values can be accessed in Table S5.

Fig. 3.

SARS-CoV-2 lineage proportion through time in different Brazilian states with codetection cases. Data were recovered from GISAID on 23 July 2021, raw data can be accessed in Table S8. Upper triangles coloured with the lineage of major consensus genomes and lower triangles with minor consensus genomes lineages.