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

Tam, Nguyen Thi Thanh; Anh, Nguyen To; Tung, Trinh Son; Thach, Pham Ngoc; Dung, Nguyen Thanh; Trang, Van Dinh; Hung, Le Manh; Dien, Trinh Cong; Ngoc, Nghiêm My; Duyet, Le Van; Cuong, Phan Manh; Phuong, Hoang Vu Mai; Thái, Phạm Quang; Tung, Nguyen Le Nhu; Man, Dinh Nguyen Huy; Phong, Nguyễn Thanh; Quang, Vo Minh; Thoa, Pham Thi Ngoc; Truong, Nguyen Thanh; Thao, Tran Nguyen Phuong; Linh, Dao Phuong; Tai, Ngo Tan; Bao, Ho The; Vuong, Vo Trong; Nhung, Huynh Thi Kim; Hong, Phan Nu Dieu; Hanh, Le Thi Phuoc; Chung, Le Thanh; Nhàn, Nguyễn Thị Thanh; Thanh, Ton That; Hung, Do Thai; Kim, Huynh; Long, Trinh Hoang; Trang, Nguyễn Thu; Thương, Nguyễn Thị; Hong, Nguyen Thi Thu; Nhu, Le Nguyen Truc; Ny, Nguyen Thi Han; Thuy, Cao Thu; Thanh, Le Kim; Nguyet, Lam Anh; Quynh, Lê; Thuong, Tang Chi; Nga, Le Hong; Thanh, Tran Tan; Thwaites, Guy; Doorn, H. Rogier van; Châu, Nguyễn Văn Vĩnh; Kesteman, Thomas; Tan, Le Van

doi:10.3201/eid2905.221787

Cited by 5 publications

(3 citation statements)

References 9 publications

(10 reference statements)

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“…Precipitation showed a significant association with the Alpha variant, the Delta variant exhibited an association with humidity and other variants showed an association with wind speed. Similar findings were also observed in other studies [ 29 , 30 ]. These findings highlight the importance of considering environmental factors alongside genomic surveillance to better understand and mitigate the spread of SARS-CoV-2 variants.…”

Section: Discussionsupporting

confidence: 93%

The Dynamics of COVID-19 in Hiroshima Prefecture Compared to Japan and Its Association With Meteorological Factors: A Comparative Analysis

Hussain,

Shaba,

Bunthen

et al. 2024

Cureus

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Introduction Despite the implementation of countermeasures and mass vaccination programs, the COVID-19 pandemic incidence was a vital public health concern. This study aimed to explore the dynamics of COVID-19 cases and assess the association of COVID-19 pandemic epidemiological data with meteorological factors in Hiroshima Prefecture compared to Japan. Methods We analyzed COVID-19 pandemic data in Japan's Hiroshima Prefecture from January 16, 2020, to May 9, 2023. Meteorological factors were examined at different time frames, and Spearman correlation coefficients were calculated for COVID-19 variables and variants based on GISAID whole genome analysis. Results Hiroshima Prefecture reported 816,788 COVID-19 cases and 1,371 fatalities, with a city-to-rural case ratio of 0.97:1. Infection rates were 17.42% for Japan and 15.83% for Hiroshima. Gender-wise, the ratio was 99:1, and the 30-39 age group in Hiroshima had the highest cases (15.5%). Among all meteorological factors, daily and 14-day average wind speed showed a weak correlation with incidence (-0.1954, P < 0.01; 0.3669 P < 0.01), fatalities (-0.1148, P < 0.01; -0.2232 P < 0.01), and incidence rate (-0.2042, P < 0.01; -0.3751, P < 0.01), respectively. Clade GRA was most frequent (39.7%), and among 61 variants, B.1.1.7, AY.29, and BA.1.1.2 were predominant. Precipitation was associated significantly with the Alpha variant (0.3373, P<0.01), while the Delta variant (0.2934, <0.05) weakly correlated with humidity. Conclusion COVID-19 pandemic trends in Hiroshima Prefecture paralleled Japan's, yet with lower incidence and fatalities compared to most prefectures. Significant associations were found between meteorological factors and COVID-19 metrics, including incidence, fatalities, incidence rate, and mutations in Hiroshima.

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Section: Discussionsupporting

confidence: 93%

The Dynamics of COVID-19 in Hiroshima Prefecture Compared to Japan and Its Association With Meteorological Factors: A Comparative Analysis

Hussain,

Shaba,

Bunthen

et al. 2024

Cureus

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“…Meanwhile across the globe, the proportion of delta variant had been dominated in neighboring and regional countries 12 including the Russian Federation, 21 South Korea, 22 and Vietnam. 23 In Mongolia, the Delta variant had apparently become dominant by September 2021, following the loosening of restrictive measures, including the resumption of commercial flights and presidential election campaigns. These patterns suggest a relatively slower introduction of globally circulating variants.…”

Section: Discussionmentioning

confidence: 99%

Molecular epidemiology of SARS‐CoV‐2 in Mongolia, first experience with nanopore sequencing in lower‐ and middle‐income countries setting

Erendereg,

Tumurbaatar,

Byambaa

et al. 2023

Immunity Inflam & Disease

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BackgroundCoronavirus disease (COVID‐19) has had a significant impact globally, and extensive genomic research has been conducted on severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) lineage patterns and its variants. Mongolia's effective response resulted in low prevalence until vaccinations became available. However, due to the lack of systematically collected data and absence of whole genome sequencing capabilities, we conducted a two‐stepped, nationally representative molecular epidemiologic study of SARS‐CoV‐2 in Mongolia for 2020 and 2021.MethodsWe used retrospective analysis of stored biological samples from November 2020 to October 2021 and a variant‐specific real‐time reverse transcription polymerase chain reaction (RT‐PCR) test to detect SARS‐CoV‐2 variants, followed by whole genome sequencing by Nanopore technology. Samples were retrieved from different sites and stored at −70°C deep freezer, and tests were performed on samples with cycle threshold <30.ResultsOut of 4879 nucleic acid tests, 799 whole genome sequencing had been carried out. Among the stored samples of earlier local transmission, we found the 20B (B.1.1.46) variant predominated in the earlier local transmission period. A slower introduction and circulation of alpha and delta variants were observed compared to global dynamics in 2020 and 2021. Beta or Gamma variants were not detected between November 2020 and September 2021 in Mongolia.ConclusionsSARS‐CoV‐2 variants of concerns including alpha and delta were delayed in circulation potentially due to public health stringencies in Mongolia. We are sharing our initial experience with whole genome sequencing of SARS‐CoV‐2 from Mongolia, where sequencing data is sparse.

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“…Interruptions between the segments were modeled in May and October 2021. May 2021 marked the beginning of the nationwide Delta wave in Viet Nam [ 39 ]. By the end of September 2021, the country reached sufficiently high levels of COVID-19 vaccination coverage for the government to issue Resolution No.…”

Section: Methodsmentioning

confidence: 99%

Ensuring Continuity of Tuberculosis Care during Social Distancing through Integrated Active Case Finding at COVID-19 Vaccination Events in Vietnam: A Cohort Study

Dinh,

Vo,

Wiemers

et al. 2024

TropicalMed

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COVID-19 significantly disrupted tuberculosis (TB) services in Vietnam. In response, the National TB Program (NTP) integrated TB screening using mobile chest X-rays into COVID-19 vaccination events. This prospective cohort study evaluated the integrated model’s yield, treatment outcomes, and costs. We further fitted regressions to identify risk factors and conduct interrupted time-series analyses in the study area, Vietnam’s eight economic regions, and at the national level. At 115 events, we conducted 48,758 X-ray screens and detected 174 individuals with TB. We linked 89.7% to care, while 92.9% successfully completed treatment. The mean costs per person diagnosed with TB was $547. TB risk factors included male sex (aOR = 6.44, p < 0.001), age of 45–59 years (aOR = 1.81, p = 0.006) and ≥60 years (aOR = 1.99, p = 0.002), a history of TB (aOR = 7.96, p < 0.001), prior exposure to TB (aOR = 3.90, p = 0.001), and symptomatic presentation (aOR = 2.75, p < 0.001). There was a significant decline in TB notifications during the Delta wave and significant increases immediately after lockdowns were lifted (IRR(γ1) = 5.00; 95%CI: (2.86, 8.73); p < 0.001) with a continuous upward trend thereafter (IRR(γ2) = 1.39; 95%CI: (1.22, 1.38); p < 0.001). Similar patterns were observed at the national level and in all regions but the northeast region. The NTP’s swift actions and policy decisions ensured continuity of care and led to the rapid recovery of TB notifications, which may serve as blueprint for future pandemics.

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

Cited by 5 publications

References 9 publications

The Dynamics of COVID-19 in Hiroshima Prefecture Compared to Japan and Its Association With Meteorological Factors: A Comparative Analysis

The Dynamics of COVID-19 in Hiroshima Prefecture Compared to Japan and Its Association With Meteorological Factors: A Comparative Analysis

Molecular epidemiology of SARS‐CoV‐2 in Mongolia, first experience with nanopore sequencing in lower‐ and middle‐income countries setting

Ensuring Continuity of Tuberculosis Care during Social Distancing through Integrated Active Case Finding at COVID-19 Vaccination Events in Vietnam: A Cohort Study

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