Genomic surveillance of SARS-CoV-2 in Thailand reveals mixed imported populations, a local lineage expansion and a virus with truncated ORF7a

Joonlasak, Khajohn; Batty, Elizabeth M.; Kochakarn, Theerarat; Panthan, Bhakbhoom; Kümpornsin, Krittikorn; Jiaranai, Poramate; Wangwiwatsin, Arporn; Huang, Angkana T.; Kotanan, Namfon; Jaru-Ampornpan, Peera; Manasatienkij, Wudtichai; Watthanachockchai, Treewat; Rakmanee, Kingkan; Jones, Anthony R.; Fernandez, Stefan; Sensorn, Insee; Sungkanuparph, Somnuek; Pasomsub, Ekawat; Klungthong, Chonticha; Chookajorn, Thanat; Chantratita, Wasun

doi:10.1016/j.virusres.2020.198233

Cited by 26 publications

(25 citation statements)

References 19 publications

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“…The deletions within the ORF7a and ORF7b region have also previously been reported [ 15 - 18 ]. ORF7a activates the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappa B) pathway and induces proinflammatory cytokine expression [ 19 , 20 ].…”

Section: Discussionmentioning

confidence: 62%

Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing ORF7a, ORF7b and ORF8, Poland, July to August 2021

et al. 2021

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Routine genomic surveillance on samples from COVID-19 patients collected in Poland during summer 2021 revealed the emergence of a SARS-CoV-2 Delta variant with a large 872 nt deletion. This change, confirmed by Sanger and deep sequencing, causes complete loss of ORF7a, ORF7b, and ORF8 genes. The index case carrying the deletion is unknown. The standard pipeline for sequencing may mask this deletion with a long stretch of N’s. Effects of this deletion on phenotype or immune evasion needs further study.

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Section: Discussionmentioning

confidence: 62%

Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing ORF7a, ORF7b and ORF8, Poland, July to August 2021

et al. 2021

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“…ORF7a is another accessory protein of SARS-CoV-2 and is thought, like its SARS-CoV orthologue, to interfere with surface expression of host restriction factor tetherin and to modulate host translation [149, 150], although others have recently suggested this tetherin inhibition may be a non-specific side effect of ORF7a-mediated Golgi fragmentation [151]. Several independent studies have detected SARS-CoV-2 isolates with unique in- and out-of-frame deletions in this protein resulting in heavily truncated versions being expressed [152–156]. It has been hypothesised that due to possible redundancy between ORF7a and ORF6 of SARS-CoV-2, which also is thought to also inhibit host translation, deletions in ORF7a may come at a low fitness cost in vivo [154].…”

Section: Sars-cov-2 Mutations Outside the Spike Glycoproteinmentioning

confidence: 99%

SARS-CoV-2 one year on: evidence for ongoing viral adaptation

Peacock

Penrice-Randal

Hiscox

et al. 2021

Journal of General Virology

143

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SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral ‘genetic drift’ or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.

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“…8 This lineage was not a part of the local transmission in Thailand outside this cohort based on routine genomic surveillance. 2,11 The virus from individual Q4 belonged to the B.1.177 lineage. The viral genetic repertoires from cases A1, A2, A3, A4, and A6 perfectly matched (100% sequence similarity) with those from individuals Q1 and Q2 (Supplemental 1; the sample list is provided in Supplemental Table 1).…”

Section: Resultsmentioning

confidence: 99%

“…The sample from case A5 was RT-PCR positive for only one out of two genes (N gene: Ct 35.91) with merely 1.92% of the genome covered by a multiplex enrichment method. 2,12 Thus, there is a possibility that case A5 could have been a false positive or could have had low levels of fragmented viral RNA recovered several weeks after an acute infection phase. 12 Contact tracing and outbreak investigations were conducted based on previous exposures to individuals Q1-Q3 (Figure 1).…”

Section: Resultsmentioning

confidence: 99%

“…Thailand has suffered from several COVID-19 importation events during the pandemic. 2 The Thai Ministry of Public Health requires every international traveler to undergo a mandatory 14-day quarantine either at state-run or private alternative state quarantine (ASQ) facilities. An ASQ facility is a hotel accredited by the Thai health authorities and partnered with a hospital to monitor quarantined individuals for signs and symptoms of COVID-19 and to collect nasopharyngeal/oropharyngeal swabs for real-time polymerase chain reaction (RT-PCR) testing twice on Days 0-5 and Days 11-13 after entering the country.…”

Section: Introductionmentioning

confidence: 99%

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COVID-19 Transmission among Healthcare Workers at a Quarantine Facility in Thailand: Genomic and Outbreak Investigations

Atsawawaranunt

Kochakarn

Kongklieng

et al. 2021

The American Journal of Tropical Medicine and Hygiene

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During the COVID-19 pandemic, Thailand implemented a quarantine program at approved quarantine facilities for every international traveler. Here, we report an epidemiological and genomic investigation of a COVID-19 cluster consisting of seven healthcare workers (HCWs) at a quarantine facility and its partnered hospital in Thailand. Outbreak investigations were implemented to obtain contact tracing data and to establish chains of transmission. Genomic sequencing of SARS-CoV-2 with samples within the cohort was performed. Investigations of 951 HCWs and staff with quarantined travelers were implemented to determine the chain of transmission. Genomic and outbreak investigations identified the international travelers infected with the B.1.1.31 SARS-CoV-2 lineage as the source of this outbreak. The genomic data and the investigated timeline revealed a putative transmission chain among HCWs, pointing toward the transmission via the use of common living quarters at the investigated quarantine site. The evaluation of this cohort has led to a policy recommendation on quarantine facility management. International travel quarantine is an important strategy to contain importation of COVID-19 cases. However, a quarantine facility is likely to become a potential hotspot, requiring thorough preventive measures. Reducing the exposure risk by providing private living quarters and scheduling clinical duties at a quarantine site separated from the conventional healthcare workforce have been implemented.

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Genomic surveillance of SARS-CoV-2 in Thailand reveals mixed imported populations, a local lineage expansion and a virus with truncated ORF7a

Cited by 26 publications

References 19 publications

Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing ORF7a, ORF7b and ORF8, Poland, July to August 2021

Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing ORF7a, ORF7b and ORF8, Poland, July to August 2021

SARS-CoV-2 one year on: evidence for ongoing viral adaptation

COVID-19 Transmission among Healthcare Workers at a Quarantine Facility in Thailand: Genomic and Outbreak Investigations

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