Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam

Phan, Lan Trong; Nguyen, Thuong Vu; Huynh, Loan K. T.; Manh, Dao Huy; Vo, Tho A. N.; Vu, Nhung H. P.; Pham, Hang; Nguyen, Huy; Nguyen, Thuc T.; Le, Hung Quoc; Nguyen, Thinh V.; Nguyen, Quan; Huynh, Thao; Nguyen, Sang Ngoc; Nguyen, Anh Hoang; Nguyen, Ngoc T.; Nguyen, Thao N. T.; Nguyễn, Long Thanh; Luong, Quang Chan; Cao, Thang M.; Pham, Quang Duy

doi:10.1002/jmv.26075

Cited by 21 publications

(24 citation statements)

References 24 publications

(45 reference statements)

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“…This difference may be due to characteristics of patients varying between a national hospital and government quarantine centres, or due to sample selection: we examined patients with Ct <30 in the real-time RT PCR, thus possibly not representing all cases at the NHTD. Common symptoms such as dry cough and fever reported in our study are similar to earlier reports of COVID-19 in China [29,30] and Vietnam [7,9,16]. However, most patients did not have underlying chronic diseases, and most (77%) had pneumonia with abnormalities on chest imaging, including one asymptomatic case.…”

Section: Discussionsupporting

confidence: 88%

“…submitted to GISAID (May 29 2020), forming the G614 SARS-CoV-2 strain [33]. Of the SARS-CoV-2 genomes from the first two patients in Vietnam (one from Wuhan who transmitted to a second case), the D614G change was not found [9]. The B.1 lineage and its sublineages have formed the majority of sequences from Vietnam since March 2020 (S1 Fig) and harbour D614G.…”

Section: Plos Onementioning

confidence: 99%

“…The cases recently detected in Da Nang have triggered the third cluster of COVID-19 in Vietnam, increasing local and hospital acquired transmission and deaths. There are a number of reports describing the clinical, epidemiological and genetic features of COVID-19 cases and SARS-CoV-2 in Vietnam, although whole genome sequencing (WGS) data is limited [6][7][8][9][10][11][12][13][14][15][16][17][18]. Here, we report the clinical, epidemiological and WGS features and correlations of 44 patients with COVID-19 in Vietnam.…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam

et al. 2020

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A second cluster of COVID-19 cases imported from Europe occured in Vietnam from early March 2020. We describe 44 SARS-CoV-2 RT-PCR positive patients (cycle threshold value <30) admitted to the National Hospital for Tropical Diseases in Hanoi between March 6 and April 15 2020. Whole SARS-CoV-2 genomes from these patients were sequenced using Illumina Miseq and analysed for common genetic variants and relationships to local and globally circulating strains. Results showed that 32 cases were Vietnamese with a median age of 37 years (range 15–74 years), and 23 were male. Most cases were acquired outside Vietnam, mainly from the UK (n = 15), other European countries (n = 14), Russia (n = 6) and countries in Asia (n = 3). No cases had travelled from China. Forty-one cases had symptoms at admission, typically dry cough (n = 36), fever (n = 20), sore throat (n = 14) and diarrhoea (n = 12). Hospitalisation was long with a median of 25 days, most commonly from 20–29 days. All SARS-CoV-2 genomes were similar (92–100% sequence homology) to the reference sequence Wuhan_1 (NC_045512), and 32 strains belonged to the B.1.1 lineage. The three most common variants were linked, and included C3037T, C14408T (nsp12: P323L) and A23403G (S: D614G) mutations. This group of mutations often accompanied variant C241T (39/44 genomes) or GGG 28881..28883 AAC (33/44 genomes). The prevalence of the former reflected probable European origin of viruses, and the transition D614G was dominant in Vietnam. New variants were identified; however, none could be associated with disease severity.

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Section: Discussionsupporting

confidence: 88%

Section: Plos Onementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam

et al. 2020

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“…The infection assays were performed in a biosafety level 3 laboratory. Vero E6 cell lines were infected with a clinical isolate SARS-CoV-2 [ 9 ]. After 72 hours, the virus medium was inactivated at 65°C for 1 hour.…”

Section: Methodsmentioning

confidence: 99%

Comparison of Primer-Probe Sets among Different Master Mixes for Laboratory Screening of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Cuong

Nguyen

Linh

et al. 2020

BioMed Research International

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Background. There is a shortage of chemical reagents for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis and a surge of SARS-CoV-2 cases, especially in limited-resource settings. Therefore, the combination of an optimal assay kit is necessary. Methods. We compared the ability to screen SARS-CoV-2 among three primer-probe sets in two different master mixes, Invitrogen™ SuperScript™ III One-Step RT-PCR and LightCycler Multiplex RNA Virus Master. Results. The assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master or Invitrogen™ SuperScript™ III One-Step RT-PCR showed positive results from a single reaction of triplicate in the three days of 4.8 copies per reaction. R squared and amplification efficiency were 0.97 and ranged from 107 to 108%, respectively. Conclusions. Our findings indicated that TIB-Molbiol, IDT, and Phu Sa primer-probe sets could be beneficial for the laboratory screening of SARS-CoV-2 by RT-qPCR assay of E gene. There is a need to consider the combination of these reagent sets as a new strategy to increase the testing capacity of screening programs for COVID-19.

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“…There have been four mutations classified as nonsynonymous mutations such as G8388A (serine to asparagine), A8987T (isoleucine to phenylalanine), and C10232T (arginine to cysteine) and a synonymous mutation is G3778A, which was published in a previous study [9].…”

Section: 2viral Preparationmentioning

confidence: 99%

Comparison of primer-probe sets among different master mixes for laboratory screening of Severe Acute Respiratory Syndrome - Coronavirus 2 (SARS-CoV-2)

Hoang

Nguyen

Hoang

et al. 2020

Preprint

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Background: The shortage of chemical reagents for severe acute respiratory syndrome - coronavirus 2 (SARS-CoV-2) diagnosis and the surge of SARS-CoV-2 cases, especially in limited-resource settings. Therefore, the combination of an optimal assay kit is necessary. Methods: We compared the ability to screen SARS-CoV-2 among three primer-probe sets added into two different master mixes (Invitrogen SuperScript III One-Step RT-PCR, and LightCycler Multiplex RNA Virus Master). Results: The assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master or Invitrogen SuperScript III One-Step RT-PCR showed positive results from a single reaction of triplicate in the three days of 4.8 copies per reaction, with R-square and amplification efficiently (AE) were 0.97 and ranged from 107 to 108%, respectively. Conclusions: Our findings indicated TIB-Molbiol, IDT, and Phu Sa primer-probe sets could be beneficial for the laboratory screening of SARS-CoV-2 by Realtime RT-PCR assay of E gene. There is a need for considering the combination of these reagent sets as a new strategy to increase testing capacity for screening programs for COVID-19.

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Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam

Cited by 21 publications

References 24 publications

Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam

Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam

Comparison of Primer-Probe Sets among Different Master Mixes for Laboratory Screening of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Comparison of primer-probe sets among different master mixes for laboratory screening of Severe Acute Respiratory Syndrome - Coronavirus 2 (SARS-CoV-2)

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