COVID-19: Vietnam finds new virus variant that’s a hybrid of India and UK strains


Vietnam has discovered a new coronavirus variant that’s a hybrid of strains first found in India and the U.K., the Vietnamese health minister said Saturday.

Nguyen Thanh Long said scientists examined the genetic makeup of the virus that had infected some recent patients, and found the new version of the virus. He said lab tests suggested it might spread more easily than other versions of the virus.

Viruses often develop small genetic changes as they reproduce, and new variants of the coronavirus have been seen almost since it was first detected in China in late 2019.

The World Health Organization has listed four global “variants of concern” – the two first found in the U.K. and India, plus ones identified in South Africa and Brazil.

Long says the new variant could be responsible for a recent surge in Vietnam, which has spread to 30 of the country’s 63 municipalities and provinces.

Vietnam was initially a standout success in battling the virus – in early May, it had recorded just over 3,100 confirmed cases and 35 deaths since the start of the pandemic.

But in the last few weeks, Vietnam has confirmed more than 3,500 new cases and 12 deaths, increasing the country’s total death toll to 47.

Most of the new transmissions were found in Bac Ninh and Bac Giang, two provinces dense with industrial zones where hundreds of thousands of people work for major companies including Samsung, Canon and Luxshare, a partner in assembling Apple products. Despite strict health regulations, a company in Bac Giang discovered that one fifth of its 4,800 workers had tested positive for the virus.

In Ho Chi Minh City, the country’s largest metropolis and home to 9 million, at least 85 people have tested positive as part of a cluster at a Protestant church, the Health Ministry said. Worshippers sang and chanted while sitting close together without wearing proper masks or taking other precautions.

Vietnam has since ordered a nationwide ban on all religious events. In major cities, authorities have banned large gatherings, closed public parks and non-essential business including in-person restaurants, bars, clubs and spas.

Vietnam so far has vaccinated 1 million people with AstraZeneca shots. Last week, it sealed a deal with Pfizer for 30 million doses, which are scheduled to be delivered in the third and fourth quarters of this year.

It is also in talks with Moderna that would give it enough shots to fully vaccine 80% of its 96 million people.

On December 14, 2020, the United Kingdom reported a newly identified variant of SARS-CoV-2 (known as VOC 202012/01 or B.1.1.7 lineage).1, 2 This carries several mutations, including the spike protein N501Y substitution and 69-70del, resulting in substantially increased transmission rates of 50-74% greater than other variants3; the variant rapidly circulates worldwide.4

In such a context, a full characterization of this variant is essential for a further development of response strategies to COVID-19. Here, we describe clinical, epidemiological characteristics, and sequencing of the B.1.1.7 variant from a patient with pneumonia imported from the United Kingdom to Vietnam. We additionally identified and reported another passenger infected with the B.1.177 strain.

A 44-year-old Vietnamese woman with a history of hypertension, living in London (Patient 1), had flown to Vietnam on December 22, 2020. She and other 304 passengers were immediately taken into a government quarantine center in southern Vietnam for 14 days as required by the current quarantine protocols for all incoming international arrivals to Vietnam.

After 2 days, she was tested positive for SARS-CoV-2 using real-time reverse-transcription polymerase chain reaction (a cycle threshold of 24). She reported that she wore a personal protection equipment (PPE) kit, including a facemask, gloves, goggles, shoe covers, and disposable coveralls bodysuit during her return to Vietnam. She additionally reported that she had not been exposed to any known COVID-19 cases in the United Kingdom before departure.

Patient 1 disclosed that she had experienced an increased sore throat with a low-grade fever on December 23. On December 25, she was referred to a designated hospital for proper isolation and care. Physical examination on admission revealed a body temperature of 37.5°C, blood pressure of 150/90 mmHg, moist crackles auscultated in both lower lung fields, and oxygen saturation of 95% while she was breathing ambient air.

Chest radiographs and other laboratory tests on admission showed no abnormalities. On Day 7th of hospitalization, a dry cough developed, and chest radiographs showed heterogeneous infiltrates in the inferior lobes of the bilateral lungs, indicating the development of pneumonia in this patient (Figure S1).

The patient’s symptoms were resolved on January 6, 2021 (Day 13th of hospitalization). None of the 10 close contacts of the patient who reported wearing PPE kits during their return to Vietnam tested positive for SARS-CoV-2. Her husband who was living in the United Kingdom tested positive for SARS-CoV-2 one day after her diagnosis.

Given the patient’s travel history, we did cell culture and successfully isolated SARS-CoV-2 from the throat and nasopharyngeal swabs of Patient 1 on Vero E6 cell line. The viral cytopathic effect was observed on the second day after inoculation, and was similar to that of the strain with D614G mutation that was observed previously (Figure S2). We then studied the full genome of the isolate using next-generation sequencing (29,823 base pairs; GISAID ID: EPI_ISL_760247), and compared the sequences with the GISAID reference strain hCoV-19/Wuhan/WIV04/2019. Sequence analysis showed that the isolate belonged to the GR clade and B.1.1.7 lineage (Figure 1), and it carried 10 mutations in the spike region: three deletions (69-70del and 144del) and seven amino acid substitutions (N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H).

Three other mutations were located in the ORF8-specific region (Q27stop, R52I, and Y73C) and four mutations in the nucleocapsid protein region (D3L, R203K, G204R, and S235F). Apart from Patient 1, we detected additional infections among passengers (Patient 2). The isolate from Patient 2, a 28-year-old man, was the GV clade, B.1.177 lineage, and it harbored two A222V and D614G mutations in the spike protein region, A220V in N protein, M125I on NS3 and P323L in NSP12 region (GISAID ID: EPI_ISL_812922). Under legal protections for a public health response to the widening epidemic of COVID-19, the present case investigation did not require human subject reviews.

FIGURE 1: Phylogenetic tree of the complete genomes of SARS-CoV-2 isolated from two patients returning to Vietnam from the United Kingdom in December 2020. Dots indicate the SARS-CoV-2 strains isolated in this study (EPI_ISL_760247 and EPI_ISL_812922). Complete genome sequences were aligned with other related coronavirus sequences archived from GenBank/GISAID using Mafft software and constructed a phylogenetic tree using the maximum likelihood method with 1000 bootstrap replicates in MEGA-X using the general time-reversible model. The bootstrap values were indicated on branches

Blood obtained from Patient 1 on admission tested negative for viral hepatitis B and C. On Day 10th of hospitalization, the serum levels of alanine aminotransferases and aspartate aminotransferases were 60 and 39 U/L, respectively, approximately two- to threefold higher than levels detected on Day 1 (20 and 17 U/L, respectively) (Table S1). It is possible that there was liver impairment directly caused by the infection of this variant in this case.5

The importation of a highly transmissible B.1.1.7 variant of SARS-CoV-2 was first detected in Vietnam. Continuing strategies for strict border control, quarantine, and testing policies of all incoming international passengers are essential for detecting and preventing the spread of new variants of SARS-CoV-2 in the general population in Vietnam.



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