An Imported Case and An Infected Close Contact of The Omicron Variant of Sars-Cov-2 - Guangdong Province, China, December 13, 2021

China CDC Weekly
Notes from the Field
An Imported Case and an Infected Close Contact of the Omicron

Variant of SARS-CoV-2 — Guangdong Province, China,
December 13, 2021
Kuibiao Li1,&; Zhonghua Zheng2,&; Xiang Zhao3; Qing Zeng1; Tengfei Zhou1; Qianfang Guo2;
Yao Hu2; Wenbo Xu3; Zhoubin Zhang1,#; Baisheng Li2,#
On November 27, 2021, a 67-year-old male spread in South Africa, becoming the dominant strain
returning from Canada via airplane was transferred to in South Africa. On November 26, 2021, it was listed
the central isolation hotel in Shanghai. During the by the World Health Organization (WHO) as a VOC
quarantine, his 1st, 4th, 7th, and 14th days of (2). The Omicron variant is a highly divergent variant
specimens returned negative for severe acute respiratory with a high number of mutations, including position
syndrome coronavirus 2 (SARS-CoV-2), which causes 26–32 in the spike protein, some of which are
coronavirus disease 2019 (COVID-19). On December concerning and may be associated with immune escape
11, he completed 14 days of centralized isolation and potential and higher transmissibility. As of December
returned to Guangzhou from Shanghai via airplane, 9, 2021, human infections with this variant had been
then he was closed-loop transferred to Yuexiu District identified in 63 countries (3).
for a 7-day home isolation. On December 12, the local Compared with the Wuhan reference sequence
Community Health Service Center routinely collected (EPI_ISL_402119) (4), the strain from the case
his throat swab and the result returned to COVID-19 displayed 59 nucleotide variation sites. The sequence
positive on December 13, 2021. He was transported to reported on the evolutionary branch is most similar to
the Guangzhou Eighth People’s Hospital for isolated those reported in England on December 4, 2021
treatment by negative pressure ambulance on the same (Figure 1). Furthermore, 48 amino acid mutation sites
day. The patient had two inflamed lungs according to and 16 amino acid deletions were detected in the
the chest computed tomography (CT) examination, protein that corresponded to the features of the
but his most recently updated condition was stable. An VOC/Omicron variant (B.1.1.529.1).
estimated 600 close contacts were identified and were Researchers have established the existence of 2
placed in centralized isolation. On December 16, one variants of Omicron. The “standard” variant is now
of the close contacts, a 70-year-old female also tested referred to as BA.1/B.1.1.529.1, and a second variant
positive for COVID-19. She lived on the lower floor of of Omicron known as BA.2/B.1.1.529.2. BA.2 has
the same type of apartment as the imported case and been nicknamed “Stealth Omicron” because it differs
spent 19 hours in the same building. from the “standard” variety by not having the
On December 13, 2021, the nasal swab was characteristic SGTF-causing deletion (Δ69–70) (5). In
sequenced using both Nanopore GridION by this study, the variant has deletion (Δ69–70) and
Guangzhou CDC and Illumina MiniSeq by belongs to sublineage BA.1/B.1.1.529.1.
Guangdong CDC. The viral RNA was reverse Funding: The Basic Research Project of Key
transcribed and amplified using ULSEN® 2019-nCoV Laboratory of Guangzhou (No.202102100001), The
Whole Genome Capture Kit (Beijing MicroFuture Key Project of Medicine Discipline of Guangzhou
Technology Co., Ltd, Beijing, China, V-090418). (No.2021–2023-11).
Then, the sequencing libraries were prepared using the doi: 10.46234/ccdcw2021.265
Illumina Nextera® XT Library Prep Kit (Illumina, Inc., #
Corresponding authors: Zhoubin Zhang, gzcdczzb@gzcdc.org.cn;
San Diego, USA, FC-131-1001) and were conducted Baisheng Li, libsn@126.com.
by Illumina sequencing. On December 14, 2021, the 1
Institute of Public Health, Guangzhou Medical University &
sequencing analysis concluded that the virus genome Guangzhou Center for Disease Control and Prevention, Guangzhou,
belonged to lineage B.1.1.529, Variant of Concern Guangdong, China; 2 Guangdong Provincial Center for Disease
(VOC)/Omicron. The Omicron (B.1.1.529) variant Control and Prevention, Guangzhou, Guangdong, China;
3
National Institute for Viral Disease Control and Prevention, Chinese
was reportedly first discovered on November 9, 2021, Center for Disease Control and Prevention, Beijing, China.
in Botswana in southern Africa (1), and then gradually &
Joint first authors.
96 CCDC Weekly / Vol. 4 / No. 5 Chinese Center for Disease Control and Prevention
China CDC Weekly
62 hCoV-19/France/OCC-SC554/2020|EPI ISL 645206|2020-04-03

hCoV-19/France/OCC-SC561/2020|EPI ISL 660728|2020-04-20
hCoV-19/France/OCC-SC563/2020|EPI ISL 660729|2020-04-22 VOC/Omicron(B.1.1.529)
67 hCoV-19/England/PHEC-3U0A8UB0/2021|EPI ISL 7583411|2021-12-04
87 XG10623 S1 (Reads) NC 045512 consensus Guangdong
48 hCoV-19/England/PHEC-3U0A4UCB/2021|EPI ISL 7509830|2021-11-26
hCoV-19/USA/AZ-ASU26315/2021|EPI ISL 7503377|2021-12-05
77
59 hCoV-19/USA/TX-HMH-MCoV-68741/2021|EPI ISL 7604480|2021-12-07
25 VOC/Omicron(BA.1)
hCoV-19/USA/TX-HMH-MCoV-68528/2021|EPI ISL 7415767|2021-12-02
61 hCoV-19/South Africa/NICD-N21751/2021|EPI ISL 7337497|2021-11-22
28 hCoV-19/Australia/QLD2568/2021|EPI ISL 7190366|2021-12-01
hCoV-19/Brazil/AM-FIOCRUZ-21896339ECF/2021|EPI ISL 2777825|2021-03-19 VOC/Omicron(BA.2)
hCoV-19/Brazil/AM-FIOCRUZ-21890984TSM/2021|EPI ISL 2777596|2021-03-26
99
25 hCoV-19/Italy/UMB-ISS-6677/2021|EPI ISL 1014545|2021-01-07
61
55 hCoV-19/Brazil/PE-NXBS509GENOV827539448543/2021|EPI ISL 3664121|2021-01-03 VOC/Gamma(P.1)
59 57 hCoV-19/Brazil/PB-BA1200-250009713/2020|EPI ISL 2241496|2020-10-01
hCoV-19/Japan/PG-14389/2020|EPI ISL 896023|2020-11-07
hCoV-19/England/MILK-9E05B3/2020|EPI ISL 601443|2020-09-20 VOC/Alpha(B.1.1.7)
65
hCoV-19/Peru/LIM-INS-869/2020|EPI ISL 1534645|2020-11-30 C.37
38
hCoV-19/India/un-IRSHA-CD210871/2020|EPI ISL 2758215|2020-03-03 B.1.617.1
72 hCoV-19/USA/ID-UNM-IBL720784/2021|EPI ISL 3275127|2021-03-31
97 hCoV-19/USA/MO-CDC-QDX24155130/2021|EPI ISL 2047029|2021-04-21
80 96 hCoV-19/USA/MS-CDC-2-4524366/2021|EPI ISL 3355089|2021-06-01 VOC/Delta(B.1.617.2)
99 hCoV-19/India/GJ-INSACOG-GBRC1238/2021|EPI ISL 3066421|2021-04-07

72 hCoV-19/Mexico/AGU-InDRE FB18599 S4467/2020|EPI ISL 2937904|2020-09-22
hCoV-19/Angola/KRISP-K009785/2020|EPI ISL 1347937|2020-12-11 B.1.525
hCoV-19/USA/CA-LACPHL-AF00986/2020|EPI ISL 2259242|2020-04-21 B.1.526
74
hCoV-19/Zimbabwe/ZW-29001/2020|EPI ISL 1191821|2020-09-01
71
99 hCoV-19/South Africa/KRISP-MDSH920888/2020|EPI ISL 736968|2020-12-06
VOC/Beta(B.1.351)
98 hCoV-19/Bangladesh/BCSIR-NILMRC-448/2021|EPI ISL 943561|2021-01-24
NC 045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1 complete genome
0.000,20
FIGURE 1. Phylogenetic tree based on the full-length genome sequences of the COVID-19 virus.
Note: The VOC/Omicron(B.1.1.529) variants are highlighted in yellow. The VOC/Omicron(BA.1) variants are highlighted in
green and the Guangdong imported VOC/Omicron(BA.1) variant is marked with an arrow. The VOC/Omicron(BA.2) variant
is highlighted in blue. The 11 distinguished COVID-19 mutants are marked on the right.
Abbreviations: VOC=variant of concern; COVID-19=coronavirus disease 2019.
Submitted: December 16, 2021; Accepted: December 17, 2021 concern. [2021-12-14].
3. World Health Organization. COVID-19 Weekly Epidemiological
Update-7 December 2021. https://www.who.int/publications/m/item/
REFERENCES weekly-epidemiological-update-on-covid-19---7-december-2021. [2021-
12-14].
4. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al. A new
1. Callaway E. Heavily mutated Omicron variant puts scientists on alert. coronavirus associated with human respiratory disease in China. Nature
Nature. 2021;600(7887):21. http://dx.doi.org/10.1038/d41586-021- 2020;579(7798):265. http://dx.doi.org/10.1038/s41586-020-2008-3.
03552-w. 5. Guardian. Scientists find ‘stealth’ version of Omicron that may be harder
2. World Health Organization. Classification of Omicron (B.1.1.529): to track. https://www.theguardian.com/world/2021/dec/07/scientists-
SARS-CoV-2 Variant of Concern. https://www.who.int/news/item/26- find-stealth-version-of-omicron-not-identifiable-with-pcr-test-covid-
11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of- variant. [2021-12-14].
Chinese Center for Disease Control and Prevention CCDC Weekly / Vol. 4 / No. 5 97

An Imported Case and An Infected Close Contact of The Omicron Variant of Sars-Cov-2 - Guangdong Province, China, December 13, 2021

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An Imported Case and An Infected Close Contact of The Omicron Variant of Sars-Cov-2 - Guangdong Province, China, December 13, 2021

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China CDC Weekly

Notes from the Field

An Imported Case and an Infected Close Contact of the Omicron

62 hCoV-19/France/OCC-SC554/2020|EPI ISL 645206|2020-04-03

99 hCoV-19/India/GJ-INSACOG-GBRC1238/2021|EPI ISL 3066421|2021-04-07

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