Post by Admin on Mar 3, 2020 6:26:24 GMT
Where are the original sources from?
The evolutionary network suggests that the hypothesized haplotype mv1 may be from an intermediate host or the first infected humans. From those connections, both H13 and H38 would be suggested as ancestral haplotypes. The SH-like approximate likelihood ratio test showed both haplotype H13’s group and H38 (with H45) could be the most basal clades in phylogenies of the 58 haplotypes (Figure S4), but phylogenetic information of the alignment was informative (Figure S5). Two main evolutionary paths of available haplotypes can be from H13 through H3 to H1, or from H38 through H3 to H1 (Figure 3C). Both scenarios demonstrate H3 was the key connection from an ancestral haplotype to H1. Neither H13 nor H38 has samples from Wuhan (Hubei) (Figure 3). H13 was only recovered from five Shenzhen (Guangdong) samples, including the father (patient 2) of the familial cluster, who was one of the first identified infected patients in Guangdong.13 Two derived haplotypes were also only found in Shenzhen (H14 from the grandson of patient 2), and the other three haplotypes were found in three samples from Japan and one sample from Arizona in the United States (Figure 3). According to an epidemiological study, the Shenzhen family traveled to Wuhan after the outbreak was announced, and they could have been infected during their visit in Wuhan from a hospital or an unknown common source13. This suggests that H13 should have originated from Wuhan, but none of the available samples from Wuhan encode haplotypes in Group A. Genetically, haplotypes of Group A have links to only Wuhan haplotype H3 (only one sample EPI_ISL_406801, with no link to the Hua Nan market).
It is possible that H13 was newly derived from H3 in the family from Shenzhen (Figure 3C) and did not spread in Wuhan, or that no samples have been sequenced yet. However, this scenario is not supported by the evolutionary network. H38 has three genomes from the same patient (Table S1), who was the first identified infected patient in the United States.14 He should have been infected while visiting his family in China. The original source of H38 can be explained as that of H13, which is also derived from H3, and the derived H45 was from a Chongqing patient who was working in Wuhan.
The H3 haplotype has only one sample from Wuhan, which was not linked to the Hua Nan market,9 and the other samples in this group were from other countries and regions (Figure 3). Noteworthily, all the samples from the Hua Nan market had the H1 haplotype or its derived haplotypes (H2, H8-H12, see Figure 2 and Table S1), indicating that there were circulated infections within the market in the short term. It is possible that SARS-CoV-2 in the Hua Nan market had been transmitted from other places (Figure 3D), or at least, that Hua Nan market did not host the original source of SARS-CoV-2. As the first identified infected patients had no link to the market,11 it is possible that infected humans transmitted SARS-CoV-2 to workers or sellers in the market, after which it rapidly circulated there. The crowded market boosted SARS-CoV-2 transmissions to buyers and spread it to the whole city in early December 2019, corresponding to the estimated population expansion time.
Regional and worldwide circulation and spread
Of the 54 genomes from patients in China, Chongqing (3 samples), Guangdong (18), Hubei (22), Taiwan (2), and Zhejiang (4) have more than two samples, and the other five provinces sequenced one sample. Hubei (Wuhan) samples from 24 December 2019 to 5 January 2020 encoded 13 haplotypes, belonging to Groups C (H1 and 11 satellite haplotypes) and B (only H3). These relationships indicate a rapid transmission and circulations of SARS-CoV-2 in Wuhan at an early stage of transmission. H1 (no satellite haplotypes) and H3 haplotypes are the ancestors of haplotypes out of Wuhan/Hubei. Eighteen Guangdong samples, collected from 10 to 23 January 2020, encoded 15 haplotypes, belonging to Groups A, C and E, showing that there were multiple sources imported into Guangdong. Three haplotypes (H14, H15 and H17) may have evolved locally, indicating that human-to-human transmissions happened when SARS-CoV-2 initially spread to Shenzhen of Guangdong.13 Two samples from Taiwan encoded H3 and H24 in Groups B and D, respectively, and three samples from Chongqing encoded H1, H40, and H45 in Groups B and C, respectively. There were two sources imported into these two provinces/regions. Four Zhejiang samples encoded H1 and H24 in Group C, which was only imported from the source of the H1 haplotype.
Phylogenetic approaches provide insight into the epidemiology of SARS-CoV-2
Epidemiological study of SARS-CoV-2 using traditional approaches is very difficult, because it was not identified as a new coronavirus until 29 December, and some infected people with mild symptoms or without symptoms16,40 may have been overlooked in late November and early December. Moreover, the Hua Nan market, which was considered as the birthplace of SARS-CoV-2, has been closed since 1 January 2020. In this study, we have used genomic data for SARS-CoV-2 to infer evolutionary relationships of the 58 haplotypes, and to suggest that H1 and its descendant haplotypes from the Hua Nan market should be derived from the H3 haplotype, which was not linked to the market (Figure 3C). This suggests that the source of the coronavirus in the Hua Nan market was imported from elsewhere, as also suggested by other researchers.12 The phylogenetic network indicated that H13 and H38 should be ancestral haplotypes that connected to the outgroup bat-RaTG13-CoV through a hypothesized intermediate haplotype. Because the currently available samples do not include the first identified infected patient and other patients from early December, the most common ancestral haplotype might be missed. If there are any frozen samples from those patients, it would be worth doing genomic sequencing for phyloepidemiologic study to help to locate the birthplace of SARS-CoV-2 in Wuhan. Meanwhile, we expect that the H13 and H38 haplotypes will be found in some samples of infected patients in Wuhan if more samples are sequenced in future. This will be very important in the search for the original sources of SARS-CoV-2, because both H13 and H38 tend to be ancestral haplotypes.
The evolutionary network of haplotypes can be used to recover the directions of human-to-human transmissions at the local scale and spread at the larger scale. The central haplotype can be considered as the super-spreader haplotype, and the tip haplotype is the most recent descendant haplotype. The transmission direction can be identified using the connection information of tips and branches. For example, the confirmed patients from the Hua Nan market shared the common ancestral haplotype H1, indicating they were infected from a common source, who may have been a super-spreader in the market. This transmission phenomenon may also have happened in Shenzhen with the patients of Group A. This approach has recovered specific directions of human-to-human transmission in the Shenzhen family (H13 → H14), the Queensland tour group (H25 → H26), the England family (H28 → H29), and the repatriated Japanese from Wuhan (H53 → H52). Most international infections link to Wuhan directly or indirectly, but for some of them it is not clear exactly where they were infected. As discussed above, we have found that some patients in Japan and United States might have been infected in Guangzhou, and one patient in France might have been infected in Chongqing or Singapore. We suspect that super-spreaders mediate the spreading from China to worldwide. At least, the infected people with H56 and mv2, as well as H54, contributed at least three haplotypes (Figure 3A).
The samples outside of China encoded 31 haplotypes belonging to Groups A-E. Of these, 27 haplotypes are private by regional samplings, only two Thailand samples were the H1 haplotype, one each from Australia and Belgium were the H3 haplotype, one sample from the United States was the H19 haplotype, and one sample from Singapore was the H40 haplotype. Twelve samples, encoding 10 haplotypes, were from patients in five countries in Asia. Seven haplotypes linked to Wuhan and three haplotypes linked to Guangdong (Shenzhen). Human-to-human transmission may have happened from patients with H53 to H52 haplotypes in Tokyo, Japan, who were repatriated Japanese from Wuhan.35 Five Oceanian samples, encoding six haplotypes in Groups B, C, and D, were from patients from three states in Australia, all with links to Wuhan. Patients with H3, with H25 and H26, and with H55 (linked to H1) were directly from Wuhan, and human-to-human transmission was from patients of H25 to H26, who were in a same tour group in Queensland.36 The connection between patients with H56 and H27 is not clear, because the patient with H56 flew to Sydney from Wuhan on 25 January 2020, and the patient with H27 flew to Melbourne from Wuhan on 15 January 2020. One possibility is that there was an intermediary spreader, who also transmitted SARS-CoV-2 to other patients in France, the United States, and Taiwan. Eight European samples, encoding seven haplotypes, were from patients in four countries. Patients in Belgium37 and Germany16 traveled to or stayed in Wuhan. Patients in England did not report a link to Wuhan,38 but a familial transmission was recovered from H28 to H29. Patients in France may have been infected by three different sources, i.e. H44 linked to Wuhan, H43 may link to Chongqing/Singapore, and H30 may link to an intermediary spreader.
Of the 13 genomes from the United States, three were from the same patient in Washington encoding the same haplotype H38, while the other three samples encoded eight haplotypes, covering all five groups (Figure 3A), so the sources of imported infections are complicated. Three haplotypes (H1 (California), H19 (Wisconsin), and H38 (Washington)) were linked to Wuhan, and three (H19 (Wisconsin), H35 (Arizona), H42 (California)) to five (H41 (California) and H58 (Illinois)) haplotypes may link to Guangdong. The remaining haplotypes (H36 (California), H37 (California), and H57 (Massachusetts)) linked to patients out of China (H54 (Vietnam) and H56 (Australia)), who were from Wuhan.15,39 It is not clear where they were infected. There is no human-to-human transmission evidence in the United States from the 11 cases.
The evolutionary network suggests that the hypothesized haplotype mv1 may be from an intermediate host or the first infected humans. From those connections, both H13 and H38 would be suggested as ancestral haplotypes. The SH-like approximate likelihood ratio test showed both haplotype H13’s group and H38 (with H45) could be the most basal clades in phylogenies of the 58 haplotypes (Figure S4), but phylogenetic information of the alignment was informative (Figure S5). Two main evolutionary paths of available haplotypes can be from H13 through H3 to H1, or from H38 through H3 to H1 (Figure 3C). Both scenarios demonstrate H3 was the key connection from an ancestral haplotype to H1. Neither H13 nor H38 has samples from Wuhan (Hubei) (Figure 3). H13 was only recovered from five Shenzhen (Guangdong) samples, including the father (patient 2) of the familial cluster, who was one of the first identified infected patients in Guangdong.13 Two derived haplotypes were also only found in Shenzhen (H14 from the grandson of patient 2), and the other three haplotypes were found in three samples from Japan and one sample from Arizona in the United States (Figure 3). According to an epidemiological study, the Shenzhen family traveled to Wuhan after the outbreak was announced, and they could have been infected during their visit in Wuhan from a hospital or an unknown common source13. This suggests that H13 should have originated from Wuhan, but none of the available samples from Wuhan encode haplotypes in Group A. Genetically, haplotypes of Group A have links to only Wuhan haplotype H3 (only one sample EPI_ISL_406801, with no link to the Hua Nan market).
It is possible that H13 was newly derived from H3 in the family from Shenzhen (Figure 3C) and did not spread in Wuhan, or that no samples have been sequenced yet. However, this scenario is not supported by the evolutionary network. H38 has three genomes from the same patient (Table S1), who was the first identified infected patient in the United States.14 He should have been infected while visiting his family in China. The original source of H38 can be explained as that of H13, which is also derived from H3, and the derived H45 was from a Chongqing patient who was working in Wuhan.
The H3 haplotype has only one sample from Wuhan, which was not linked to the Hua Nan market,9 and the other samples in this group were from other countries and regions (Figure 3). Noteworthily, all the samples from the Hua Nan market had the H1 haplotype or its derived haplotypes (H2, H8-H12, see Figure 2 and Table S1), indicating that there were circulated infections within the market in the short term. It is possible that SARS-CoV-2 in the Hua Nan market had been transmitted from other places (Figure 3D), or at least, that Hua Nan market did not host the original source of SARS-CoV-2. As the first identified infected patients had no link to the market,11 it is possible that infected humans transmitted SARS-CoV-2 to workers or sellers in the market, after which it rapidly circulated there. The crowded market boosted SARS-CoV-2 transmissions to buyers and spread it to the whole city in early December 2019, corresponding to the estimated population expansion time.
Regional and worldwide circulation and spread
Of the 54 genomes from patients in China, Chongqing (3 samples), Guangdong (18), Hubei (22), Taiwan (2), and Zhejiang (4) have more than two samples, and the other five provinces sequenced one sample. Hubei (Wuhan) samples from 24 December 2019 to 5 January 2020 encoded 13 haplotypes, belonging to Groups C (H1 and 11 satellite haplotypes) and B (only H3). These relationships indicate a rapid transmission and circulations of SARS-CoV-2 in Wuhan at an early stage of transmission. H1 (no satellite haplotypes) and H3 haplotypes are the ancestors of haplotypes out of Wuhan/Hubei. Eighteen Guangdong samples, collected from 10 to 23 January 2020, encoded 15 haplotypes, belonging to Groups A, C and E, showing that there were multiple sources imported into Guangdong. Three haplotypes (H14, H15 and H17) may have evolved locally, indicating that human-to-human transmissions happened when SARS-CoV-2 initially spread to Shenzhen of Guangdong.13 Two samples from Taiwan encoded H3 and H24 in Groups B and D, respectively, and three samples from Chongqing encoded H1, H40, and H45 in Groups B and C, respectively. There were two sources imported into these two provinces/regions. Four Zhejiang samples encoded H1 and H24 in Group C, which was only imported from the source of the H1 haplotype.
Phylogenetic approaches provide insight into the epidemiology of SARS-CoV-2
Epidemiological study of SARS-CoV-2 using traditional approaches is very difficult, because it was not identified as a new coronavirus until 29 December, and some infected people with mild symptoms or without symptoms16,40 may have been overlooked in late November and early December. Moreover, the Hua Nan market, which was considered as the birthplace of SARS-CoV-2, has been closed since 1 January 2020. In this study, we have used genomic data for SARS-CoV-2 to infer evolutionary relationships of the 58 haplotypes, and to suggest that H1 and its descendant haplotypes from the Hua Nan market should be derived from the H3 haplotype, which was not linked to the market (Figure 3C). This suggests that the source of the coronavirus in the Hua Nan market was imported from elsewhere, as also suggested by other researchers.12 The phylogenetic network indicated that H13 and H38 should be ancestral haplotypes that connected to the outgroup bat-RaTG13-CoV through a hypothesized intermediate haplotype. Because the currently available samples do not include the first identified infected patient and other patients from early December, the most common ancestral haplotype might be missed. If there are any frozen samples from those patients, it would be worth doing genomic sequencing for phyloepidemiologic study to help to locate the birthplace of SARS-CoV-2 in Wuhan. Meanwhile, we expect that the H13 and H38 haplotypes will be found in some samples of infected patients in Wuhan if more samples are sequenced in future. This will be very important in the search for the original sources of SARS-CoV-2, because both H13 and H38 tend to be ancestral haplotypes.
The evolutionary network of haplotypes can be used to recover the directions of human-to-human transmissions at the local scale and spread at the larger scale. The central haplotype can be considered as the super-spreader haplotype, and the tip haplotype is the most recent descendant haplotype. The transmission direction can be identified using the connection information of tips and branches. For example, the confirmed patients from the Hua Nan market shared the common ancestral haplotype H1, indicating they were infected from a common source, who may have been a super-spreader in the market. This transmission phenomenon may also have happened in Shenzhen with the patients of Group A. This approach has recovered specific directions of human-to-human transmission in the Shenzhen family (H13 → H14), the Queensland tour group (H25 → H26), the England family (H28 → H29), and the repatriated Japanese from Wuhan (H53 → H52). Most international infections link to Wuhan directly or indirectly, but for some of them it is not clear exactly where they were infected. As discussed above, we have found that some patients in Japan and United States might have been infected in Guangzhou, and one patient in France might have been infected in Chongqing or Singapore. We suspect that super-spreaders mediate the spreading from China to worldwide. At least, the infected people with H56 and mv2, as well as H54, contributed at least three haplotypes (Figure 3A).
The samples outside of China encoded 31 haplotypes belonging to Groups A-E. Of these, 27 haplotypes are private by regional samplings, only two Thailand samples were the H1 haplotype, one each from Australia and Belgium were the H3 haplotype, one sample from the United States was the H19 haplotype, and one sample from Singapore was the H40 haplotype. Twelve samples, encoding 10 haplotypes, were from patients in five countries in Asia. Seven haplotypes linked to Wuhan and three haplotypes linked to Guangdong (Shenzhen). Human-to-human transmission may have happened from patients with H53 to H52 haplotypes in Tokyo, Japan, who were repatriated Japanese from Wuhan.35 Five Oceanian samples, encoding six haplotypes in Groups B, C, and D, were from patients from three states in Australia, all with links to Wuhan. Patients with H3, with H25 and H26, and with H55 (linked to H1) were directly from Wuhan, and human-to-human transmission was from patients of H25 to H26, who were in a same tour group in Queensland.36 The connection between patients with H56 and H27 is not clear, because the patient with H56 flew to Sydney from Wuhan on 25 January 2020, and the patient with H27 flew to Melbourne from Wuhan on 15 January 2020. One possibility is that there was an intermediary spreader, who also transmitted SARS-CoV-2 to other patients in France, the United States, and Taiwan. Eight European samples, encoding seven haplotypes, were from patients in four countries. Patients in Belgium37 and Germany16 traveled to or stayed in Wuhan. Patients in England did not report a link to Wuhan,38 but a familial transmission was recovered from H28 to H29. Patients in France may have been infected by three different sources, i.e. H44 linked to Wuhan, H43 may link to Chongqing/Singapore, and H30 may link to an intermediary spreader.
Of the 13 genomes from the United States, three were from the same patient in Washington encoding the same haplotype H38, while the other three samples encoded eight haplotypes, covering all five groups (Figure 3A), so the sources of imported infections are complicated. Three haplotypes (H1 (California), H19 (Wisconsin), and H38 (Washington)) were linked to Wuhan, and three (H19 (Wisconsin), H35 (Arizona), H42 (California)) to five (H41 (California) and H58 (Illinois)) haplotypes may link to Guangdong. The remaining haplotypes (H36 (California), H37 (California), and H57 (Massachusetts)) linked to patients out of China (H54 (Vietnam) and H56 (Australia)), who were from Wuhan.15,39 It is not clear where they were infected. There is no human-to-human transmission evidence in the United States from the 11 cases.