Abstract
To assess the relative transmissibility of the SARS-CoV-2 Alpha variant compared to the pre-existing SARS-CoV-2 in Japan, we performed a cross-sectional study to determine the secondary attack rate of COVID-19 in household contacts before and after the Alpha variant became dominant in Osaka. We accessed 290 household contacts whose index cases were diagnosed between 1 and 20 December 2020 (the third epidemic group), at a time when Osaka was free of the Alpha variant. We also accessed 398 household contacts whose index cases were diagnosed between 20 April and 3 May 2021 (the fourth epidemic group), by which time the Alpha variant had become dominant. We identified 124 household contacts whose index case was determined positive for the Alpha variant (Alpha group) in this fourth group. The secondary attack rates in the fourth group (34.7%) and the Alpha group (38.7%) were significantly higher than that in the third group (19.3%, p < 0.001). Multivariable Poisson regression analysis with a robust error variance showed a significant excess risk in the fourth group (1.90, 95% CI = 1.47–2.48) and the Alpha group (2.34, 95% CI = 1.71–3.21). This finding indicates that the SARS-CoV-2 Alpha variant has an approximately 1.9–2.3-fold higher transmissibility than the pre-existing virus in the Japanese population.
Keywords: SARS-CoV-2, Alpha variant, N501Y, transmissibility, household contact, Japanese
1. Introduction
Japan faced the fourth wave of the COVID-19 epidemic caused by infection with the novel Corona virus SARS-CoV-2 from April to May 2021 [1]. At this time, across the country, the pre-existing virus was rapidly replaced by the SARS-CoV-2 variant known as Alpha or B.1.1.7 [2] in many areas [3]. The Osaka Prefectural Government monitored the expansion of this new variant and reported that the Alpha variant positive rate among COVID-19 PCR positive samples increased from 28% in the week 1–7 March [4] to 83% in the week 26 April–2 May [3]. Previous ecological studies estimating the reproductive numbers conducted in England and the UK showed that the SARS-CoV-2 lineage B.1.1.7 (variant Alpha), which has the N501Y mutation, has a 35% to 100% higher transmissibility than the pre-existing SARS-CoV-2 [5,6,7,8]. In the Osaka Prefecture (population 8.8 million), we also experienced a marked increase in the weekly peak incidence of COVID-19, from 43.5 per 100,000 in the week 7–13 January (third epidemic wave) to 89.7 in the week 23–29 April (fourth epidemic wave) [9]. Therefore, we hypothesized that this increase was attributed to a higher transmissibility of the Alpha variant than the pre-existing SARS-CoV-2 in Japan, at a time when the transmissibility of this variant had not been well documented in an Asian population.
The present study aimed to quantify the relative transmissibility of the SARS-CoV-2 Alpha variant compared with the pre-existing SARS-CoV-2 in the setting of household contacts in the Osaka population before vaccination against COVID-19 became available to the public.
2. Materials and Methods
2.1. Subjects
When a Public Health Center (PHC) in Japan received an incidence report of COVID-19 from a physician, the PHC immediately performed contact tracing of the index case to identify persons with whom that person was in close contact during their infectious period. All the individuals who had close contact with the index case were tested by COVID-19 PCR at least once during a 14-day observation from the time of diagnosis of that case. For this study, we selected COVID-19 index cases who were diagnosed between 1 and 20 December 2020 and their household contacts (the 3rd epidemic group), and those who were diagnosed between 20 April and 3 May 2021 and their household contacts (the 4th epidemic group) from three different PHCs (total residents: 1.16 million) in the Osaka Prefecture.
Informed consent was not required from patients and contacts because active epidemiological investigation data analyses were performed in accordance with the Infectious Diseases Control Law. The Ethics Committee of Osaka University Hospital approved this study (T20114).
2.2. Data Items
We collected index cases’ demographic data, date of onset, occurrence of high fever (38.0 °C and over), date of diagnosis and test results for the Alpha variant. Data on the household contacts were obtained following contact tracing of the corresponding index cases. The PHC obtained PCR positive results of the household contacts even when the first test was negative, but subsequent tests received in the clinic were positive from the incidence report documented by physicians.
2.3. Determination of the SARS-CoV-2 Alpha Variant
The Osaka Prefectural Government started to monitor the spread of the Alpha variant using randomly selected SARS-CoV-2 positive samples at the beginning of March 2021 (testing approximately 30% of these). Identification of the N501Y was performed by real-time one-step RT-PCR assays following the guideline of the National Institute of Infectious Diseases, Tokyo. The determination of the N501Y mutation focused on the point mutation from 23,102 A (wild type) to T using two probes: 501Y-1c_VIC-MGB and N501-1c_FAM-MGB.
The Osaka Prefectural Government randomly selected 137 samples from 3406 positive N501Y mutations determined between 20 April and 3 May 2021 to be examined via whole-genome sequences of the strain at the National Institute of Infectious Diseases, Tokyo. The National Institute confirmed that all 137 samples were positive for the SARS-CoV-2 Alpha variant. Therefore, we determined the SARS-CoV-2 Alpha variant via the determination of the N501Y mutation in this setting.
2.4. Statistical Methods
We calculated the household secondary attack rate by analyzing the characteristics of the contacts including the diagnostic period of the index cases (3rd epidemic/4th epidemic). A Chi-square test was used for each variable to assess the influences on the secondary attack rate. A multivariable Poisson regression model with a robust error variance [10] was used to compare the rate between the 3rd and the 4th epidemic groups. To quantify the relative transmissibility of the Alpha variant with the pre-existing SARS-CoV-2, we calculated the risk ratio for the secondary attack rate in the 4th group where the index cases were Alpha positive (Alpha group) to the 3rd epidemic group with the pre-existing virus using a Poisson regression model. Possible confounding factors were the contacts’ ages (0–29, 30–59, 60 and over), their relationship to the index case (spouse or others) and the index cases’ fever (at least 38.0 °C), which were adjusted for the analysis.
3. Results
We extracted anonymized data on 290 household contacts of 139 index cases during the third epidemic wave and 398 contacts of 168 index cases during the fourth epidemic wave. There were 124 household contacts with the 54 index cases of people infected with the Alpha variant in the latter.
Table 1 shows the secondary attack rate among a total of 687 household contacts according to their characteristics. Individuals aged 60 and over were most susceptible to SARS-CoV-2 infection (38.8%). Spouses of the index cases showed a significantly higher secondary attack rate (42.1%) than the other contacts. The presence of a high fever (at least 38.0 °C) in the index case was significantly correlated with a secondary attack rate among household contacts (33.2% vs. 21.7%).
Table 1.
Secondary attack rate (SAR) of SARS-CoV-2 for Japanese household contacts according to their characteristics.
| Characteristics | No. Household Contacts | No. SARS-CoV-2 Positive | SAR % | p-Value | |
|---|---|---|---|---|---|
| Sex | Female | 396 | 110 | 27.8% | 0.754 |
| Male | 291 | 84 | 28.9% | ||
| Unknown | 1 | 0 | NA | ||
| Age | 0–29 years | 278 | 66 | 22.3% | 0.002 |
| 30–59 years | 276 | 78 | 29.7% | ||
| 60 years+ | 134 | 50 | 38.8% | ||
| Relationship to index case | Spouse | 176 | 74 | 42.1% | <0.001 |
| Parent | 179 | 39 | 21.8% | ||
| Children | 220 | 55 | 25.0% | ||
| Others | 112 | 25 | 22.3% | ||
| Fever of index case | <38.0 °C | 308 | 67 | 21.7% | 0.003 |
| ≥38.0 °C | 337 | 112 | 33.2% | ||
| Unknown | 43 | 15 | 34.9% | ||
| Time from symptom onset to diagnosis of the index case | 2 days or less | 331 | 95 | 28.7% | 0.494 |
| 3 to 5 days | 224 | 56 | 25.0% | ||
| 6 days and over | 103 | 34 | 22.0% | ||
| Unknown | 30 | 9 | 30.0% | ||
| Epidemic phase based on diagnosis of index case | 1 to 20 December 2020 | 290 | 56 | 19.3% | <0.001 |
| 20 April to 3 May 2021 | 398 | 138 | 34.7% | ||
| Viral type of index case | Pre-existing virus * | 290 | 56 | 19.3% | <0.001 |
| Alpha variant | 124 | 48 | 38.7% | ||
* Index cases who were diagnosed with COVID-19 from 1 to 20 December 2020 were assumed not to be infected with the variant of concern.
The household contacts of cases in the fourth epidemic group were significantly more likely to become infected than those in the third epidemic group (34.7% vs. 19.3%, p < 0.001). The Alpha group showed a significantly higher rate than those in the third epidemic group (38.7% vs. 19.3%, p < 0.001) (Table 1).
In the multivariable regression analysis, the secondary attack rate in the fourth epidemic group was significantly higher than the third epidemic group (risk ratio: 1.90, 95% confidence interval; 1.47–2.48, p < 0.001) (Table 2). A significant excess risk in the Alpha group was observed in comparison with the third epidemic group (risk ratio: 2.34, 95% CI; 1.71–3.21, p < 0.001) (Table 3).
Table 2.
Factors associated with the secondary attack rate of SARS-CoV-2 for Japanese household contacts focusing on the epidemic wave using multivariable Poisson regression analysis.
| Factors | Risk Ratio | p-Value | 95% Confidence Interval | |||
|---|---|---|---|---|---|---|
| Epidemic wave based on diagnosis of index cases | 1 to 20 December 2020 | ref | ||||
| 20 April to 3 May 2021 | 1.90 | <0.001 | 1.47 | - | 2.48 | |
| Age | 0–29 years | ref | ||||
| 30–59 years | 1.15 | 0.353 | 0.85 | - | 1.56 | |
| 60 years+ | 1.62 | 0.003 | 1.18 | - | 2.23 | |
| Relationship to index case | Spouse | 1.56 | 0.001 | 1.21 | - | 2.02 |
| Others | ref | |||||
| Fever of index case | <38.0 °C | ref | ||||
| ≥38.0 °C | 1.51 | 0.002 | 1.17 | - | 1.94 | |
| Unknown | 1.50 | 0.078 | 0.96 | - | 2.34 | |
Table 3.
Factors associated with the secondary attack rate of SARS-CoV-2 for Japanese household contacts focusing on viral type using multivariable Poisson regression analysis.
| Factors | Risk Ratio | p-Value | 95% Confidence Interval | |||
|---|---|---|---|---|---|---|
| Viral type of index case | Pre-existing virus * | ref | ||||
| Alpha variant | 2.34 | <0.001 | 1.71 | - | 3.21 | |
| Age | 0–29 years | ref | ||||
| 30–59 years | 1.50 | 0.071 | 0.97 | - | 2.34 | |
| 60 years+ | 2.56 | <0.001 | 1.64 | - | 4.00 | |
| Relationship to index case | Spouse | 1.41 | 0.044 | 1.01 | - | 1.98 |
| Others | ref | |||||
| Fever of index case | <38.0 °C | ref | ||||
| ≥38.0 °C | 1.48 | 0.021 | 1.06 | - | 2.07 | |
| Unknown | 1.11 | 0.824 | 0.44 | - | 2.82 | |
* Index cases who were diagnosed with COVID-19 from 1 to 20 December 2020 were assumed not to be infected with the variant of concern.
4. Discussion
Our results revealed that household contacts whose index cases were diagnosed with COVID-19 in the week 20 April to 3 May 2021, when the SARS-CoV-2 Alpha variant was dominant in Osaka, had a 1.9-fold higher secondary attack rate than those whose index cases were diagnosed in the week 1 to 20 December 2020, when Osaka was free of this variant. Moreover, contacts whose index cases were infected with this variance had a 2.3-fold higher secondary attack rate than the third epidemic group. The cumulative incidence rate of COVID-19 among the population of Osaka was still only 1.02% in 10 May 2021 (90,213 cases in a population of 8.8 million) [9]. This was before the SARS-CoV-2 vaccination became available to the general population in mid-May 2021. Therefore, the risk ratios calculated in the present analysis are considered reflective of the relative degree of increased transmissibility of the SARS-CoV-2 Alpha variant in comparison with the pre-existing SARS-CoV-2 in the Japanese population. To the best of our knowledge, this is the first report assessing the transmissibility of the SARS-CoV-2 Alpha variant in a contact tracing setting.
The N501Y mutation is a key contact residue in the receptor binding domain and enhances binding to human angiotensin-converting enzyme 2 [11]. The relative transmissibility of the SARS-CoV-2 Alpha variant was assessed by comparing the reproduction number with other lineages and was reported to range from 35 to 100%, being more transmissible in England and the UK [5,6,7,8]. The risk ratio of the Alpha group (2.34) seems to be higher than the estimated relative transmissibility in England and the UK, but these estimations were based on ecological studies. A plausible explanation of these different estimations may be that Japanese individuals had a lower likelihood of transmitting the pre-existing SARS-CoV-2 than the UK population. Of note, the secondary attack rate among household contacts in December 2020 was 19.1% in the present study, which is lower than the rate among household contacts determined in London (43%) [12] and the UK (34%) [13] in 2020. The secondary attack rates in household contacts among East Asian populations reported in 2020 were also relatively lower, such as 17% in Thailand [14], 16% in Wuhan, China [15], 12% in South Korea [16], 7% in Taiwan [17] and 19% in Japan [18]. Ethnic differences resulting in a lower susceptibility to the pre-existing virus in the Japanese population might have modified the relative transmissibility of the SARS-CoV-2 Alpha variant.
In the multivariable Poisson regression analysis, we showed that spouses had an increased risk of SARS-CoV-2 infection compared with other household contacts. This is probably because spouses had closer or longer daily contact with his/her index case than the other contacts.
Our study has some limitations. The study design was cross-sectional in order to compare secondary attack rates among household contacts between a pre- and post-Alpha variant-dominant phase. Although we adjusted for some possible confounding factors in both the index cases and contacts, other factors such as seasonality could not be adjusted for and might have biased the findings. In addition, this study did not have any information on the SARS-CoV-2 vaccination because the vaccine was not officially available to the general Japanese population until mid-May 2021. This lack of information might have resulted in an underestimation of the relative transmissibility of the SARS-CoV-2 Alpha variant in this analysis. An increasing cumulative incidence of COVID-19 in Osaka residents might also have resulted in underestimating the relative transmissibility of this variant in this setting. We used the N501Y mutation as a factor to define the Alpha variant. Other variants (P.1 and B.1.351) also contain this mutation, whereas these variants were not detected in the fourth wave in Osaka
5. Conclusions
This study indicates that the SARS-CoV-2 Alpha variant has an approximately 1.9–2.3-fold higher transmissibility than the pre-existing virus in the Japanese population.
Acknowledgments
The authors thank the infection control staff of Fujiidera PHC and Ibaraki PHC of Osaka Prefectural Government and Hirakata City PHC for releasing the data required for our study.
Author Contributions
Conceptualization, H.T., A.H. and T.O.; methodology, H.T.; software, C.T.; validation, H.N., C.S. and Y.T.; formal analysis, C.T.; investigation, H.T.; resources, H.N., C.S. and Y.T.; data curation, H.T. and C.T.; writing—original draft preparation, H.T.; writing—review and editing, A.H., H.S. and T.O.; visualization, C.T.; supervision, T.O. and H.S.; project administration, H.T.; funding acquisition, H.T. All authors have read and agreed to the published version of the manuscript.
Funding
This study was financially supported by a grant-in aid for “Public Health Research on COVID-19 in Comprehensive Programs on Community Health” sponsored by the Ministry of Health, Labour and Welfare, Japan.
Institutional Review Board Statement
The study was conducted according to the guidelines of the Declaration of Helsinki and approved by the Ethics Committee of Osaka University Hospital approved this study (T20114).
Informed Consent Statement
Informed consent was not required from patients and contacts because active epidemiological investigation data analyses were performed in accordance with the Infectious Diseases Control Law.
Data Availability Statement
The data presented here is not publicly available due to the privacy policy of the Osaka Prefectural Government.
Conflicts of Interest
The authors declare no conflict of interest.
Footnotes
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.
References
- 1.National Institute of Infectious Diseases, Japan Recent Descriptive Epidemiology of COVID-19 in Japan. [(accessed on 16 June 2021)]; Available online: https://www.niid.go.jp/niid/ja/diseases/ka/corona-virus/2019-ncov/10431-covid19-ab38th.html.
- 2.World Health Organization Naming SARS-CoV-2 Variants. [(accessed on 29 June 2021)]; Available online: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/
- 3.Ministry of Health, Labor and Welfare COVID-19 Variant of Concern (1 June 2021) [(accessed on 16 June 2021)]; Available online: https//www.mhlw.go.jp/content/10900000/000787862.pdf.
- 4.Ministry of Health, Labor and Welfare COVID-19 Variant of Concern (19 April 2021) [(accessed on 16 June 2021)]; Available online: https//www.mhlw.go.jp/stf/seikakunitsuite/bunya/0000121431_00256.html.
- 5.Graham M.S., Sudre C.H., May A., Antonelli M., Murray B., Varsavsky T., Klaser K., Canas L.S., Molteni E., Modat M., et al. Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: An ecological study. Lancet Public Health. 2021;6:e335–e345. doi: 10.1016/S2468-2667(21)00055-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Davies N.G., Abbott S., Barnard R.C., Jarvis C.I., Kucharski A.J., Munday J.D., Pearson C.A.B., Russell T.W., Tully D.C., Washburne A.D., et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science. 2021;372:6538. doi: 10.1126/science.abg3055. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Volz E., Mishra S., Chand M., Barrett J.C., Johnson R., Geidelberg L., Hinsley W.R., Laydon D.J., Dabrera G., O’Toole A., et al. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature. 2021;593:266–269. doi: 10.1038/s41586-021-03470-x. [DOI] [PubMed] [Google Scholar]
- 8.Leung K., Shum M.H., Leung G.M., Lam T.T., Wu J.T. Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. Eurosurveillance. 2021;26:2002106. doi: 10.2807/1560-7917.ES.2020.26.1.2002106. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Osaka Prefectural Government Incident of COVID-19 in Osaka, from 2 November 2020. [(accessed on 16 June 2021)]; Available online: https://www.pref.osaka.lg.jp/iryo/osakakansensyo/happy_kako.html.
- 10.Barros A.J., Hirakata V.N. Alternatives for logistic regression in cross-sectional studies: An empirical comparison of models that directly estimate the prevalence ratio. BMC Med. Res. Methodol. 2003;3:21. doi: 10.1186/1471-2288-3-21. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Starr T.N., Greaney A.J., Hilton S.K., Ellis D., Crawford K.H.D., Dingens A.S., Navarro M.J., Bowen J.E., Tortorici M.A., Walls A.C., et al. Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding. Cell. 2020;182:1295–1310.e20. doi: 10.1016/j.cell.2020.08.012. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Patel A., Charani E., Ariyanayagam D., Abdulaal A., Denny S.J., Mughal N., Moore L.S.P. New-onset anosmia and ageusia in adult patients diagnosed with SARS-CoV-2 infection. Clin. Microbiol. Infect. 2020;26:1236–1241. doi: 10.1016/j.cmi.2020.05.026. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Bernal J.L., Panagiotopoulos N., Byers C., Vilaplana T.G., Boddington N., Zhang X., Charlett A., Elgohari S., Coughlan L., Whillock R., et al. Transmission dynamics of COVID-19 in household and community settings in the United Kingdom. medRxiv. 2020 doi: 10.1101/2020.08.19.20177188. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Doung-Ngern P., Suphanchaimat R., Panjangampatthana A., Janekrongtham C., Ruampoom D., Daochaeng N., Eungkanit N., Pisitpayat N., Srisong N., Yasopa O., et al. Case-Control Study of Use of Personal Protective Measures and Risk for SARS-CoV 2 Infection, Thailand. Emerg. Infect. Dis. 2020;26:2607–2616. doi: 10.3201/eid2611.203003. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Li F., Li Y.Y., Liu M.J., Fang L.Q., Dean N.E., Wong G.W.K., Yang X.B., Longini I., Halloran M.E., Wang H.J., et al. Household transmission of SARS-CoV-2 and risk factors for susceptibility and infectivity in Wuhan: A retrospective observational study. Lancet Infect. Dis. 2021;21:617–628. doi: 10.1016/S1473-3099(20)30981-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Park Y.J., Choe Y.J., Park O., Park S.Y., Kim Y.M., Kim J., Kweon S., Woo Y., Gwack J., Kim S.S., et al. Contact Tracing during Coronavirus Disease Outbreak, South Korea, 2020. Emerg. Infect. Dis. 2020;26:2465–2468. doi: 10.3201/eid2610.201315. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.Cheng H.Y., Jian S.W., Liu D.P., Ng T.C., Huang W.T., Lin H.H., for the Taiwan COVID-19 Outbreak Investigation Team Contact Tracing Assessment of COVID-19 Transmission Dynamics in Taiwan and Risk at Different Exposure Periods before and after Symptom Onset. JAMA Intern. Med. 2020;180:1156–1163. doi: 10.1001/jamainternmed.2020.2020. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18.Miyahara R., Tsuchiya N., Yasuda I., Ko Y.K., Furuse Y., Sando E., Nagata S., Imamura T., Saito M., Morimoto K., et al. Familial Clusters of Coronavirus Disease in 10 Prefectures, Japan, February–May 2020. Emerg. Infect. Dis. 2021;27:915–918. doi: 10.3201/eid2703.203882. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The data presented here is not publicly available due to the privacy policy of the Osaka Prefectural Government.