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

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.

Spatiotemporal Evolution of SARS-CoV-2 Alpha and Delta Variants during Large Nationwide Outbreak of COVID-19, Vietnam, 2021.

We analyzed 1,303 SARS-CoV-2 whole-genome sequences from Vietnam, and found the Alpha and Delta variants were responsible for a large nationwide outbreak of COVID-19 in 2021. The Delta variant was confined to the AY.57 lineage and caused >1.7 million infections and >32,000 deaths. Viral transmission was strongly affected by nonpharmaceutical interventions.

Human infection with highly pathogenic avian influenza virus (H5N1) in northern Vietnam, 2004-2005.

We performed a retrospective case-series study of patients with influenza A (H5N1) admitted to the National Institute of Infectious and Tropical Diseases in Hanoi, Vietnam, from January 2004 through July 2005 with symptoms of acute respiratory tract infection, a history of high-risk exposure or chest radiographic findings such as pneumonia, and positive findings for A/H5 viral RNA by reverse transcription-PCR. We investigated data from 29 patients (mean age 35.1 years) of whom 7 (24.1%) had died. Mortality rates were 20% (5/25) and 50% (2/4) among patients treated with or without oseltamivir (p = 0.24), respectively, and were 33.3% (5/15) and 14.2% (2/14) among patients treated with and without methylprednisolone (p = 0.39), respectively. After exact logistic regression analysis was adjusted for variation in severity, no significant effectiveness for survival was observed among patients treated with oseltamivir or methylprednisolone.