Transmissibility of SARS-CoV-2 B.1.1.214 and Alpha Variants during 4 COVID-19 Waves, Kyoto, Japan, January 2020-June 2021

Abstract

Household transmission is a primary source of SARS-CoV-2 spread. We used COVID-19 epidemiologic investigation data and viral genome analysis data collected in the city of Kyoto, Japan, during January 2020-June 2021 to evaluate the effects of different settings and viral strains on SARS-CoV-2 transmission. Epidemiologic investigations of 5,061 COVID-19 cases found that the most common category for close contact was within households (35.3%); this category also had the highest reverse transcription PCR positivity. The prevalent viral lineage shifted from B.1.1.214 in the third wave to the Alpha variant in the fourth wave. The proportion of secondary cases associated with households also increased from the third to fourth waves (27% vs. 29%). Among 564 contacts from 206 households, Alpha variant was significantly associated with household transmission (odds ratio 1.52, 95% CI 1.06-2.18) compared with B.1.1.214. Public health interventions targeting household contacts and specific variants could help control SARS-CoV-2 transmission.

Keywords: COVID-19; Japan; SARS; SARS-CoV-2; contact tracing; coronavirus; coronavirus disease; epidemiology; household contact; respiratory infections; severe acute respiratory syndrome coronavirus 2; viral genome; viruses; zoonoses.

Figure 1

Seven-day moving average of cases during 4 COVID-19 waves, Kyoto, Japan, January 2020–June 2021. Solid black represents averages in Kyoto City and dashed lines represent averages in Japan. Arrows indicate the state of emergency designation in Kyoto Prefecture, in which Kyoto is located. Scales for the y-axes differ substantially to underscore patterns but do not permit direct comparisons.

Figure 2

Prevalence of major SARS-CoV-2 viral lineages detected among respiratory tract specimens collected during 4 COVID-19 waves in Japan, January 2020–June 2021. A) Lineages detected in Kyoto City. B) Lineages detected from 62,703 genomes obtained in Japan and downloaded from the GISAID database (https://www.gisaid.org). Number of available genomes analyzed per month is shown above each bar. The most common lineages during each wave in Kyoto were B.1 (n = 8, 47.1%) during the first wave; B.1.1.284 (n = 156, 88.6%) during the second; B.1.1.214 (n = 766, 86.0%) during the third; and B.1.1.7 (Alpha; n = 983, 93.4%) during the fourth. B.1.48 was the second most common lineage during the first wave (n = 7, 41.2%) and R.1 was the most common lineage during March 2021 (n = 14, 53.8%), between the third and fourth waves. The most common lineages during each wave in Japan were B.1.1 (n = 2,561, 78.1%) during the first wave; B.1.1.284 (n = 5,641, 73.3%) during the second; B.1.1.214 (n = 10,970, 72.1%) during the third; and B.1.1.7 (Alpha; n = 19,630, 78.8%) during the fourth. B.1.48 was the second most common lineage during the first wave (n = 313, 9.5%) and R.1 was the second most common lineage during March 2021 (n = 2,217, 40.0%).