As of April 02, 2021, 43 unique lineages were identified with Pangolin Lineage Assigner from the 1,431 total sequences deposited in the GenBank and GISAID from Hawai’i (Table 1). Based on this analysis, the B.1.429, B.1.427, B.1.1.7, and B.1.351 were 14.47%, 2.38%, 0.98%, and 0.35%, respectively, prevalent in Hawai’i. Moreover, the SARS-CoV-2 VOC, as classified by the CDC, were overall 18.2% (260/1,431) prevalent among all SARS-CoV-2 sequences in Hawai’i (Table 1). As of May 20, 2021, the VOC prevalence had increased overall to 45.2% (1,069/2,367) (Table 1). This increase includes the emergence of the P.1 VOC, a 11.78% increase in B.1.1.7, and a 14.13% increase in B.1.429 (Table 1).
Variants of Concern Consensus
Figure 1, shows the phylogenetic analysis of all VOC prevalent in Hawai’i reported worldwide rooted with the Lineage A reference sequence (EPI_ISL_406801).2 These trees were generated using FastTree in MANA HPC and Geneious Prime.15 Based on this analysis, 228 of the 260 (87.69%) VOC found in Hawai’i have identifiable origins. Figure 2, shows the states in the continental United States, as well as the countries worldwide, that were identified as being the source of the B.1.429, B.1.427, B.1.1.7, and B.1.351 SARS-CoV-2 VOC introductions into Hawai’i. The consensus (>90%) of the B.1.429 MSA, B.1.427 MSA, B.1.1.7 MSA, and B.1.351 MSA revealed 20, 16, 27, and 19, respectively, genomic mutations as compared to the MN908947 Lineage B reference sequence (Table 2).
B.1.429 California VOC
In the GenBank, as of April 02, 2021, 21 of 97 Hawai’i sequences were of lineage B.1.429 as determined with the Pangolin Lineage Assigner. One-hundred eighty-six sequences in GISAID from Hawai’i were identified as the B.1.429 VOC. Total B.1.429 VOC reported worldwide in GISAID was 15,393 as determined by applying the GISAID lineage filter. Thus, the starting sequence count was 15,416 (21 GenBank + 15,393 GISAID + 2 lineage origin = 15,416). Of the 15,416 sequences, 11,648 sequences were removed for being uninformative and containing incomplete sequences . Further, the sRNAtoolbox server removed 944 sequences containing duplicate sequences and 15 sequences of duplicate ID. The final alignment of 2,809 (15,416 - 11,648 ambiguous - 959 duplicate sequence and ID = 2,809) strains and subsequent phylogenetic analysis defined the origin of the B.1.429 variant introduced into Hawai’i (Figure 1A). Using this method, we were able to identify the origin of 183 of 207 B.1.429 sequences introduced into Hawai’i (Figure 2).
B.1.427 California VOC
In the GenBank, as of April 02, 2021, 8 of 97 Hawai’i sequences were B.1.427 VOC as determined with the Pangolin Lineage Assigner. Twenty-six sequences in GISAID from Hawai’i were identified as the B.1.427 VOC. Total B.1.427 lineages reported worldwide in GISAID were 6,562 as determined by applying the GISAID lineage filter. Thus, the starting sequence count was 6,572 (8 GenBank + 6,562 GISAID + 2 lineage origin = 6,572). Of the 6,572 sequences, 5,273 sequences were removed for being ambiguous. Further, the sRNAtoolbox server removed 278 sequences containing duplicate sequences and 3 sequences of duplicate ID. One duplicate ID was created by the duplicate sequence merger. The final alignment of 1,019 strains (6,572 - 5,273 ambiguous - (281 duplicate sequence and ID - 1 duplicate ID created by duplicate sequence merger) = 1,019) and subsequent phylogenetic analysis defined the origin of the B.1.427 variant introduced into Hawai’i (Figure 1B). Using this method, we were able to identify the origin of 22 of 34 B.1.427 sequences introduced into Hawai’i (Figure 2).
B.1.1.7 United Kingdom VOC
In the GenBank, as of April 02, 2021, 0 of 97 Hawai’i sequences were of lineage B.1.1.7 as determined with the Pangolin Lineage Assigner. Fourteen strains in GISAID from Hawai’i were identified as the B.1.1.7 VOC. Total B.1.1.7 lineages reported worldwide in GISAID were 272,730 as determined by applying the GISAID lineage filter. Thus, the starting sequence count was 272,734 (272,730 GISAID sequences + 4 lineage origin). The aforementioned method was applied to each of the seven sub-MSA, thereby removing a total of 113,685 ambiguous sequences, and 75,590 duplicate sequences and ID. Twelve duplicate IDs were created by the duplicate sequence merger. The final alignment of 83,471 sequences (272,734 - 113,685 ambiguous - (75,590 duplicate sequence and ID - 12 duplicate ID created by duplicate sequence merger) = 83,471) and subsequent phylogenetic analysis defined the origin of the B.1.1.7 VOC introduced into Hawai’i using phylogenetic analysis (Figure 1C). Using this method, we were able to identify the origin of 10 of 14 B.1.1.7 sequences introduced into Hawai’i (Figure 2).
B.1.351 South Africa VOC
In the GenBank, as of April 02, 2021, 0 of 97 Hawai’i sequences were B.1.351 VOC as determined with the Pangolin Lineage Assigner. Five sequences in GISAID from Hawai’i were identified as the B.1.351 VOC. Total B.1.351 sequences reported worldwide in GISAID were 6,961 as determined by applying the GISAID lineage filter. Of the 6,963 sequences aligned, 5,758 sequences were removed for being uninformative and containing incomplete sequences. Further, the sRNAtoolbox server removed 373 sequences containing duplicate sequences and 55 sequences of duplicate ID. One duplicate ID was created by the duplicate sequence merger. The final alignment of 778 strains (6,961 GISAID + 2 lineage origin - 5,758 ambiguous - (428 duplicate sequence and ID - 1 duplicate ID created by duplicate sequence merger) = 778) and subsequent phylogenetic analysis defined the origin of the B.1.1.7 VOC introduced into Hawai’i using phylogenetic analysis (Figure 1D). Using this method, we were able to identify the origin of all five B.1.351 sequences introduced into Hawai’i (Figure 2).
High-Quality Sequencing
Several published sequences worldwide have missing nucleotides between the 5’ UTR and 3’ UTR, such as 41.7%, 82.7%, 80.2%, and 75.6% of B.1.1.7, B.1.351, B.1.427, and B.1.429 sequences, respectively. Therefore, these sequences are not useful for phylogenetic analysis.
Quarantine
As of May 20, 2021, the first reported collection dates worldwide for B.1.429, B.1.427, B.1.1.7, B.1.351, and P.1 VOC, respectively, are 2020-04-15,22 2020-09-17,23 2020-02-07,24 2020-05-11,25 and 2020-11-03.26 In Hawai’i, the first reported collection dates for B.1.429, B.1.427, B.1.1.7, B.1.351, and P.1 VOC were on 2020-12-31, 2020-12-07, 2021-01-21, 2021-02-16, and 2021-03-21, respectively.27 From first reported worldwide collection date to first reported collection date in Hawai’i, for the B.1.429, B.1.427, B.1.1.7, B.1.351, and P.1 VOC, are 260, 81, 349, 281, and 138 days, respectively (Figure 3).
Partitioning days to VOC arrival in Hawai’i into quarantine (2020-03-11 to 2020-06-16) (M = 320 days, SD = 45) and post-quarantine (2020-06-16 to 2021-05-20) (M = 132 days, SD = 21) time periods demonstrates that quarantine significantly delayed the arrival of VOC to Hawai’i, t(45) = 17.38 , p = 1.38e-21 (Figure 4A). Utah, a non-quarantine state, also demonstrated difference in days to VOC arrival between the time period defined by the collective quarantine of the 43 states (2020-03-11 to 2020-06-16) (M = 285 days, SD = 71) when compared to the nationwide no-quarantine time period (2020-06-16 to 2021-05-20) (M = 116 days, SD = 40), t(40) = 9.37, p = 1.2e-11 (Figure 4B). Comparing the group defined by the collective 43-state quarantine demonstrates that VOC arrival in Hawai’i (M = 320 days, SD = 45) was delayed when compared to Utah (M = 285 days, SD = 71) , t(47) = 2.11 , p = 0.04 (Figure 4C). Comparing the group defined by the time period following the collective 43-state quarantine demonstrates no significant difference in days to VOC arrival between Hawai’i (M = 132 days, SD =21) when compared to Utah (M = 116 days, SD = 40), t(38) = 1.59, p = 0.12 (Figure 4D).