| Literature DB >> 34903718 |
Frederik Plesner Lyngse1,2,3, Kåre Mølbak4,5, Robert Leo Skov4, Lasse Engbo Christiansen6, Laust Hvas Mortensen7,8, Mads Albertsen9, Camilla Holten Møller4, Tyra Grove Krause4, Morten Rasmussen4, Thomas Yssing Michaelsen9, Marianne Voldstedlund4, Jannik Fonager4, Nina Steenhard4, Carsten Thure Kirkeby5.
Abstract
New lineages of SARS-CoV-2 are of potential concern due to higher transmissibility, risk of severe outcomes, and/or escape from neutralizing antibodies. Lineage B.1.1.7 (the Alpha variant) became dominant in early 2021, but the association between transmissibility and risk factors, such as age of primary case and viral load remains poorly understood. Here, we used comprehensive administrative data from Denmark, comprising the full population (January 11 to February 7, 2021), to estimate household transmissibility. This study included 5,241 households with primary cases; 808 were infected with lineage B.1.1.7 and 4,433 with other lineages. Here, we report an attack rate of 38% in households with a primary case infected with B.1.1.7 and 27% in households with other lineages. Primary cases infected with B.1.1.7 had an increased transmissibility of 1.5-1.7 times that of primary cases infected with other lineages. The increased transmissibility of B.1.1.7 was multiplicative across age and viral load.Entities:
Mesh:
Year: 2021 PMID: 34903718 PMCID: PMC8669007 DOI: 10.1038/s41467-021-27202-x
Source DB: PubMed Journal: Nat Commun ISSN: 2041-1723 Impact factor: 14.919
Summary Statistics.
| Primary Cases | Potential | Positive | Attack | |||||
|---|---|---|---|---|---|---|---|---|
| Selected | With | With | Secondary | Secondary | Rate | |||
| Total | for WGS | Genome | B.1.1.7 | Cases | Cases | (%) | (95%-CI) | |
| Total | 8093 | 6632 | 5241 | 808 | 16,612 | 4133 | 25 | (24–26) |
| Sex | ||||||||
| Male | 3648 | 3013 | 2406 | 419 | 8905 | 2190 | 25 | (24–26) |
| Female | 4445 | 3619 | 2835 | 389 | 7707 | 1943 | 25 | (24–26) |
| Age | ||||||||
| 0–10 | 419 | 327 | 237 | 54 | 3490 | 822 | 24 | (22–25) |
| 10–20 | 795 | 670 | 557 | 91 | 3270 | 755 | 23 | (21–25) |
| 20–30 | 1531 | 1294 | 1020 | 204 | 2347 | 494 | 21 | (19–23) |
| 30–40 | 1353 | 1101 | 870 | 143 | 1876 | 483 | 26 | (24–28) |
| 40–50 | 1464 | 1182 | 920 | 119 | 2167 | 521 | 24 | (22–26) |
| 50–60 | 1443 | 1166 | 917 | 132 | 2020 | 536 | 27 | (25–29) |
| 60–70 | 669 | 539 | 449 | 38 | 919 | 315 | 34 | (31–37) |
| 70–80 | 300 | 255 | 190 | 23 | 392 | 150 | 38 | (33–43) |
| >80 | 119 | 98 | 81 | <5 | 131 | 57 | 44 | (37–54) |
| Household | ||||||||
| Size | ||||||||
| 2 | 3308 | 2716 | 2108 | 298 | 3308 | 1019 | 31 | (29–32) |
| 3 | 1886 | 1549 | 1235 | 189 | 3635 | 843 | 23 | (22–25) |
| 4 | 1848 | 1486 | 1178 | 193 | 5368 | 1292 | 24 | (23–26) |
| 5 | 790 | 661 | 534 | 92 | 3042 | 714 | 23 | (21–26) |
| 6 | 261 | 220 | 186 | 36 | 1259 | 265 | 21 | (17–25) |
Notes: This table provides summary statistics for the number of primary cases, potential secondary cases, positive secondary cases, and attack rates in the study, stratified by sex, age and household sizes Summary statistics for five-year age groups are shown in Table S2. Summary statistics stratified by the primary cases are shown in Table S3 and S4. 95%-Confidence intervals are clustered on the household level.
Intra-household correlation of lineages between primary and positive secondary cases.
| Positive secondary cases | Potential | Attack | ||||||
|---|---|---|---|---|---|---|---|---|
| Primary cases | Other | No | secondary | Rate | ||||
| Lineage | B.1.1.7 | lineages | Genome | Total | cases | (%) | (95%-CI) | |
| B.1.1.7 | 808 | 472 | 19 | 165 | 656 | 1719 | 38 | (35–41) |
| Other lineages | 4433 | 18 | 1750 | 721 | 2489 | 9115 | 27 | (26–28) |
| No Genome | 2852 | 133 | 540 | 315 | 988 | 5778 | 17 | (16–18) |
| Total | 8093 | 623 | 2309 | 1201 | 4133 | 16,612 | 25 | (24–26) |
Notes: There were 8093 primary cases, of which 808 (10%) where infected with B.1.1.7, 4433 (55%) were infected with other lineages, and 2852 (35%) did not have a successfully sequenced genome. The 808 primary cases infected with B.1.1.7 had 656 positive secondary cases. Of these cases, 75% (472 + 19 = 491) were successfully sequenced. Of these, 96% (472) were infected with B.1.1.7 and 4% (19) with other lineages. 95%-Confidence intervals are clustered on the household level.
Fig. 1Age structured transmissibility stratified by lineage of the primary case.
a The transmission rate describes the proportion of potential secondary cases within the household that were infected. b The transmission risk describes the proportion of infected primary cases that infected at least one secondary case. Figure S7 provides the same graphs for five-year age groups. The markers show the estimates of the mean. The shaded areas show the 95% confidence bands of the estimates clustered on the household level.
Odds ratio estimates for transmissibility for B.1.1.7 compared with other lineages.
| Transmission Rate | Transmission Risk | ||||||
|---|---|---|---|---|---|---|---|
| I | II | III | IV | V | VI | VII | |
| B.1.1.7 | 1.50 | 1.68 | 1.69 | 1.63 | 1.52 | 1.66 | 1.61 |
| 95%-CI | (1.30–1.72) | (1.46–1.94) | (1.47–1.95) | (1.39–1.91) | (1.31–1.77) | (1.42–1.93) | (1.36–1.90) |
| Constant | ✔ | ✔ | ✔ | ✔ | ✔ | ✔ | ✔ |
| Age, Primary Case | ✔ | ✔ | ✔ | ✔ | ✔ | ||
| Age, Pot. Sec. Case | ✔ | ✔ | |||||
| Ct Value | ✔ | ✔ | |||||
| Observations | 10,834 | 10,834 | 10,834 | 8762 | 10,834 | 10,834 | 8762 |
| Households | 5241 | 5241 | 5241 | 4172 | 5241 | 5241 | 4172 |