Identification and Analysis of SARS-CoV-2 Alpha Variants in the Largest Taiwan COVID-19 Outbreak in 2021

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is believed to have originated in Wuhan City, Hubei Province, China, in December 2019. Infection with this highly dangerous human-infecting coronavirus via inhalation of respiratory droplets from SARS-CoV-2 carriers results in coronavirus disease 2019 (COVID-19), which features clinical symptoms such as fever, dry cough, shortness of breath, and life-threatening pneumonia. Several COVID-19 waves arose in Taiwan from January 2020 to March 2021, with the largest outbreak ever having a high case fatality rate (CFR) (5.95%) between May and June 2021. In this study, we identified five 20I (alpha, V1)/B.1.1.7/GR SARS-CoV-2 (KMUH-3 to 7) lineage viruses from COVID-19 patients in this largest COVID-19 outbreak. Sequence placement analysis using the existing SARS-CoV-2 phylogenetic tree revealed that KMUH-3 originated from Japan and that KMUH-4 to KMUH-7 possibly originated via local transmission. Spike mutations M1237I and D614G were identified in KMUH-4 to KMUH-7 as well as in 43 other alpha/B.1.1.7 sequences of 48 alpha/B.1.1.7 sequences deposited in GISAID derived from clinical samples collected in Taiwan between 20 April and July. However, M1237I mutation was not observed in the other 12 alpha/B.1.1.7 sequences collected between 26 December 2020, and 12 April 2021. We conclude that the largest COVID-19 outbreak in Taiwan between May and June 2021 was initially caused by the alpha/B.1.1.7 variant harboring spike D614G + M1237I mutations, which was introduced to Taiwan by China Airlines cargo crew members. To our knowledge, this is the first documented COVID-19 outbreak caused by alpha/B.1.1.7 variant harboring spike M1237I mutation thus far. The largest COVID-19 outbreak in Taiwan resulted in 13,795 cases and 820 deaths, with a high CFR, at 5.95%, accounting for 80.90% of all cases and 96.47% of all deaths during the first 2 years. The high CFR caused by SARS-CoV-2 alpha variants in Taiwan can be attributable to comorbidities and low herd immunity. We also suggest that timely SARS-CoV-2 isolation and/or sequencing are of importance in real-time epidemiological investigations and in epidemic prevention. The impact of D614G + M1237I mutations in the spike gene on the SARS-CoV-2 virus spreading as well as on high CFR remains to be elucidated.

Keywords: COVID-19; SARS-CoV-2; alpha/B.1.1.7; clade replacements; next-generation sequencing; phylogenetic analysis; qRT-PCR; virus culture.

FIGURE 1

Monthly COVID-19 data between January 2020 and December 2021 in Taiwan. Monthly data of confirmed COVID-19 cases and deaths resulting from COVID-19 between 1 January 2020 and 31 December 2021. These data were retrieved from the notifiable diseases surveillance system maintained by the Taiwan CDC. Source of data: https://nidss.cdc.gov.tw/nndss/disease?id=19CoV.

FIGURE 2

Geographical distribution of autochthonous COVID-19 cases between January 2020 and December 2021 in Taiwan. Confirmed COVID-19 case numbers are shown in each city of the second-level administrative division in Taiwan. The numbers in the brackets are fatal cases. This figure was generated using QGIS v3.16.14 (QGIS Development Team, 2022, QGIS Geographic Information System, Open Source Geospatial Foundation, http://www.qgis.org/). Taiwan map data were retrieved from the Taiwan Geospatial One-Stop Portal developed by the Information Center of the Taiwan Ministry of The Interior and used under the Open Government Data License.

FIGURE 3

Phylogenetic analysis of KMUH-3 to KMUH-7 SARS-CoV-2 using UShER. UShER enables real-time sequence placement for the SARS-CoV-2 pandemic using an existing phylogenetic tree generated by the sarscov2phylo pipeline, which contains 6,624,590 genomes from GISAID, GenBank, COG-UK, and CNCB (2 January 2022). The phylogenetic subtree data are visualized using Interactive Tree Of Life (iTOL) version 6.4.3 (https://itol.embl.de/) (73). The 200 nearest neighboring GISAID EpiCoV and/or other publicly available SARS-CoV-2 sequences, including the sequences uploaded for analysis, already in the existing phylogenetic tree were output for visualization. Only partial results are shown in each subtree panel. (A) The 200 nearest neighboring sequences to the KMUH-3 are all retrieved from Japan. (B) The 200 nearest neighboring sequences to KMUH-4 to KMUH-7 were retrieved from Taiwan, Australia, and European countries.

FIGURE 4

Clades replaced over time between January 2020 and December 2021 in Taiwan.

FIGURE 5

Phylogenetic tree of 247 SARS-CoV-2 genomes collected in Taiwan between January 2020 and December 2021. The phylogenetic analysis was inferred by using the maximum likelihood and fits of 286 different nucleotide substitution models, and the results suggested GTR + F + I as the best-fitting model with the lowest Bayesian information criterion (BIC) scores of 107,672.091 among the 286 models tested. The tree topology was automatically computed to estimate maximum likelihood values. The optimal log-likelihood for this computation was –50,857.073. There was a total of 29,867 positions in the final dataset. The original tree is displayed using iTOL v 6.4.3 (https://itol.embl.de/) (73) with an indicator of bootstrap values and a scale bar. Viruses are shown as the virus name| Accession ID| Collection date| City/Nextstrain_clade/pangolin_lineage/GISAID_clade). (A) An original phylogenetic tree of 247 SARS-CoV-2 sequences obtained from GISAID which samples were collected between January 2020 and December 2021 in Taiwan. (B) A partial tree exhibited phylogenetic correlation between Nextstrain clades 20H beta-V2, 20C, 21C epsilon, and 20G. (C) A partial tree exhibited phylogenetic correlation between Nextstrain clades 20A, 21A delta, 21I delta, 21J delta, and 20E EU1. (D) A partial tree exhibited phylogenetic correlation between Nextstrain clades 19A and 19B. (E) A partial tree exhibited phylogenetic correlation between Nextstrain clades 20B, 20J, and 20I alpha-V1. KMUH-3 was clustered with alpha/B.1.1.7 variant strain sequences without spike M1237I mutation collected between 26 December 2020 and 21 April 2021. KMUH-4 to KMUH-7 were clustered with alpha/B.1.1.7 variant strain sequences with spike M1237I mutation collected between 20 April 2021 and 28 July 2021. *Alpha/B.1.1.7 without spike M1237I mutation; ^**alpha/B.1.1.7 with spike M1237I mutation.

FIGURE 6

Phylogenetic tree of all 60 alpha/B.1.1.7 sequences deposited in GISAID EpiCoV from samples collected in Taiwan between January 2020 and December 2021. The phylogenetic analysis was inferred by using the maximum likelihood and fits of 286 different nucleotide substitution models, and the results suggested TN + F as the best-fitting model with the lowest Bayesian information criterion (BIC) scores of 85,071.899 among the 286 models tested. The tree topology was automatically computed to estimate the maximum likelihood values. The optimal log-likelihood for this computation was –42,000.232. There was a total of 29,796 positions in the final dataset. The original tree is displayed using iTOL v 6.4.3 (https://itol.embl.de/) (73) with an indicator of bootstrap values and a scale bar. Viruses are shown as the virus name| collection date.

FIGURE 7

Phylogenetic analysis results of cases 1078/1079, KMUH-4 to KMUH-7, and 62 alpha/B.1.1.7 sequences with D614G and M1237I mutations deposited in GISAID from samples collected between 14 April 2021 and 16 April 2021. The phylogenetic analysis was inferred by using the maximum likelihood and fits of 286 different nucleotide substitution models, and the results suggested TN + F + I as the best-fitting model with the lowest BIC scores of 86,786.332 among the 286 models tested. The tree topology was automatically computed to estimate the maximum likelihood values. The optimal log-likelihood for this computation was –42,677.481. There was a total of 29,662 positions in the final dataset. The original tree is displayed using iTOL v 6.4.3 (https://itol.embl.de/) (73) with an indicator of bootstrap values and a scale bar. Viruses are shown as the virus name.