Detection of co-infection and recombination cases with Omicron and local Delta variants of SARS-CoV-2 in Vietnam
Trang NT., Dien TC., Tam NT., Cuong PM., Van Duyet L., Thuong NTH., Trang VD., Thach PN., van Doorn HR., Kesteman T., Mary C., Marc C., Trinh DHK., Tam DTH., Duc DH., Viet DVT., Jaom F., Barney F., Ronald G., Kim HVT., Chanh HQ., Hai HTB., Van Hien H., Bao HV., Thao HD., le Anh Huy H., Ha HN., Trieu HT., Yen HX., Evelyne K., Thomas K., Nguyet LA., Katrina L., Jones L., Thanh LK., Van Khoa LD., Nhat LTH., Van Tan L., Odette LS., Yen LM., Nhu LNT., Lan LTH., Nguyen NV., Hoa NT., Tran NB., Manh ND., Yen NH., Le Thao My N., Nguyet NM., Anh NT., Ha NT., Quyen NTH., Ngoc NT., Nhien NTT., Ny NTH., Thuong NTH., Yen NTH., Trang NTH., Ngoc NTK., Tuyen NTK., Diep NTN., Dung NTP., Tam NT., Hong NTT., Trang NT., Thuong Thuong NT., Truong NX., Phuong ND., Van NTT., Thinh OP., Thanh PN., Khanh PNQ., Kim PHT., Lam PK., Le Kim Yen P., Nhat PTH., Motiur R., Huyen TNT., Guy T., Louise T., Huyen TB., Han TDT., Van Anh TK., Hien TM., Thao TP., Thanh TT., Ngoc TTB., Hang TT., Hien TT., Tung TS., Rogier VDH., Jennifer VN., Pascale VC., Bich VTN., Hang VTT., Sophie Y.
AbstractThe 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.