Novel Mutation of SARS-CoV-2, Vietnam, July 2020

Characteristics and long-term health outcomes of the first domestic COVID-19 outbreak cases in Da Nang, Vietnam: a longitudinal cohort study

BACKGROUND

Vietnam experienced the first COVID-19 domestic outbreak due to the Wuhan strain (B.1.1) in Da Nang from July 2020. COVID-19 can cause acute as well as long-term health problems. We aimed to characterise clinical features and risk factors related to severe illness of COVID-19 among Da Nang outbreak cases and to describe long-term health outcomes among survivors of this outbreak.

METHODS

We conducted an ambidirectional cohort study. Study subjects were all hospitalised cases with positive real-time PCR test of SARS-CoV-2 in the three major hospitals in Da Nang from 25 July to 28 August 2020. Clinical and demographic information was retrospectively collected from medical charts. Then, the survivors were followed-up prospectively at 6 and 16 months after acute infection to assess their health status via standardized questionnaires, physical examinations, chest X-rays and pulmonary function tests.

RESULTS

A total of 362 cases including 20 fatal cases were enrolled into the study retrospectively. The median age of the participants included in the medical chart review was 46.5 years and 60.8% were female. Overall, 7.8% of the participants required respiratory support during hospitalisation and 20 of them died. Compared to the survivors, the fatal cases were significantly older (median age of survivors 45.0 yr vs fatal cases 66.5 yr, P < 0.001) and more likely to have underlying conditions. The proportions of participants who had at least one long COVID symptom within the 7 days of each follow-up at 6 and 16 months were 72.0% (134/186) and 63.5% (47/74), respectively. We also found that females and adults reported symptoms more often in the follow-up surveys, 78.9% (90/114) [females] vs 61.1% (44/72) [males] at 6 months, P = 0.008; 68.7% (46/67) [ ≥ 20 years] vs 14.3% (1/7) [ < 20 years] at 16 months, P = 0.004.

CONCLUSIONS

In the first domestic COVID-19 outbreak in Vietnam, the mortality rate was approximately 6% and associated with underlying medical conditions. In the follow-up surveys, a substantial proportion of participants reported long COVID related health problems, although the prevalence declined over time. Females and adults reported symptoms more often, which might be due to the pathophysiological differences according to sex and age.

Molecular characterisation and tracking of severe acute respiratory syndrome coronavirus 2 in Thailand, 2020-2022

The global COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected in China in December 2019. To date, there have been approximately 3.4 million reported cases of COVID-19 and over 24,000 deaths in Thailand. In this study, we investigated the molecular characteristics and evolution of SARS-CoV-2 in Thailand from 2020 to 2022. Two hundred sixty-eight SARS-CoV-2 isolates, collected mostly in Bangkok from COVID-19 patients, were characterised by partial genome sequencing. Moreover, the viruses in 5,627 positive SARS-CoV-2 samples were identified as viral variants - B.1.1.7 (Alpha), B.1.617.2 (Delta), B.1.1.529 (Omicron/BA.1), or B.1.1.529 (Omicron/BA.2) - by multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) assays. The results revealed that B.1.36.16 caused the predominant outbreak in the second wave (December 2020-January 2021), B.1.1.7 (Alpha) in the third wave (April-June 2021), B.1.617.2 (Delta) in the fourth wave (July-December 2021), and B.1.1.529 (Omicron) in the fifth wave (January-March 2022). The evolutionary rate of the viral genome was 2.60 × 10-3 (95% highest posterior density [HPD], 1.72 × 10-3 to 3.62 × 10-3) nucleotide substitutions per site per year. Continued molecular surveillance of SARS-CoV-2 is crucial for monitoring emerging variants with the potential to cause new COVID-19 outbreaks.

Occurrence of the Omicron variant of SARS-CoV-2 in northern Viet Nam in early 2022

The Omicron variant caused a surge of infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Viet Nam in early 2022, signalling community transmission. We report on active whole-genome sequencing surveillance of positive SARS-CoV-2 samples collected at that time in northern Viet Nam from international arrivals and community clusters. We used an amplicon protocol developed with 14 polymerase chain reaction products and the Illumina iSeq 100 platform. Overall, 213 nasopharyngeal or throat swabs were analysed, of which 172 samples were identified with the Omicron variant. Of these, 80 samples were collected from community cases in February 2022, among which 59 samples were sublineage BA.2 and one sample was the recombinant XE variant. Our results indicated that Omicron had replaced Delta as the dominant variant in a very short period of time and that continuously conducting active whole-genome sequencing surveillance is necessary in monitoring the evolution and genomic diversity of SARS-CoV-2 in Viet Nam.