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Department of Infectious Diseases, National Children's Medical Center, Children's Hospital of Fudan University, 399 Wanyuan Road, Min-hang District, Shanghai 201102, ChinaShanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 201102, China
Department of Clinical Laboratory, National Children's Medical Center, Children's Hospital of Fudan University, 399 Wanyuan Road, Min-hang District, Shanghai 201102, ChinaShanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 201102, China
Shanghai, as the largest economic center and metropolitan city in China, is always facing greater pressure of SARS-CoV-2 importation from abroad. Although the strict implementation of dynamic zero strategies against SARS-CoV-2 infection is in effect in China, the sudden surge of SARS-CoV-2 Omicron variant caused a large wave of COVID-19 pandemic in Shanghai, China, since the late February, 2022.
The outbreaks of Omicron variant peaked in April, despite the strict implementation of lockdown. As of June 30th, 2022, more than 630,000 confirmed cases and nearly 600 fatal cases have been reported in Shanghai.
little is known about its clinical and virological characteristics as yet. Thus, we carried out the study to understand the clinical features, viral shedding and genetic characteristics of SARS-CoV-2 Omicron variant in Shanghai.
Herein, a total of 191 child-parent pairs’ households including 230 children and 465 parents with SARS-CoV-2 infection admitted in the designated Children's Hospital of Fudan University for COVID-19 in Shanghai, during April 1st to May 5th, 2022, were included. Nasopharyngeal swab samples were collected from these patients. Viral RNA was extracted from 200 μl of the samples using viral RNA extraction kit (DAAN, China). SARS-CoV-2 RNA was detected by the dual-target (ORF1ab and N genes) detection kits (DAAN), and the Ct value < 35 in either target gene was determined as a positive detection.
The median age of patients was 23.5 years and 45.6% of them was male. Most of patients presented to be mild (91.8%) to asymptomatic (8.2%) (Table 1). A vast majority of the children had fever (92.2%), followed by cough (36.5%), nausea/vomiting/diarrhea (22.2%), nasal congestion (10.9%), sore throat (9.1%) and loss of taste or smell (1.7%), while adults were predominated with fever (68.4%) and cough (37.4%), followed by sore throat (22.8%), fatigue (12.7%), nasal congestion (4.3%) and loss of taste or smell (3.2%) (Table 1). Of the patients, 51 (22.2%) children and 362 (77.8%) adults have received at least one dose vaccines. These findings were consistent with the other studies that the Omicron BA.2 variant caused milder diseases.
After the symptom onset, the viral RNA load in patients showed a rapid increase in about one to two days, being faster in children with about one-day interval compared with 2 days in adults (Fig. 1A). During the first week, the median viral RNA load remained high levels, and then had a significant decline both in children and adults (Fig. 1A), which was similar to those of other studies regarding Omicron variants.
We observed that the median peak viral RNA loads (p = 0.0008) were significantly higher and the median duration days of viral RNA shedding (Ct value < 35) (p = 0.0009) were 2 days longer in children than in adults (Fig. 1B, C). Notably, higher median peak viral RNA loads and longer median duration days of shedding were found in children aged < 1 year than most of the other age groups of children with significant differences (Fig. 1D, E). It emphasized the importance of stringent infection control and early treatment for high-risk young children.
Using the sequencing strategy, hybrid capture based enrichment of SARS-CoV-2,
we succeeded in obtaining 42 viral genomes from the SARS-CoV-2 cases. The cases represented throughout 12 districts of Shanghai, between April and May, 2022. All these viral genome sequences belonged to the 21 L/BA.2.2 Omicron variant. Combining the previous report,
we concluded that COVID-19 pandemic in Shanghai were predominately attributable to Omicron BA.2.2 sub-lineage. Furthermore, a maximum likelihood (ML) tree was reconstructed using 254 BA.2.2 genomic sequences including 42 strains in our study and 212 strains available from GISAID. The ML tree showed that the BA.2.2 strains obtained in our study and identified in other provinces from mainland of China clustered together, but separated from the strains in other regions, indicated that BA.2.2 strain had regionally evolved into an emerging cluster (SH2022) circulating in Shanghai (Fig. 1F). Besides, SH2020 was most closely related to the strains from Hong Kong, indicating that SH2022 strain was most likely originated from the strain of Hong Kong. Additionally, the tree showed that the BA.2.2 strains identified in other provinces in China were transmitted from Shanghai (Fig. 1F), suggesting that the BA.2.2 variant in Shanghai had spread across the provinces in China.
Analysis of those BA.2.2 genomic sequences obtained in the study showed the presence of a mean of 51 aa substitutions and 12 aa deletions, compared with the reference SARS-CoV-2 strain Wuhan-Hu-1/2019 (MN908947). These included 29, 2, 1 and 4 aa mutations in the S, M, E and N proteins, respectively; 10, 4, 1, 1 and 1 aa mutations in the ORF1a, ORF1b, ORF3a, ORF6 and ORF9 proteins (Fig. 1G), respectively. However, compared with other known BA.2.2 strains, eight reversion mutations (N405D, S408R, N417K, K440N, N477S, K478T, G614D and Y655H) in S protein and one mutation (T63A) in M protein were found as Shanghai BA.2.2 strain-specific (Fig. 1G). Among these reversion mutation residues, Y655H in S protein and T63A in M protein presented with a high occur frequency of 42.9% and 88.1% in 42 strains, while other reversion mutations were almost shown at the frequency of more than 7.1%. Furthermore, a unique new mutation I76V within the ORF8 protein was identified in 21.4% of Shanghai BA.2.2 strains. In addition, three unique new nucleotide silent mutations of G7393T in ORF1a, C26789T in M and T28897A in N genes were also found, with the occur frequency of 42.7%, 33.3% and 92.9%, respectively. Thus, the roles of these unique mutations, especially when combined, deserve urgent and further investigations in Shanghai BA.2.2 strains.
Collectively, we not only provide more virologic evidence for the recent upsurge in Shanghai COVID-19 outbreaks caused by the newly identified BA.2.2 variants, but also offer the important understandings for the epidemiology of BA.2.2 variant. Continuing surveillance on complete genome information could facilitate the understandings of SARS-CoV-2 evolutionary patterns and of genotype replacement and, ultimately, in the control and development of effective vaccines and antiviral drugs against SARS-CoV-2 variant infections.
The study was supported by the Key Development Program of the Children's Hospital of Fudan University (Grant No. EK2022ZX05 ), the General Project of Natural Science Foundation of Shanghai (Grant No. 22ZR1408200 ), the Science and Technology Commission of Shanghai Municipality (No. 20JC141020002 ) and Three-Year Action Plan for Strengthening the Construction of Public Health System in Shanghai (2020-2022) (GWV-3.2).
J. X. and M. Z. led the design , conduct and analysis of the clinical study and the development of the manuscript. Y.Y. A., performed the trial. J. J. L., Z.Q. W., Z. L. W., H. T., Y. Q., X. M. F., W. J. M., and L. T. L. collected the clinical samples and data. Y.Y. A. and J. J. L. contributed to the protocol design and data analysis. All authors were involved in interpreting the data and in ensuring the accuracy and completeness of the data and the fidelity of the trial to the protocol. Y.Y. A. wrote the first draft of the manuscript. The manuscript was subsequently revised by J. X. and M. Z., and approved by all authors, who agreed to submit the manuscript for publication.
Declaration of Competing Interest
All the authors declared no conflicts of interest.
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