Infection of dogs with SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in Wuhan in December 2019 and caused coronavirus disease 2019 (COVID-19)1,2. In 2003, the closely related SARS-CoV had been detected in domestic cats and a dog3. However, little is known about the susceptibility of domestic pet mammals to SARS-CoV-2. Here, using PCR with reverse transcription, serology, sequencing the viral genome and virus isolation, we show that 2 out of 15 dogs from households with confirmed human cases of COVID-19 in Hong Kong were found to be infected with SARS-CoV-2. SARS-CoV-2 RNA was detected in five nasal swabs collected over a 13-day period from a 17-year-old neutered male Pomeranian. A 2.5-year-old male German shepherd was positive for SARS-CoV-2 RNA on two occasions and virus was isolated from nasal and oral swabs. Antibody responses were detected in both dogs using plaque-reductionneutralization assays. Viral genetic sequences of viruses from the two dogs were identical to the virus detected in the respective human cases. The dogs remained asymptomatic during quarantine. The evidence suggests that these are instances of human-to-animal transmission of SARS-CoV-2. It is unclear whether infected dogs can transmit the virus to other animals or back to humans.

Risk of air and surface contamination of SARS-CoV-2 in isolation wards and its relationship with patient and environmental characteristics.

Air and surface contamination of the SARS-CoV-2 have been reported by multiple studies. However, the evidence is limited for the change of environmental contamination of this virus in the surrounding of patients with COVID-19 at different time points during the course of disease and under different conditions of the patients. Therefore, this study aims to understand the risk factors associated with the appearance of SARS-CoV-2 through the period when the patients were staying in the isolation wards. In this study, COVID-19 patients admitted to the isolation wards were followed up for up to 10 days for daily collection of air and surface samples in their surroundings. The positivity rate of the environmental samples at different locations was plotted, and multiple multi-level mixed-effect logistic regressions were used to examine the association between the positivity of environmental samples and their daily health conditions and environmental factors. It found 6.6 % of surface samples (133/2031 samples) and 2.1 % of air samples (22/1075 samples) were positive, and the positivity rate reached to peak during 2-3 days after admission to the ward. The virus was more likely to present at bedrail, patients' personal items and medical equipment, while less likely to be detected in the air outside the range of 2 m from the patients. It also revealed that higher positivity rate is associated with lower environmental temperature, fever and cough at the day of sampling, lower Ct values of latest test for respiratory tract samples, and pre-existing respiratory or cardiovascular conditions. The finding can be used to guide the hospital infection control strategies by identifying high-risk areas and patients. Extra personal hygiene precautions and equipment for continuously environmental disinfection can be used for these high-risk areas and patients to reduce the risk of hospital infection.

Evaluation of SARS-CoV-2 transmission in COVID-19 isolation wards: On-site sampling and numerical analysis.

Although airborne transmission has been considered as a possible route for the spread of SARS-CoV-2, the role that aerosols play in SARS-CoV-2 transmission is still controversial. This study evaluated the airborne transmission of SARS-CoV-2 in COVID-19 isolation wards at Prince of Wales Hospital in Hong Kong by both on-site sampling and numerical analysis. A total of 838 air samples and 1176 surface samples were collected, and SARS-CoV-2 RNA was detected using the RT-PCR method. Testing revealed that 2.3% of the air samples and 9.3% of the surface samples were positive, indicating that the isolation wards were contaminated with the virus. The dispersion and deposition of exhaled particles in the wards were calculated by computational fluid dynamics (CFD) simulations. The calculated accumulated number of particles collected at the air sampling points was closely correlated with the SARS-CoV-2 positive rates from the field sampling, which confirmed the possibility of airborne transmission. Furthermore, three potential intervention strategies, i.e., the use of curtains, ceiling-mounted air cleaners, and periodic ventilation, were numerically investigated to explore effective control measures in isolation wards. According to the results, the use of ceiling-mounted air cleaners is effective in reducing the airborne transmission of SARS-CoV-2 in such wards.

Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong.

Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission. By analyzing 1899 genome sequences (>18% of confirmed cases) from 23-January-2020 to 26-January-2021, we reveal the effects of fluctuating control measures on the evolution and epidemiology of SARS-CoV-2 lineages in Hong Kong. Despite numerous importations, only three introductions were responsible for 90% of locally-acquired cases. Community outbreaks were caused by novel introductions rather than a resurgence of circulating strains. Thus, local outbreak prevention requires strong border control and community surveillance, especially during periods of less stringent social restriction. Non-adherence to prolonged preventative measures may explain sustained local transmission observed during wave four in late 2020 and early 2021. We also found that, due to a tight transmission bottleneck, transmission of low-frequency single nucleotide variants between hosts is rare.

Whole genome amplicon sequencing and phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from lineage B.1.36.27 isolated in Hong Kong.

BACKGROUND: The import of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.36.27 has sparked the fourth wave of COVID-19 outbreak in Hong Kong. This strain has been circulating in Hong Kong since September 2020 but rarely found in other countries (<1%). RESEARCH DESIGN AND METHODS: A total of 14 SARS-CoV-2 genome sequences collected from patients in Hong Kong between July 2020 and March 2021 were determined by whole viral genome sequencing using Illumina next-generation sequencing platform, followed by phylogenetic analysis. RESULTS: Of the 14 SARS-CoV-2 genome sequences analyzed, 9 strains belonged to the PANGO lineage B.1.36.27, GISAID clade GH, and Nextclade clade 20A. Compared to the reference genome, 31 nucleotide differences and 11 amino acid differences were identified in the genome of the SARS-CoV-2 from PANGO lineage B.1.36.27. CONCLUSIONS: We reported the nucleotides and amino acids mutations identified in the SARS-CoV-2 from PANGO lineage B.1.36.27. Our viral genome sequences enriched the understanding of SARS-CoV-2 mutational landscape and improved the repertoire of known SARS-CoV-2 variants for tracking and tracing. From this study, we found no evidence to show that SARS-CoV-2 from lineage B.1.36.27 can compromise existing vaccines and antibody therapies.

Assessment of SARS-CoV-2 viral loads in combined nasal-and-throat swabs collected from COVID-19 individuals under the Universal Community Testing Programme in Hong Kong.

BACKGROUND: Combined nasal-and-throat swabs (CNTS) is less invasive and easy to execute. CNTS also induces lower risk to healthcare workers upon collection. However, there is a lack of data on viral load assessment for population-wide testing. OBJECTIVE: This study assessed if CNTS is suitable as an alternative specimen type for the detection of SARS-CoV-2. METHODS: We assessed the viral load of SARS-CoV-2 in CNTS collected from COVID-19 individuals through the 2-week period of the Universal Community Testing Programme (UCTP) conducted in Hong Kong. In addition, we compared viral loads of SARS-CoV-2 for the paired CNTS and non-CNTS specimens among these individuals. RESULTS: This UCTP identified 48 COVID-19 individuals from nearly 2 million specimens collected. The viral loads of SARS-CoV-2 varied widely, cycle threshold values Ct 16.28-36.94, among symptoms and asymptomatic individuals. The viral loads for the paired CNTS and non-CNTS specimens were comparable. CONCLUSIONS: This study demonstrated that CNTS could be a specimen of choice for diagnosis of SARS-CoV-2.

Coronavirus Disease 2019 (COVID-19) Re-infection by a Phylogenetically Distinct Severe Acute Respiratory Syndrome Coronavirus 2 Strain Confirmed by Whole Genome Sequencing.

BACKGROUND: Waning immunity occurs in patients who have recovered from Coronavirus Disease 2019 (COVID-19). However, it remains unclear whether true re-infection occurs. METHODS: Whole genome sequencing was performed directly on respiratory specimens collected during 2 episodes of COVID-19 in a patient. Comparative genome analysis was conducted to differentiate re-infection from persistent viral shedding. Laboratory results, including RT-PCR Ct values and serum Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) IgG, were analyzed. RESULTS: The second episode of asymptomatic infection occurred 142 days after the first symptomatic episode in an apparently immunocompetent patient. During the second episode, there was evidence of acute infection including elevated C-reactive protein and SARS-CoV-2 IgG seroconversion. Viral genomes from first and second episodes belong to different clades/lineages. The virus genome from the first episode contained a a stop codon at position 64 of ORF8, leading to a truncation of 58 amino acids. Another 23 nucleotide and 13 amino acid differences located in 9 different proteins, including positions of B and T cell epitopes, were found between viruses from the first and second episodes. Compared to viral genomes in GISAID, the first virus genome was phylogenetically closely related to strains collected in March/April 2020, while the second virus genome was closely related to strains collected in July/August 2020. CONCLUSIONS: Epidemiological, clinical, serological, and genomic analyses confirmed that the patient had re-infection instead of persistent viral shedding from first infection. Our results suggest SARS-CoV-2 may continue to circulate among humans despite herd immunity due to natural infection. Further studies of patients with re-infection will shed light on protective immunological correlates for guiding vaccine design.

Genetic Diversity of SARS-CoV-2 among Travelers Arriving in Hong Kong.

We sequenced 10% of imported severe acute respiratory syndrome coronavirus 2 infections detected in travelers to Hong Kong and revealed the genomic diversity of regions of origin, including lineages not previously reported from those countries. Our results suggest that international or regional travel hubs might be useful surveillance sites to monitor sequence diversity.

Air travel-related outbreak of multiple SARS-CoV-2 variants.

BACKGROUND: A large cluster of 59 cases were linked to a single flight with 146 passengers from New Delhi to Hong Kong in April 2021. This outbreak coincided with early reports of exponential pandemic growth in New Delhi, which reached a peak of > 400 000 newly confirmed cases on 7 May 2021. METHODS: Epidemiological information including date of symptom onset, date of positive-sample detection and travel and contact history for individual cases from this flight were collected. Whole genome sequencing was performed, and sequences were classified based on the dynamic Pango nomenclature system. Maximum-likelihood phylogenetic analysis compared sequences from this flight alongside other cases imported from India to Hong Kong on 26 flights between June 2020 and April 2021, as well as sequences from India or associated with India-related travel from February to April 2021 and 1217 reference sequences. RESULTS: Sequence analysis identified six lineages of SARS-CoV-2 belonging to two variants of concern (Alpha and Delta) and one variant of public health interest (Kappa) involved in this outbreak. Phylogenetic analysis confirmed at least three independent sub-lineages of Alpha with limited onward transmission, a superspreading event comprising 37 cases of Kappa and transmission of Delta to only one passenger. Additional analysis of another 26 flights from India to Hong Kong confirmed widespread circulation of all three variants in India since early March 2021. CONCLUSIONS: The broad spectrum of disease severity and long incubation period of SARS-CoV-2 pose a challenge for surveillance and control. As illustrated by this particular outbreak, opportunistic infections of SARS-CoV-2 can occur irrespective of variant lineage, and requiring a nucleic acid test within 72 hours of departure may be insufficient to prevent importation or in-flight transmission.

Evaluation of automated antigen detection test for detection of SARS-CoV-2.

RT-PCR is the gold standard to detect SARS-CoV-2, however, its capacity is limited. We evaluated an automated antigen detection (AAD) test, Elecsys SARS-CoV-2 Antigen (Roche, Germany), for detecting SARS-CoV-2. We compared the limit of detection (LOD) between AAD test, rapid antigen detection (RAD) test; SARS-CoV-2 Rapid Antigen Test (SD Biosensor, Korea), and in-house RT-PCR test. LOD results showed that the AAD test was 100 fold more sensitive than the RAD test, while the sensitivity of the AAD test was comparable to the RT-PCR test. The AAD test detected between 85.7% and 88.6% of RT-PCR-positive specimens collected from COVID-19 patients, false negative results were observed for specimens with Ct values >30. Although clinical sensitivity for the AAD test was not superior or comparable to the RT-PCR test in the present study, the AAD test may be an alternative to RT-PCR test in terms of turn-around time and throughput.

Early detection of community acquired of SARS-CoV-2 lineage B.1.351 in Hong Kong.

Background: Prior to this report, variants of concern for SARS-CoV-2 were only detected from imported cases in Hong Kong. Objective: Multiple cases of SARS-CoV-2 lineage B.1.351 have been identified in local community. We reported the phylogenetic relationship of these cases. Study design: SARS-CoV-2 cases were screened for the key non-synonymous substitutions in spike protein by different assays. Preliminary positive cases were further tested by whole genome sequencing. Results: From Dec 2020 to May 2021, 55 SARS-CoV-2 cases belonged to lineage B.1.351. Among them, eight genomes were clustered together, all of them were local cases with epidemiological link. Conclusions: To track variants of SARS-CoV-2 and to allow early implementation of control measures, SARS-CoV-2 genomic surveillance must be consistently performed.

Serum Antibody Profile of a Patient With Coronavirus Disease 2019 Reinfection.

We recently reported a patient with coronavirus disease 2019 reinfection. Here, we show that serum neutralizing antibodies could be detected during the first episode but not at the presentation of the second episode. During reinfection, neutralizing antibodies and high avidity immunoglobulin G were found within 8 days after hospitalization, whereas immunoglobulin M response was absent.

The surveillance of spike protein for patients with COVID-19 detected in Hong Kong in 2020.

In 2020, numerous fast-spreading severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have been reported. These variants had unusually high genetic changes in the spike (S) protein. In an attempt to understand the genetic background of SARS-CoV-2 viruses in Hong Kong, especially before vaccination, the purpose of this study is to summarize the S protein mutations detected among coronavirus disease 2019 (COVID-19) patients in Hong Kong in 2020. COVID-19 cases were selected every month in 2020. One virus from each case was analyzed. The full encoding region of the S proteins was sequenced. From January 2020 to December 2020, a total of 340 COVID-19 viruses were sequenced. The amino acids of the S protein for 44 (12.9%) were identical to the reference sequence, WIV04 (GenBank accession MN996528). For the remaining 296 sequences (87.1%), a total of 43 nonsynonymous substitution patterns were found. Of the nonsynonymous substitutions found, some of them were only detected at specific time intervals and then they disappeared. The ongoing genetic surveillance system is important. It would facilitate early detection of mutations that can increase infectivity as well as mutations that are selected for the virus to escape immunological restraint.

Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China.

We describe an introduction of clade GH severe acute respiratory syndrome coronavirus 2 causing a fourth wave of coronavirus disease in Hong Kong. The virus has an ORF3a-Q57H mutation, causing truncation of ORF3b. This virus evades induction of cytokine, chemokine, and interferon-stimulated gene expression in primary human respiratory cells.

Evaluation of rapid antigen detection kit from the WHO Emergency Use List for detecting SARS-CoV-2.

BACKGROUND: Currently, there are two rapid antigen detection (RAD) kits from the WHO Emergency Use List for detecting SARS-CoV-2. OBJECTIVE: The Panbio COVID-19 Ag Rapid Test Device was selected to evaluate the performance for detecting SARS-CoV-2. STUDY DESIGN: Analytical sensitivity for the detection of SARS-CoV-2 virus was determined by limit of detection (LOD) using RT-PCR as a reference method. Clinical sensitivity was evaluated by using respiratory specimens collected from confirmed COVID-19 patients. RESULTS: The LOD results showed that the RAD kit was 100 fold less sensitive than RT-PCR. Clinical sensitivity of the RAD kit was 68.6 % for detecting specimens from COVID-19 patients. CONCLUSIONS: The RAD kit evaluated in the present study shared similar performance with another kit from the WHO Emergency Use List, the Standard Q COVID-19 Ag. Understanding the clinical characteristics of RAD kits can guide us to decide different testing strategies in different settings.

Analytical sensitivity and clinical sensitivity of the three rapid antigen detection kits for detection of SARS-CoV-2 virus.

BACKGROUND: Numerous rapid antigen detection (RAD) kits for diagnosing COVID-19 patients are available in the market recently. OBJECTIVE: To compare analytical sensitivity and clinical sensitivity for the three commercially available RAD kits. STUDY DESIGN: Analytical sensitivity for the detection of SARS-CoV-2 virus was determined by limit of detection (LOD) using RT-PCR as a reference method. Clinical sensitivity was evaluated by using respiratory specimens collected from confirmed COVID-19 patients. RESULTS: The LOD results showed that the three RAD kits varied from 102-105 fold less sensitive than RT-PCR. Clinical sensitivity of RAD kits ranged from 22.9 %-71.4 % for detecting specimens from COVID-19 patients. CONCLUSIONS: Although RAD kits were less sensitive than RT-PCR, understanding the clinical characteristics of different RAD kits can guide us to obtain suitable specimens for testing. The likelihood of positive results for RAD kits will be higher.

In-Flight Transmission of SARS-CoV-2.

Four persons with severe acute respiratory syndrome coronavirus 2 infection had traveled on the same flight from Boston, Massachusetts, USA, to Hong Kong, China. Their virus genetic sequences are identical, unique, and belong to a clade not previously identified in Hong Kong, which strongly suggests that the virus can be transmitted during air travel.