Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Clinical Samples
2.3. Diagnostic Tests
2.4. Whole-Genome Sequencing of SARS-CoV-2
2.5. Phylogenetic Analysis
2.6. Mutation Site Identification
2.7. Haplotype Network Construction
2.8. Pairwise Distance Calculation and Genetic Diversity Analysis
3. Results
3.1. Phylogenetic Analysis of SARS-CoV-2 Detected in a Cruise Ship Cluster
3.2. Characterization of Mutation Sites and Substitution Patterns in CA Strains
3.3. Haplotype Diversity in SARS-CoV-2 Strains Detected in Cruise Ship Clusters
3.4. Pairwise Genetic Distance between Cruise Ship Strains and Isolates from Lockdown Cities or Superspreading Events
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Group | Sample | Strain | Mutations | Amino Acid Substitutions | ||
---|---|---|---|---|---|---|
Total Number | Number /Strain | Total Number | Number/Strain | |||
FJ Japan | Clinical tests | 82 | 1191 | 14.52 | 612 | 7.46 |
Costa Atlantica | Cruise ship | 94 | 1175 | 12.50 | 755 | 8.03 |
Diamond Princess | Cruise ship | 71 | 149 | 2.10 | 110 | 1.55 |
FJ Japan (n = 82) | Costa Atlantica (n = 94) | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Position 1 | Ref 2 | Mut 3 | Protein | Substitution | n | Position | Ref | Mut | Protein | Substitution | n |
14408 | C | T | ORF1b NSP12b | P314L | 82 | 3373 | C | A | ORF1a NSP3 | D218E | 94 |
23403 | A | G | S | D614G | 82 | 14408 | C | T | ORF1b NSP12b | P314L | 94 |
28881 | GGG | AAC | N | RG203KR | 82 | 23403 | A | G | S | D614G | 94 |
4346 | T | C | ORF1a NSP3 | S543P | 35 | 28881 | GGG | AAC | N | RG203KR | 94 |
10376 | C | T | ORF1a NSP5 | P108S | 35 | 11195 | C | T | ORF1a NSP6 | L75F | 92 |
14708 | C | T | ORF1b NSP12b | A414V | 35 | 25437 | G | T | ORF3a | L15F | 64 |
28725 | C | T | N | P151L | 35 | 23604 | C | A | S | P681H | 44 |
22020 | T | C | S | M153T | 23 | 10755 | C | T | ORF1a NSP5 | A234V | 7 |
28975 | G | T | N | M234I | 13 | 376 | G | C | ORF1a NSP1 | E37D | 6 |
21518 | G | T | ORF1b NSP16 | R287I | 7 | 6660 | G | A | ORF1a NSP3 | S1314N | 5 |
18167 | C | T | ORF1b NSP14 | P43L | 6 | 17876 | C | T | ORF1b NSP13 | T547I | 4 |
7728 | C | T | ORF1a NSP3 | S1670F | 4 | 25445 | G | T | ORF3a | G18V | 4 |
12869 | A | T | ORF1a NSP9 | T62S | 3 | 2901 | T | C | ORF1a NSP3 | V61A | 2 |
2167 | G | T | ORF1a NSP2 | K454N | 2 | 3230 | G | T | ORF1a NSP3 | G171C | 2 |
2910 | C | T | ORF1a NSP3 | T64I | 2 | 3514 | G | T | ORF1a NSP3 | M265I | 2 |
4309 | G | T | ORF1a NSP3 | K530N | 2 | 5018 | G | T | ORF1a NSP3 | D767Y | 2 |
11083 | G | T | ORF1a NSP6 | L37F | 2 | 13080 | T | C | ORF1a NSP10 | F19S | 2 |
21575 | C | T | S | L5F | 2 | 13624 | G | T | ORF1b NSP12b | D53Y | 2 |
21614 | C | T | S | L18F | 2 | 13922 | A | G | ORF1b NSP12b | D152G | 2 |
23481 | C | T | S | S640F | 2 | 19885 | AA | CG | ORF1b NSP15 | K89R | 2 |
26966 | T | A | M | H148Q | 2 | 27688 | C | T | ORF7a | P99S | 2 |
27925 | C | A | ORF8 | T11K | 2 | 28302 | G | T | N | R10L | 2 |
Diamond Princess (n = 71) | |||||||||||
Position | Ref | Mut | Protein | Substitution | n | ||||||
11083 | G | T | ORF1a NSP6 | L37F | 71 | ||||||
18656 | C | T | ORF1b NSP14 | T206I | 8 | ||||||
4127 | G | A | ORF1a NSP3 | G470S | 2 | ||||||
5845 | A | T | ORF1a NSP3 | K1042N | 2 |
FJ Japan (n = 82) | Costa Atlantica (n = 94) | Diamond Princess (n = 71) | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Pos 1 | Ref 2 | Mut 3 | Sub 4 | n | Pos | Ref | Mut | Sub | n | Pos | Ref | Mut | Sub | n |
21575 | C | T | L5F | 2 | 21721 | C | A | D53E | 1 | 21575 | C | T | L5F | 1 |
21614 | C | T | L18F | 2 | 21765 | T | G | I68R | 1 | 21917 | A | G | I119V | 1 |
21707 | C | T | H49Y | 1 | 22021 | G | T | M153I | 1 | 22104 | G | T | G181V | 1 |
22020 | T | C | M153T | 23 | 22275 | T | A | F238Y | 1 | 23856 | G | T | R765L | 1 |
22199 | G | C | V213L | 1 | 22289 | G | T | A243S | 1 | 24797 | C | A | P1079T | 1 |
22317 | G | T | G252V | 1 | 23403 | A | G | D614G | 94 | 24819 | A | G | K1086R | 1 |
23403 | A | G | D614G | 82 | 23604 | C | A | P681H | 44 | 25244 | G | T | V1228L | 1 |
23481 | C | T | S640F | 2 | 23705 | C | A | P715T | 1 | |||||
24328 | G | C | L922F | 1 | ||||||||||
25088 | G | T | V1176F | 1 | ||||||||||
25317 | C | A | S1252Y | 1 |
Group | FJ | CA | DP | England | California | France | Paris-LD | Milan-LD | Moscow-LD | Austria-SSE |
---|---|---|---|---|---|---|---|---|---|---|
Fu’s Fs | −24.7827 | −10.2815 | −9.5685 | −23.9885 | −23.7186 | −23.4760 | −24.4464 | −24.5018 | −25.1710 | −13.5053 |
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Abe, H.; Ushijima, Y.; Amano, M.; Sakurai, Y.; Yoshikawa, R.; Kinoshita, T.; Kurosaki, Y.; Yanagihara, K.; Izumikawa, K.; Morita, K.; et al. Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. Microorganisms 2022, 10, 99. https://doi.org/10.3390/microorganisms10010099
Abe H, Ushijima Y, Amano M, Sakurai Y, Yoshikawa R, Kinoshita T, Kurosaki Y, Yanagihara K, Izumikawa K, Morita K, et al. Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. Microorganisms. 2022; 10(1):99. https://doi.org/10.3390/microorganisms10010099
Chicago/Turabian StyleAbe, Haruka, Yuri Ushijima, Murasaki Amano, Yasuteru Sakurai, Rokusuke Yoshikawa, Takaaki Kinoshita, Yohei Kurosaki, Katsunori Yanagihara, Koichi Izumikawa, Kouichi Morita, and et al. 2022. "Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan" Microorganisms 10, no. 1: 99. https://doi.org/10.3390/microorganisms10010099
APA StyleAbe, H., Ushijima, Y., Amano, M., Sakurai, Y., Yoshikawa, R., Kinoshita, T., Kurosaki, Y., Yanagihara, K., Izumikawa, K., Morita, K., Kohno, S., & Yasuda, J. (2022). Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. Microorganisms, 10(1), 99. https://doi.org/10.3390/microorganisms10010099