Abstract
The coronavirus disease 2019 (COVID-19) has caused a serious disease burden and poses a tremendous public health challenge worldwide. Here, we report a comprehensive epidemiological and genomic analysis of SARS-CoV-2 from 63 patients in Niigata City, a medium-sized Japanese city, during the early phase of the pandemic, between February and May 2020. Among the 63 patients, 32 (51%) were female, with a mean (±standard deviation) age of 47.9 ± 22.3 years. Fever (65%, 41/63), malaise (51%, 32/63), and cough (35%, 22/63) were the most common clinical symptoms. The median Ct value after the onset of symptoms lowered within 9 days at 20.9 cycles (interquartile range, 17–26 cycles), but after 10 days, the median Ct value exceeded 30 cycles (p < 0.001). Of the 63 cases, 27 were distributed in the first epidemic wave and 33 in the second, and between the two waves, three cases from abroad were identified. The first wave was epidemiologically characterized by a single cluster related to indoor sports activity spread in closed settings, which included mixing indoors with families, relatives, and colleagues. The second wave showed more epidemiologically diversified events, with most index cases not related to each other. Almost all secondary cases were infected by droplets or aerosols from closed indoor settings, but at least two cases in the first wave were suspected to be contact infections. Results of the genomic analysis identified two possible clusters in Niigata City, the first of which was attributed to clade S (19B by Nexstrain clade) with a monophyletic group derived from the Wuhan prototype strain but that of the second wave was polyphyletic suggesting multiple introductions, and the clade was changed to GR (20B), which mainly spread in Europe in early 2020. These findings depict characteristics of SARS-CoV-2 transmission in the early stages in local community settings during February to May 2020 in Japan, and this integrated approach of epidemiological and genomic analysis may provide valuable information for public health policy decision-making for successful containment of chains of infection.
Highlights
Since the first report of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China at the end of 2019, the coronavirus disease 2019 (COVID-19) pandemic has become an unprecedented threat to public health on a global scale (Heymann and Shindo, 2020; Wang et al, 2020)
We report the clinical characteristics of 63 COVID-19 cases, including ribonucleic acid (RNA) viral load over the course of the disease, as well as an integrated approach of epidemiological and virological genomic data to investigate the transmission dynamics and patterns of SARS-CoV-2 in a local city, Niigata City (Niigata Prefecture, Japan), between February and May 2020
All of the cases identified were infected with the Clade S (19B) virus from China, which was prevalent in Japan in February and March (Wagatsuma et al, 2021), with the majority of these patients spreading the infection from a single index group to their family members or colleagues
Summary
Since the first report of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China at the end of 2019, the coronavirus disease 2019 (COVID-19) pandemic has become an unprecedented threat to public health on a global scale (Heymann and Shindo, 2020; Wang et al, 2020). Based on the framework of the Infectious Disease Control Law, the Japanese government began implementing a cluster-based approach based on active epidemiological surveillance as part of the response to control the spread of the virus (Oshitani, 2020; Imamura et al, 2021). The aim of this strategy is to conduct intensive tracing of super-spreading events (i.e., clusters) of COVID-19 cases to investigate the activities of multiple infected individuals and to identify common sources of infection. By the end of April 2020, the Task Force reported three situations that could increase the risk of COVID-19 and started to advise the public to avoid the “three Cs”: closed spaces with poor ventilation, crowded places, and close-contact settings, which led to the initial successful containment of many chains of infection in Japan (Oshitani, 2020)
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