Detection of co-infection and recombination cases with Omicron and local Delta variants of SARS-CoV-2 in Vietnam
Authors: Trang Nguyen Thu , Dien Trinh Cong , Tam Nguyen Thi , Cuong Phan Manh , Van Duyet Le , Thuong Nguyen Thi Hong , Trang Van Dinh , Thach Pham Ngoc , van Doorn H. Rogier , Kesteman Thomas ,   OUCRU COVID-19 research group, Mary Chambers , Marc Choisy , Trinh Dong Huu Khanh , Tam Dong Thi Hoai , Duc Du Hong , Viet Dung Vu Tien , Jaom Fisher , Barney Flower , Ronald Geskus , Kim Hang Vu Thi , Chanh Ho Quang , Hai Ho Thi Bich , Van Hien Ho , Bao Hung Vu , Thao Huong Dang , le Anh Huy Huynh , Ha Huynh Ngan , Trieu Huynh Trung , Yen Huynh Xuan , Evelyne Kestelyn , Thomas Kesteman , Nguyet Lam Anh , Katrina Lawson , Jones Leigh , Thanh Le Kim , Van Khoa Le Dinh , Nhat Le Thanh Hoang , Van Tan Le , Odette Lewycka Sonia , Yen Lam Minh , Nhu Le Nguyen Truc , Lan Le Thi Hoang , Nguyen Nam Vinh , Hoa Ngo Thi , Tran Nguyen Bao , Manh Nguyen Duc , Yen Nguyen Hoang , Le Thao My Nguyen , Nguyet Nguyen Minh , Anh Nguyen To , Ha Nguyen Thanh , Quyen Nguyen Than Ha , Ngoc Nguyen Thanh , Nhien Nguyen Thanh Thuy , Ny Nguyen Thi Han , Thuong Nguyen Thi Hong , Yen Nguyen Thi Hong , Trang Nguyen Thi Huyen , Ngoc Nguyen Thi Kim , Tuyen Nguyen Thi Kim , Diep Nguyen Thi Ngoc , Dung Nguyen Thi Phuong , Tam Nguyen Thi , Hong Nguyen Thi Thu , Trang Nguyen Thu , Thuong Thuong Nguyen Thuy , Truong Nguyen Xuan , Phuong Nhung Doan , Van Ninh Thi Thanh , Thinh Ong Phuc , Thanh Pham Ngoc , Khanh Phan Nguyen Quoc , Kim Phung Ho Thi , Lam Phung Khanh , Le Kim Yen Phung , Nhat Phung Tran Huy , Motiur Rahman , Huyen Thuong Nguyen Thi , Guy Thwaites , Louise Thwaites , Huyen Tran Bang , Han Tran Dong Thai , Van Anh Tran Kim , Hien Tran Minh , Thao Tran Phuong , Thanh Tran Tan , Ngoc Tran Thi Bich , Hang Tran Thi , Hien Tran Tinh , Tung Trinh Son , Rogier van Doorn H. , Jennifer Van Nuil , Pascale Vidaillac Celine , Bich Vu Thi Ngoc , Hang Vu Thi Ty , Sophie Yacoub 
Published: June 2024

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.