|Year : 2022 | Volume
| Issue : 1 | Page : 17
Characteristics and containment of the outbreak caused by the SARS-CoV-2 Omicron variants in Shanghai, China: A retrospective study
Hongrang Zhou1, Xiaoling Wang2, Guifu Li1, Xiaoming Wang3, Zhe Zhou1, Wen Kong1, Yinjun Pan1, Xingxing Xu1, Kaiyou Ye1, Junfeng Pan1, Ning Xiao2
1 Qingpu District Center for Disease Control and Prevention, Shanghai 201799, China
2 National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasitic and Vector Biology, National Health Commission of China; The School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Huangpu, Shanghai 200336, China
3 Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine 92697, USA
|Date of Submission||23-Aug-2022|
|Date of Decision||04-Nov-2022|
|Date of Acceptance||29-Nov-2022|
|Date of Web Publication||09-Dec-2022|
Qingpu District Center for Disease Control and Prevention, Shanghai 201799
National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasitic and Vector Biology, National Health Commission of China; The School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Huangpu, Shanghai 200336
Source of Support: None, Conflict of Interest: None
Objective: The study aimed to describe the characteristics and containment of the Omicron variants in Shanghai compared with the previous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in China.
Methods: We summarized the data retrieved from the Shanghai Municipal Health Commission from January to June 2022 and the National Health Commission of the People’s Republic of China from March 2020 to August 2021. Epidemiological analysis was utilized to describe the differences among SARS-CoV-2 variants and the infection situation in the outbreaks in China.
Results: The Omicron variants had the characteristics of high insidiousness, rapid transmission, high infectivity, and short incubation period, which were consistent with the characteristics of outbreaks caused by Omicron in other regions in China and abroad. There were 568978 asymptomatic infections in Shanghai from Feburary 26 to June 30, 2022, accounting for 90.73% of the SARS-CoV-2 infections in this outbreak wave. It’s significantly different from a total of 23277 SARS-CoV-2 infections in China between March 31, 2020 and August 8, 2021, of which 41.97% of the cases were asymptomatic infections.
Conclusions: Compared with previous outbreaks emerged in China, the Omicron outbreak in Shanghai was characterized by multiple point dissemination, wide coverage, a large number of close contacts of confirmed infections and asymptomatic carriers, and difficult source tracing. The lessons from Shanghai’s response to Omicron showed that the dynamic zero-COVID policy is still the most suitable response to the virus which can quickly find the infections and curb the transmission route.
Keywords: Omicron BA.2/BA.2.2; SARS-CoV-2 variants; Outbreak; Shanghai
|How to cite this article:|
Zhou H, Wang X, Li G, Wang X, Zhou Z, Kong W, Pan Y, Xu X, Ye K, Pan J, Xiao N. Characteristics and containment of the outbreak caused by the SARS-CoV-2 Omicron variants in Shanghai, China: A retrospective study. One Health Bull 2022;2:17
|How to cite this URL:|
Zhou H, Wang X, Li G, Wang X, Zhou Z, Kong W, Pan Y, Xu X, Ye K, Pan J, Xiao N. Characteristics and containment of the outbreak caused by the SARS-CoV-2 Omicron variants in Shanghai, China: A retrospective study. One Health Bull [serial online] 2022 [cited 2023 Feb 5];2:17. Available from: http://www.johb.info/text.asp?2022/2/1/17/362641
Hongrang Zhou, Xiaoling Wang. These authors contributed equally to this work.
| 1. Introduction|| |
The COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which belongs to the β genus of coronaviruses with an envelope and round or ovalshaped particles, 60-140 nm in diameter,, and has five essential genes targeting four structural proteins of nucleoprotein (N), viral envelope (E), matrix protein (M) and spinosin (S) and RNA-dependent RNA polymerase (RdRp),. Like other viruses, the novel coronavirus genome has undergone mutations, which affects the biological properties of the virus. For example, the binding affinity of the S protein with ACE-2 affects the ability of the virus to invade cells, replicate, and spread.
SARS-CoV-2 is thought to spread via respiratory droplet, aerosol particles in poorly ventilated space and contaminated surfaces, etc,,,,,,14]. People of any age can catch COVID-19, but the risk of developing dangerous symptoms increases with age and underlying health conditions like lung, heart disease, and diabetes, etc. Symptoms may appear 2-14 days after exposure to the virus,,. The most common symptoms of COVID-19 include fever, headache, dry cough and shortness of breath, tiredness, muscle or body aches, loss of taste or smell, sore throat, congestion or runny nose, nausea or vomiting, diarrhea, etc. Dyspnea and hypoxemia are the most common symptoms of severe disease that typically begin approximately one week after the onset of the symptoms, and some severe patients may even develop acute respiratory distress syndrome, septic shocks, metabolic acidosis and multifunctional organ failure, etc,,,. Most patients have a favourable prognosis while others may become very sick, or even die, mainly older people (≥60), people with chronic diseases, late pregnant women and people with obesity,,,,. The diagnosis is established based on a comprehensive analysis of the epidemiological history, clinical manifestations, and laboratory tests. Nucleic acid detection is currently regarded as the golden standard for COVID-19 diagnosis, and it is an effective method for clinical diagnosis and precautionary screening.
Up to now, the World Health Organization (WHO) has proposed five “variants of concern”, namely Alpha, Beta, Gamma, Delta and Omicron,. Since November 2021, the Omicron variant has rapidly become the most dominant SARS-CoV-2 variant due to its high transmission rate, many mutations and significant immune response evasion capabilities. As of June 2022, more than 500 million confirmed cases of COVID-19 have been reported globally, resulting in more than 6.3 million deaths. The data from Global Initiative on Sharing Avian Influenza Data (GISAID) database showed that this variant was endemic in 118 countries as of January 17, 2022, and 195 countries before this article was submitted.
While the new variants have emerged across the globe, China has effectively contained multiple COVID-19 outbreaks since the initial Wuhan outbreak by adhering the containment policies which focus on stopping the transmission of coronavirus. From late February to June 2022, a major outbreak of SARS-CoV-2 Omicron variant spread rapidly throughout Shanghai, China. The rapid mutations of the Omicron variant has brought new challenges to China’s fight against the epidemic.
| 2. Subjects and methods|| |
2.1. Data source and collection
The data on the number of confirmed infections were gathered from the websites of the Shanghai Municipal Health Commission from January to June 2022 and the National Health Commission of the People’s Republic of China from March 2020 to August 2021. The dynamic prevention and control strategies and measures taken were collected from press release for media briefing of the Shanghai Municipal Government by manual downloads.
2.2. Study design
A comparative analysis of the Omicron variants in this epidemic wave and the previous SARS-CoV-2 variants since 2020 was performed. Epidemiological analysis was utilized to describe the differences of epidemici situation at different stages of the outbreak. A discussion and analysis of the prevention and control strategies were conducted.
2.3. Statistical analysis
The data were graphed statistically by Microsoft Office Excel 2013. The number of infections outside quarantine, confirmed cases, asymptomatic cases and pre-symptomatic cases were shown and compared. A pre-symptomatic case was defined as an infected individual who hasn’t yet developed symptoms at the time, but who later shows symptoms.
| 3. Results|| |
According to the data released by the Shanghai Municipal Health Commission from January 1 to February 28, 2022, a total of 1243 cases were imported from abroad (the exact distribution of infectious variants was not published), which accounted for 80% of the total number of cases in Shanghai in 2021 and 38% of the total number of cases in China during the same period. As of July 1, 2022, there were 627115 cases of SARS-CoV-2 infection, including 568978 asymptomatic infections and 58137 confirmed cases, 22545 asymptomatic infections converted to confirmed cases and 588 deaths in total [Table 1].
|Table 1: SARS-CoV-2 infections reported in China from March 31, 2020 to August 8, 2021 and in Shanghai from Feburary 26 to June 30, 2022.|
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According to the epidemic situation and the prevention and control measures taken, three phases of the epidemic were defined [Figure 1]. The first phase started on Feburary 28, 2022, a 56-year-old woman came to Tongji Hospital with a fever. She became the index case in this outbreak after being confirmed positive on March 1. Shanghai reported a surging number of new local COVID-19 cases since then and raised the risk levels of some areas from “low risk” to “middle risk”. The second phase covered the period from March 15 to May 31, 2022. The number of infected people continued to rise. The highest number of positive cases of community transmission (1364 cases) reached on April 2. Although Shanghai started to implement whole-city lockdown on March 30, 2022, the new local cases started to rise exponentially from April 5. During the period from April 5 to April 25, the cumulative daily cases in Shanghai exceeded 15000 and reached a higher level (27719 cases) on April 13. The cumulative daily cases began to decline around mid-April and the epidemic reached a controllable level in May. The third phase started from June 1, the citywide lockdown was lifted. But, sporadic community infections were still reported.
|Figure 1: Number of SARS-CoV-2 infected cases in Shanghai from February 28 to June 25, 2022.|
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| 4. Discussion|| |
Omicron BA.2 and BA.2.2 of SARS-CoV-2 were the main causes of this wave of outbreak in Shanghai, China. Compared with the previous SARS-CoV-2 variants, Omicron variants have the characteristics of high insidiousness, rapid transmission, high infectivity, and short incubation period, which are consistent with the characteristics of outbreaks caused by Omicron in other regions in China and abroad [Table 2]. Therefore, asymptomatic transmission has occured in the early stages of this epidemic wave before the positive infections were found. Compared with previous outbreaks emerged in China, the Omicron outbreak in Shanghai was characterized by multiple point dissemination, wide coverage, a large number of close contacts of confirmed infections and asymptomatic carriers, and difficult source tracing. In addition, the new Omicron variants caused significantly lower rates of severe disease compared to the previous variants, and people vaccinated and previously infected were less likely to develop severe infection,,,. Nevertheless, the ability to rapidly mutate makes the Omicron variants remain a major health threat for the large cities like Shanghai, which is a densely populated city.
|Table 2: Comparison of the epidemic variants of SARS-CoV-2 in Shanghai with the previous variants.|
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The cases in this COVID-19 epidemic in Shanghai were predominantly asymptomatic infections (about 90.73%). And it’s significantly different from relevant studies reporting a total of 23277 SARS-CoV-2 infections in China between March 31, 2020, and August 8, 2021, of which nearly half of the cases were asymptomatic infections, and the specific data were shown in [Table 1] . The reasons for this phenomenon may be related to prevention and control measures for early diagnosis and treatment, vaccination of the population, and the characteristics of the mutated virus itself, etc. Moreover, statistical analysis revealed that 22545 asymptomatic carriers were converted to confirmed cases, accounting for 38.78% of the confirmed cases, and the conversion rate of asymptomatic infection was 3.81%.
According to the official statistics, it was found that there were 588 cumulative deaths in this period, the average age of death was 82.89 years old (the youngest of which was 33 and the oldest 101). Furthermore, the vaccination rate among the deaths was only about 5.3%, with 86.2% of the population over 80 years old; and the causes of the deaths were all underlying diseases except for one case of sudden cardiac death among the total deaths. This suggests that to some extent, once infected with SARS-CoV-2, the risk of death due to the underlying disease is higher, especially in the unvaccinated population. Data from Hong Kong, China, which was also affected by the Omicron BA.2 and BA.2.2 outbreaks, from December 31, 2021 to July 27, 2022, showed that 95% of the 9275 COVID-19 deaths were in people aged 60 years and older, and the overall mortality rate of the fifth wave of the epidemic was 0.71% while the mortality rate was 2.93% in unvaccinated patients. Current study found that vaccination significantly reduced the morbidity and mortality rates of SARS-CoV-2 infections in the elderly. And the recent statistical analysis of outbreaks in Hong Kong and Shanghai caused by the Omicron variant indicated that for infected persons aged 18 to 59 years who completed full vaccination and booster shot, the risk of developing from mild to moderate was 63% and 65% lower than that of unvaccinated infected persons, and the risk of developing from mild and moderate to severe disease was 91% and 94% lower, respectively. As for infected patients aged 60 years or older who completed the full course of vaccination and booster vaccination, the risk of developing from mild to moderate was 73% and 82% lower than that of unvaccinated infected patients, and the risk of developing from moderate to severe disease was 89% and 95% lower than that of unvaccinated infected patients, showing that vaccination is effective in preventing morbidity, severe disease, and even death. As of April 15, 2022, the full basic immunization rate of 62% and the booster immunization rate of 38% for those aged 60 years and older in Shanghai, it is suggested that eligible elderly people should be vaccinated in a timely manner,.
As shown in [Figure 1], the new local cases continued to rise in March and hit a record high of 27719 cases on April 13 although the whole-city lockdown was implemented in March. The reasons for this situation mainly included the scattered infections in communities before lockdown, hidden vrius spread chains such as the household transmission (If one person was infected in the household, other family members might expect to develop the infection who will be detected in the subsequent screening) and contact with items or goods contaminated by the virus. After three months of joint efforts by people from all walks of life in Shanghai and across the country, the resumption of work and production was promoted in an orderly manner in early June (except for the key control areas where positive cases were still found).
It’s estimated that if China did not take active preventive measures, it would result in about 1.5 million deaths. Three factors are necessary for the infection to spread: source, susceptible people and transmission, and the corresponding basic principles for prevention and control are controlling the source of infection, cutting off the transmission route, and protecting susceptible population. Of course, the levels of prevention and control measures taken are also related to the infectivity and severity of the pathogen, and the degree of social harm, etc. The development and implementation of various prevention and control measures during the COVID-19 epidemic in China were in more strict compliance with the three principles as shown in [Figure 2], which was an important factor in achieving zero community transmission in Shanghai.
|Figure 2: Specific measures to implement the three principles of COVID-19 epidemic prevention and control.|
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In this paper, we summarized and described the policy changes in the three phases of the response to Omicron in Shanghai. The initial phase of this outbreak was dominated by dynamic zero-COVID policy, including contact tracing, mass nucleic acid screening, border quarantine, and digital management for a matrix of urban communities. However, due to the high infectivity and high covertness of Omicron BA.2/BA.2.2, as well as the high population density and high population mobility in Shanghai, the number of new infections has continued to rise with authorities reporting. In the second phase of the epidemic, control measures such as blocking and grid-based nucleic acid screening were implemented, further strengthening the prevention and control of the epidemic at the social level; subsequently, at the end of March, control measures such as region-wide static management were implemented, including home isolation, antigen self-testing, early detection, and early treatment. With the gradual decline in the number of infected cases during the epidemic, the city implemented control measures such as a region-specific, multi-level targeted approach to epidemic prevention and control until the epidemic reached a controllable level. In the third phase, an alert system has been created to normalize epidemic prevention and control with nucleic acid and antigen screening, venue code and digital sentry scanning as well as monitoring at local fever clinics and pharmacies to detect any suspected cases timely.
In the Shanghai Omicron wave, the strict prevention and control measures effectively cut off COVID-19 transmission routes and dynamic zero-COVID approach has been proven successfully in containing the spread of the virus. In this paper, we analyzed the epidemiogical characteristics and containment measures for the outbreak caused by the new Omicron variants in order to provide a reference for the prevention and control of the later COVID-19 epidemic and other infectious diseases with high infectiousness and pathogenicity.
| 5. Conclusions|| |
It took nearly three months to contain the Omicron outbreak in Shanghai. With the government’s determination to enforce “dynamic zero-COVID” control measures, Shanghai has implemented the strict prevention and control measures such as citywide lockdown, large scale viral nucleic acid and antigen screening, and quarantine of infected cases and close contacts in makeshift hospitals. Shanghai’s efforts and experiences showed that it is possible to successfully contain the Omicron outbreak in China by implementation of stringent interventions.
In the early stage of the outbreak, Shanghai implemented the closings of targeted buildings and neighborhoods instead of the total lockdown to avoid damaging the economy. However, the lack of preparation for the new Omicron variant and fatigue in fighting the epidemic put Shanghai in a grim situation for a time. The lessons from Shanghai’s response to Omicron showed that the dynamic zero-COVID policy is still the most suitable response to the virus which can quickly find the infections and curb the transmission route. It also indicated that we should effectively increase the capacity of the multi-sectors to respond to severe emergencies and boost the development of early warning and emergency response systems for major emergencies in the follow-up work. In the context of normalization of epidemic situation, many provinces and cities across China took more decisive preventive measures to screen the infection cases through mass nucleic acid testing and accelerating the design and construction of makeshift hospitals to make the full preparation in wartime.
Currently, the global epidemic of COVID-19 is still serious, and the CDC reported on July 16, 2022 that two new subvariants of Omicron BA.4 and BA.5, which are probably the most infectious SARS-CoV-2 viruses to date. In the context of the global pandemic of COVID-19, there is always a continuous risk of importation of the epidemic from abroad, and the continuous mutation and upgrading of SARS-CoV-2 variants reminded us that prevention and control of the epidemic can not be relaxed. We should concurrently step up our monitoring efforts, examine the epidemic patterns, conduct genomic surveillance, and develop effective vaccines and efficient treatments in order to provide solid scientific backing for the fundamental prevention and control of the epidemic.
Conflict of interest statement
The authors declare that they have no conflict of interest.
The study received no extramural funding.
Zhou HR, Pan JF, Xiao N and Li GF discussed the framework of the article. Zhou HR and Wang XL were responsible for manuscript writing. Wang XM, Zhou Z, Kong W, Pan YJ, Xu XX and Ye KY contributed to the critical revision of the article. Zhou HR, Pan JF and Xiao N reviewed and edited the content of the whole paper.
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