Saturday, December 04, 2021

EID Journal: Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong


Given how early we are in the `Omicron Phase' of the COVID pandemic, it is remarkable that we already have an early release research letter, published in the CDC's EID Journal, describing the transmission of this emerging coronavirus variant in a Hong Kong Quarantine hotel. 

The two travelers, who arrived in Hong Kong one day apart, were quarantined in the same hotel, with rooms across the hallway from one another.  They had no direct contact - or apparent indirect contact - besides the proximity of their rooms. 

The both tested positive for Omicron, albeit 4 days apart.  Genomic sequencing showed their infections only varied by 1 nt. (nucleotide), strongly suggesting transmission from case A to case B.  A review of this case leads the authors to conclude that: "Airborne transmission across the corridor is the most probable mode of transmission."

While it is true we've seen robust transmission of previous COVID variants aboard cruise ships, and occasionally even in quarantine facilities, Hong Kong's public health agency has a lot of experience - and success - in dealing with quarantined, and potentially infected, individuals. 

The fact that one of the earliest imported Omicron cases to enter Hong Kong managed to evade their quarantine measures is worth noting.  Additionally, both patients were fully vaccinated - yet had low Ct values (indicating high viral loads) - which raises additional concerns on the ability of Omicron to infect, and  spread, among vaccinated individuals. 

I've posted excerpts from the research letter (slightly reformatted for readability). Follow the link to read it in its entirety. 

Research Letter
Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China, November 2021

Haogao Gu, Pavithra Krishnan, Daisy Y.M. Ng, Lydia D.J Chang, Gigi Y.Z. Liu, Samuel S.M. Cheng, Mani M.Y. Hui, Mathew C.Y. Fan, Jacob H.L. Wan, Leo H.K. Lau, Benjamin J. Cowling, Malik Peiris, and Leo L.M. Poon

Author affiliation: The University of Hong Kong, Hong Kong, China


We report detection of severe acute respiratory syndrome coronavirus 2 Omicron variant (B.1.1.529) in an asymptomatic, fully vaccinated traveler in a quarantine hotel in Hong Kong, China. The Omicron variant was also detected in a fully vaccinated traveler staying in a room across the corridor from the index patient, suggesting transmission despite strict quarantine precautions.

A new variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), B.1.1.529, was identified in Botswana and South Africa in early November 2021 and was designated as variant of concern (VOC) Omicron by the World Health Organization on November 26, 2021 (1). As of December 1, 2021, ≈220 sequences were available on GISAID (, and this variant has been detected in countries in Africa and beyond since mid-November (2,3).
This variant contains >30 spike protein amino acid mutations that might be associated with increased transmissibility, severity, and capacity for immune escape. With supporting evidence of epidemiologic and molecular epidemiologic findings, we report the probable transmission of Omicron in a quarantine hotel in Hong Kong, China. We also compare its mutational profile with other VOCs and variants of interest.

Two cases of infection with VOC Omicron (cases A and B) were detected in Hong Kong. Case-patient A arrived in Hong Kong from South Africa on November 11, 2021, and case-patient B arrived in Hong Kong from Canada on November 10, 2021.

Both case-patients had previously received 2 vaccine doses (Pfizer-BioNTech,; the second dose was given on June 4, 2021, for case-patient A and on May 25, 2021, for case-patient B. Both case-patients tested negative by reverse transcription PCR (RT-PCR) for SARS-CoV-2 within 72 hours before arrival. On arrival at the Hong Kong airport, both case-patients stayed in the same quarantine hotel and had rooms across the corridor from each other on the same floor.

Case-patient A showed a positive result for SARS-CoV-2 without symptoms on November 13, 2021 (cycle threshold [Ct] value 18). He was hospitalized and isolated the next day. Case-patient B had mild symptoms develop on November 17, 2021. He showed a positive result for SARS-CoV-2 (Ct value 19) on November 18, 2021, and was hospitalized on the same day. The 2 Ct values indicate high viral loads. None of the 12 persons staying in nearby rooms on the same floor during the study or related hotel staff have tested positive in repeated tests for SARS-CoV-2 (4).

Viral genomes deduced from these 2 SARS-CoV-2‒positive cases differed only by 1 nt.

Retrospective investigation, including closed-circuit television camera footage, confirmed that neither case-patient left their room during the quarantine period. No items were shared between rooms, and other persons did not enter either room. The only time the 2 quarantined persons opened their respective doors was to collect of food that was placed immediately outside each room door. The only other time they might have opened their doors would be for RT-PCRs, which were conducted in 3-day intervals. However, because these 2 case-patients arrived 1 day apart, it is unlikely that they would be tested on the same day. Airborne transmission across the corridor is the most probable mode of transmission.


The laboratory and epidemiologic features of the Omicron variant are yet to be fully characterized and cannot be determined on the basis of sequence features alone. Nonetheless, compared with other VOCs, the number of mutations found in the spike of the Omicron variant is unprecedented. This finding results in false-negative results in some diagnostic RT-PCRs specific for the S gene (3). Many of the mutations found in the S protein are known to alter SARS-CoV-2 antigenicity and transmissibility (5). The R203K and G204R mutations in the nucleocapsid protein are also associated with enhanced virus replication (6).

It is not known whether these detected mutations might have affect the effectiveness of existing vaccines and virus transmissibility. However, detection of Omicron variant transmission between 2 fully vaccinated persons across the corridor of a quarantine hotel has highlighted this potential concern. Further experimental characterizations and epidemiologic investigations of this newly found VOC are urgently needed. Increased precautions or additional measures might be warranted while awaiting more data.

Dr. Gu is a postdoctoral fellow at The University of Hong Kong, Hong Kong, China. His primary research interests are bioinformatics and virus evolution.