key: cord-1001177-o7lqzvqq
authors: Buathong, Rome; Chaifoo, Walairat; Iamsirithawon, Sopon; Wacharapluesadee, Supaporn; Joyjinda, Yutthana; Rodpan, Apaporn; Ampoot, Weenassarin; Putcharoen, Opass; Paitoonpong, Leilani; Suwanpimolkul, Gompol; Jantarabenjakul, Watsamon; Petcharat, Sininat; Bunprakob, Saowalak; Ghai, Siriporn; Prasithsirikul, Wisit; Mungaomklang, Anek; Plipat, Tanarak; Hemachudha, Thiravat
title: Multiple clades of SARS‐CoV‐2 were introduced to Thailand during the first quarter of 2020
date: 2021-04-09
journal: Microbiol Immunol
DOI: 10.1111/1348-0421.12883
sha: 9e08e04830be63d154ff7d1fd99c91c7a88759fe
doc_id: 1001177
cord_uid: o7lqzvqq

Early in January 2020, Thailand became the first country where a Coronavirus disease 19 (COVID‐19) patient was identified outside China. In this study, 23 whole genomes of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) from patients who were hospitalized during January to March 2020 were analyzed, along with their travel histories. Six lineages were identified including A, A6, B, B.1, B.1.8 and B.58; lineage A.6 was dominant. Seven patients were from China who travelled to Thailand in January and early of February, five of them were infected with B lineage virus, the other two cases were infected with different lineages including A and A.6. These findings represent clear evidence of the early introduction of diverse SARS‐CoV‐2 clades in Thailand. This article is protected by copyright. All rights reserved.

The Corona Virus Disease 2019 (COVID-19) pandemic has had devastating consequences globally, due in part to the greater infectivity of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as compared to other pathogens encountered over the past century. Thailand was the first country to report a confirmed COVID-19 case outside of China, identified in a traveler arriving at Suvarnabhumi airport in Bangkok from Wuhan, China on January 8, 2020 [1] [2] Table 1 . Five viral Nextstrain clades were found in Thailand from the specimens collected between January and March 2020, as was publicized in GISAID on November 13, 2020 6 (n=243) (Figure 1 and supplement Table 1 Travel histories of 23 patients were obtained from the outbreak investigation records from the Thai Ministry of Public Health (Table 1 ). All 6 patients in January 2020 traveled from China, 5 were infected with B lineage virus (including the first COVID-19 case in Thailand 1,2 , MT447155.1), while another case was infected with lineage A.6 ( Table 1) . SARS-CoV-2 from 9 Thai (7 with no travel history outside Thailand within the past 3 months, 1 of whom had recently returned from Japan, and 1 from Cambodia), from this study belonged to A.6 lineage, the most prevalent lineage found in this study (9/23, 39.13%) and in Thailand (125/243, 51.44%) during This article is protected by copyright. All rights reserved.

Article the first quarter of 2020 (from GISAID database on 13 November 2020). On the other hand, lineages B.1.8 and B.58 were identified from European travelers (Belgium and UK, respectively) who travelled to Thailand on March 2020 (Table 1) .

This study finds evidence of the early introduction of multiple SARS-CoV-2 viral clades into Thailand (Figure 1 ), all five current viral Nextstrain clades were identified among 243 viral sequences sampled during January to March 2020, reflecting considerable viral diversity since early on in the spread of the virus outside China. Three different viral lineages were identified from 7 Chinese travelers in January and early February 2020 revealed the evidence of early introduction of multiple SARS-CoV-2 viral lineages into Thailand ( Table 1 ). The earliest lineage A virus, the root of the pandemic 5 , was found in one patient from Wuhan who travelled to Thailand in early February 2020, while the viral lineage found in locally transmitted Thai cases was A.6, the derived lineage from lineage A (Figure 1 and Table 1 ).

The GISAID GV clade, the most recent clade identified on October 30, 2020, was first detected in UK on March 22, 2020 (GISAID ID EPI_ISL_420498, lineage B.1.153) but not found among the Thai entries in GISAID that were sampled between January and March 2020 ( Figure 1 ). However, the first GV clade (lineage B.1.177) reported from Thailand was from a patient travelling from Belgium, whose specimen was collected on October 16, 2020. It may be that the GV clade of SARS-CoV-2 evolved in Europe in late March, 2020, when Thailand went into national lock down with strict curfews beginning April 3, 2020, thus the Thai specimens during the early stages of the outbreak predated the evolution of GV. Alternatively, the number of WGS among the Thai entries in GISAID is inadequate (6.6%, 258 available WGS of 3,866 confirmed cases to date as of November 13, 2020) as compared to Scotland This article is protected by copyright. All rights reserved.

Article where 49% of laboratory-confirmed cases before 31 March 2020 were sequenced for WGS 8 . Since there was increasing inbound international air travel allowing specific groups to enter to Thailand in July 2020 according to the Emergency Decree, it is possible that new viral lineages may be evident among specimens collected subsequently in the state quarantine. Continued surveillance with WGS could help clarify the COVID-19 transmission dynamics worldwide and facilitate mutation identifications that will have an impact on the disease severity, transmissibility, development of diagnostic and therapeutic techniques, and certainly vaccine efficacy [9] [10] [11] .

A more detailed study integrating clinical data, epidemiology including comprehensive travel history, and a larger set of complete viral genome isolates from the continued outbreak is needed to further inform the understanding of SARS-CoV-2 transmission. 

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Nextstrain: real-time tracking of pathogen evolution

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Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020

Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland

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