SARS-CoV-2 genomic surveillance enables the identification of Delta/Omicron co-infections in Argentina

Abstract

Molecular surveillance of SARS-CoV-2 is crucial to early detect new variants and lineages. In addition, detection of coinfections with more than one SARS-CoV-2 lineage have been sporadically reported. In this work, surveillance of SARS-CoV-2 variants was performed on 2067 RNA samples (Ct>30) obtained during December 2021 and January 2022 from Cordoba province, Argentina, by real time RT-PCR specific for VOC/VOI relevant mutations (TaqMan SARS-CoV-2 Mutation Panel, Applied Biosystems). The following distribution of variants was obtained: Omicron (54.9%), Delta (44.2%) and Lambda (0.8%). Three samples (0.1%), obtained the last week of December, presented a profile compatible with a Delta/Omicron co-infection. One of them was sequenced by NGS-Illumina, obtaining reads for both VOCs. One of the studied patients presented severe symptoms, although he was not vaccinated and presented risk factors (older than 60 years, arterial hypertension). We describe for the first time in Argentina, the identification of cases of co-infection with two SARS-CoV-2 lineages, VOCs Delta and Omicron, during the third COVID-19 wave in the country (a high viral circulation period), when Delta and Omicron co-circulated. Our findings highlight the importance of continuing with molecular surveillance and co-detection studies of VOC/VOIs, in order to elucidate possible recombination events and the emergence of new variants.

Assessing the hidden diversity underlying consensus sequences of SARS-CoV-2 using VICOS, a novel bioinformatic pipeline for identification of mixed viral populations.

“…During this period, we found two SARS-CoV-2 coinfections involving at least one VOC/VOI (Alpha + Lambda, N.3 + Lambda). As expected, these cases showed a high number of iSNVs (47 and 30, respectively) and are usually easier to identify even by non-sequencing methods such as real time qPCR specific for SARS-CoV-2 VOCs [36] . In light of recent findings that show that 2.7% of SARS-CoV-2 genomes have detectable recombinant ancestry [37] , our results further highlight the importance of recognizing SARS-CoV-2 coinfections in real-time to monitor the spread of emerging recombinant variants with improved transmission efficiency and ability to evade immune response.…”

Systematic genomic analysis of SARS-CoV-2 co-infections throughout the pandemic and segregation of the strains involved

“…At the same time, the same stringent measures may be responsible for missing SARS-CoV-2 co-infections associated with the presence of HZ calls. Apart from a few isolated descriptions of SARS-CoV-2 co-infections [20][21][22][23][24][25], there has been a recent surge of Fig. 4 within-host dynamics of co-infecting strains for the five patients with more than one specimen available from different periods.…”

“…However, due to the fact that the first SARS-CoV-2 recombinant alerts involved the Delta and Omicron BA.1 and BA.2 lineages, very few studies have described co-infections prior to this point in time [14,15]. Most studies have focused on more systematic analyses of mixed infections [11,13], and many others reporting individual anecdotal cases [20][21][22][23][24] have confined themselves to tracking co-infections involving those lineages and the particular time period when they were co-circulating (mainly end of 2021-first quarter of 2020). As a result of this, analytical approaches designed to identify co-infections have tended to rely on selecting the set of phylogenetically informative SNPs that differentiate between lineages and using them to drive the identification of HZ calls as a proxy for the identification of co-infection.…”

Using Haplotype-Based Artificial Intelligence to Evaluate SARS-CoV-2 Novel Variants and Mutations

“…Among all recombinants, the likely most well-known and controversial recombinant is the Omicron-Delta recombinant. 29 , 30 , 31 Profiling Delta and Omicron polymutants on these 2 recombinants (eTable 19 in Supplement 1 ), we found that the virus carried L452R and I82T polymutants unique to Delta, while the remaining polymutants were unique to Omicron. Similarly, the Omicron-Alpha recombinants carried T183I, S982A, R52I, D3L, and S235F mutations unique to Alpha, while Omicron-Zeta recombinants carried L71F, A119S, and M234I mutations unique to Zeta (eTable 20 in Supplement 1 ).…”