Detection of co-infection and recombination cases with Omicron and local Delta variants of SARS-CoV-2 in Vietnam

Abstract

The first nationwide outbreak of COVID-19 in Vietnam started in late April 2021 and was caused almost exclusively by a single Delta lineage, AY.57. In early 2022, multiple Omicron variants co-circulated with Delta variants and quickly became dominant. The co-circulation of Delta and Omicron happened leading to possibility of co-infection and recombination events which can be revealed by viral genomic data. From January to October 2022, a total of 1028 viral RNA samples out of 4852 positive samples (Ct < 30) were sequenced by the long pooled amplicons method on Illumina platforms. All sequencing data was analysed by the workflow for SARS-CoV-2 on CLC genomics workbench and Illumina Dragen Covid application. Among those sequenced samples, we detected a case of Delta AY.57/Omicron BA.1 co-infection and two cases of infection with Delta AY.57/Omicron BA.2 recombinants which were nearly identical and had different epidemiological characteristics. Since the AY.57 lineage circulated almost exclusively in Vietnam, these results strongly suggest domestic events of co-infection and recombination. These findings highlight the strengths of genomic surveillance in monitoring the circulating variants in the community enabling rapid identification of viral changes that may affect viral properties and evolutionary events.

Figure 1

COVID-19 pandemic timeline in Vietnam. The figure shows main events of fourth waves of COVID-19 pandemic in Vietnam.

Figure 2

Distribution of circulating variants between January and October 2022 from the patients at NHTD, Vietnam.

Figure 3

Co-infection with Delta and Omicron variants. The graph shows the frequency and relative location of each specific mutation of each variant type along the viral genome (GISAID accession No. EPI_ISL_ 11632985). The coloured dots represent the specificity of the mutations: light orange for mutations of Delta AY.57; orange for mutations of Delta AY*; light brown for common mutations of all Delta; navy blue for mutations of Omicron BA.1; light blue for common mutaions of all Omicron; purple for mutation shared by both Delta and Omicron. The vertical axis is the frequency of the mutation. The x axis is divided into functional regions of SARS-CoV-2 and highlighted by corresponding colours.

Figure 4

Recombination of Delta and Omicron variants. The graph shows the frequency and relative location of each specific mutation of each variant type along the viral genome (GISAID accession No.: EPI_ISL_14934965, EPI_ISL_15579330 for sample 3220 and 3461 respectively). The coloured dots represent the specificity of the mutations: light orange for mutations of Delta AY.57; orange for mutations of Delta AY*; light brown for common mutations of all Delta; navy blue for mutations of Omicron BA.1; light blue for common mutaions of all Omicron; purple for mutation shared by both Delta and Omicron. The vertical axis is the frequency of the mutation. The x axis is divided into functional regions of SARS-CoV-2 and highlighted by corresponding colorus.