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.

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.

Virulence potential of fusogenic orthoreoviruses.

Several severe respiratory virus infections that have emerged during the past decade originated in animals, including bats. In Indonesia, exposure to bats has been associated with increased risk of acquiring orthoreovirus infection. Although orthoreovirus infections are mild and self-limiting, we explored their potential for evolution into a more virulent form. We used conventional virus culture, electron microscopy, and molecular sequencing to isolate and identify orthoreoviruses from 3 patients in whom respiratory tract infection developed after travel to Indonesia. Virus characterization by plaque-reduction neutralization testing showed antigenic similarity, but sequencing of the small segment genes suggested virus reassortment, which could lead to increased virulence. Bats as a reservoir might contribute to virus evolution and genetic diversity, giving orthoreoviruses the potential to become more virulent. Evolution of this virus should be closely monitored so that prevention and control measures can be taken should it become more virulent.

Coxsackievirus B3-associated aseptic meningitis: an emerging infection in Hong Kong.

Enterovirus (EV) infection is a common disease of childhood and associated not uncommonly with aseptic meningitis. In the summer of 2008, laboratory surveillance has detected increased number of coxsackievirus B3 (CVB3) associated aseptic meningitis in Hong Kong, constituting 11.6% of those infected. This study analyzed the epidemiology, circulating pattern, and clinical presentations of CVB3 in Hong Kong over the last 10 years with reference to the circulation of EV in the locality. Enteroviruses (EV) were isolated from respiratory, cerebrospinal fluid (CSF), stool, and vesicular samples using human rhabdomyosarcoma, human laryngeal carcinoma (HEp2-C), human lung fibroblast (MRC-5), and African green monkey kidney (Vero) cell lines. Virus isolates were identified and characterized by indirect immunofluorescence (IF) using monoclonal antibodies (mAB), neutralization test as well as partial VP1 sequencing. Different from previous years, IF test result showed that majority of the isolates from 2008 were untypeable by the mAB suggesting antigenic change. Sequence analysis revealed that these isolates were clustered with recent isolate from Fuyang, China. Review of data from 1999 to 2008 showed increased activity of CVB3 in the years 2005 and 2008, and isolates in these 2 years displayed an amino acid change from threonine to alanine at codon 277 of the VP1 gene, which may be associated with central nervous system (CNS) disease.

Comparison of laboratory diagnostic methods for measles infection and identification of measles virus genotypes in Hong Kong.

The sensitivities of IgM detection, virus isolation, and RT-PCR for the diagnosis of measles infection were assessed using samples collected from confirmed measles cases from 2006 to 2009. The optimal timing of specimen collection and the preferred specimen type(s) for these tests were also determined. IgM detection showed highest sensitivity when serum samples were collected >or=5 days after rash onset. Virus isolation gave the highest sensitivity when samples were collected

Performance of laboratory diagnostics for the detection of influenza A(H1N1)v virus as correlated with the time after symptom onset and viral load.

BACKGROUND: To diagnose influenza A(H1N1)v virus infection, accurate and rapid detection are important. However, there is scanty data on the performance of various laboratory diagnostics. OBJECTIVE: To compare the performance of rapid antigen test (RAT), viral culture and RT-PCR for the detection of influenza A(H1N1)v virus and to correlate their performance with the time after symptom onset and viral load. STUDY DESIGN: From May 1, 2009 to June 25, 2009, respiratory samples were collected from 5740 individuals suspected of having influenza A(H1N1)v infection. The performance of viral culture and RT-PCR were investigated and correlated with the time after symptom onset. The sensitivity of RAT ESPLINE influenza A & B-N (Fujirebio Inc, Tokyo) was evaluated using a subset of 60 samples from patients diagnosed as having influenza A(H1N1)v infection. RESULTS: Using respiratory samples from 587 patients diagnosed with influenza A(H1N1)v infection, comparison of laboratory diagnostics showed viral culture and RT-PCR gave comparable results with overall sensitivity of 93.9% and 98.1%, respectively. For RAT, when testing a subset of 60 samples collected < or =3 days following symptom onset, the sensitivity was 62%. CONCLUSIONS: Although viral shedding is prolonged and of higher titre in influenza A(H1N1)v infection, RAT showed a low sensitivity of 62% among patients presenting < or =3 days after symptom onset. Viral culture showed comparable performance with RT-PCR and with sensitivity better than that documented for seasonal influenza.

Oseltamivir- and amantadine-resistant influenza viruses A (H1N1).

Surveillance of amantadine and oseltamivir resistance among influenza viruses was begun in Hong Kong in 2006. In 2008, while both A/Brisbane/59/2007-like and A/Hong Kong/2652/2006-like viruses (H1N1) were cocirculating, we detected amantadine and oseltamivir resistance among A/Hong Kong/2652/2006-like viruses (H1N1), caused by genetic reassortment or spontaneous mutation.

Molecular epidemiology of hepatitis E virus in Hong Kong.

Hepatitis E virus (HEV) is one of the major causes of acute and self-limiting hepatitis in human. In Hong Kong, the number of notifications increased from 26 to 62 from year 2001 to 2007. This study describes the molecular epidemiology of HEV in Hong Kong in order to determine the movement and distribution of HEV. HEV in 171 serum samples from HEV IgM positive cases from year 2001 to 2007 were amplified using RT-PCR and subjected to nucleotide sequencing. Phylogenetic analysis showed 162 of 171 HEV detected cases (94.7%) belonged to genotype IV and 8 (4.7%) to genotype I. Interestingly, a cluster of 10 cases in year 2007 that had the same sequence of HEV was identified. Epidemiological data however did not detect any relationship between these cases. Since zoonotic transmission is a well known route of HEV infection, close monitoring of the circulating HEV strains in human and food source animals may help to provide additional information on the transmission of HEV and possible source of infection in Hong Kong.

Atypical norovirus epidemic in Hong Kong during summer of 2006 caused by a new genogroup II/4 variant.

An atypically high level of norovirus activity was noticed in Hong Kong beginning in early May 2006. A study was carried out to investigate whether this was caused by a new norovirus variant. Epidemiological data including monthly positivity rates and the numbers of outbreaks per month from January to July 2006 were analyzed and compared to those from 2002 to 2005. In a comparison with the epidemiological data from 2001 to 2005, an atypical peak of norovirus-associated gastroenteritis outbreak was observed beginning in May 2006, concurring with a striking increase in norovirus activity. Most of the outbreaks (>60%) were located in homes for the elderly. Phylogenetic analysis for both RdRp and 5' capsid regions showed that this epidemic was caused by a new genogroup II/4 variant. This variant was genetically distinct from the predominant variants of 2002 and 2004 but was closely related to one of the 95/96-subset variants which caused an epidemic in Hong Kong in 2001, suggesting that the 95/96 subset may be starting to recirculate.

One-step rapid reverse transcription-PCR assay for detecting and typing dengue viruses with GC tail and induced fluorescence resonance energy transfer techniques for melting temperature and color multiplexing.

BACKGROUND: Dengue fever is an arthropod-borne infection caused by dengue viruses (DVs; DEN-1 to DEN-4). Early diagnosis is critical to prevent severe disease progression and the spreading of DV because no vaccine or specific treatment is available; therefore, a rapid and specific diagnostic assay capable of detecting and typing all serotypes would be ideal. METHODS: We amplified RNA samples from all 4 DV serotypes and Japanese encephalitis virus with 4 serotype-specific forward primers and a universal species-specific reverse primer. DEN-1 and DEN-3 forward primers were labeled at their 5' ends with BODIPY 630/650 and Cy5.5, respectively. DEN-1 and DEN-3 amplicons were detected by their characteristic emission generated from induced fluorescence resonance energy transfer. The presence of DEN-2 and DEN-4 amplicons was indicated by SYBR Green I (SGI) signals at specific amplicon melting temperatures (T(m)s). RESULTS: Fluorescence signals with specific emission wavelengths were obtained from DEN-1 and DEN-3. SGI melting profiles showed a T(m) difference between DEN-2 and DEN-4 of 4.7 degrees C, which was sufficient for differentiating these 2 serotypes. The primers did not amplify the Japanese encephalitis virus. The detection limits of DEN-1 to DEN-4 were 1.64 x 10(-4), 1.05 x 10(-3), 8.15 x 10(-4), and 5.80 x 10(-3) plaque-forming units per reaction, respectively. The assay had a dynamic range of 10(3)-10(8) plaque-forming units/L and could be performed in 2 h. CONCLUSIONS: A single-tube, 1-step reverse transcription-PCR assay based on T(m) and color multiplexing was developed for detecting and typing all 4 DV serotypes.

Correlation of norovirus variants with epidemics of acute viral gastroenteritis in Hong Kong.

Norovirus (NV) (formerly called Norwalk-like virus) is the most common etiological agent of acute viral gastroenteritis outbreaks worldwide. Recent reports have shown that two new GII.4 variants caused epidemics in Europe. To investigate if it is also the case in Hong Kong, a molecular epidemiological study was undertaken between January 2002 and June 2005. During this period, there was a substantial increase in acute cases of gastroenteritis caused by NV. Phylogenetic analysis showed that GII.2 and GII.4 are the major circulating genotypes. Two new GII.4 variants (variants C and D) were identified in 2002 and 2004, which quickly became the predominant strains. They were almost identical to the variants causing epidemics in Europe recently. Since geographically distinct areas were involved within a short period of time, it is possible that GII.4 has a particular propensity for causing pandemics.

Survival of severe acute respiratory syndrome coronavirus.

BACKGROUND: The primary modes of transmission of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) appear to be direct mucus membrane contact with infectious droplets and through exposure to formites. Knowledge of the survival characteristics of the virus is essential for formulating appropriate infection-control measures. METHODS: Survival of SARS-CoV strain GVU6109 was studied in stool and respiratory specimens. Survival of the virus on different environmental surfaces, including a laboratory request form, an impervious disposable gown, and a cotton nondisposable gown, was investigated. The virucidal effects of sodium hypochlorite, house detergent, and a peroxygen compound (Virkon S; Antec International) on the virus were also studied. RESULTS: SARS-CoV GVU6109 can survive for 4 days in diarrheal stool samples with an alkaline pH, and it can remain infectious in respiratory specimens for >7 days at room temperature. Even at a relatively high concentration (10(4) tissue culture infective doses/mL), the virus could not be recovered after drying of a paper request form, and its infectivity was shown to last longer on the disposable gown than on the cotton gown. All disinfectants tested were shown to be able to reduce the virus load by >3 log within 5 min. CONCLUSIONS: Fecal and respiratory samples can remain infectious for a long period of time at room temperature. The risk of infection via contact with droplet-contaminated paper is small. Absorbent material, such as cotton, is preferred to nonabsorptive material for personal protective clothing for routine patient care where risk of large spillage is unlikely. The virus is easily inactivated by commonly used disinfectants.

Influenza A H5N1 detection.

We developed a sensitive and rapid real-time reverse transcription-polymerase chain reaction (RT-PCR) assay to detect influenza A H5N1 virus in clinical samples. This assay was evaluated with samples from H5N1-infected patients and demonstrated greater sensitivity and faster turnaround time than nested RT-PCR.

Norovirus contamination found in oysters worldwide.

Noroviruses (Norwalk-like viruses) are recognized as major causes of acute gastroenteritis worldwide. Outbreaks of norovirus gastroenteritis are often associated with consumption of oysters. In this study, oysters imported into Hong Kong from 11 countries over a 3-year period were screened by RT-PCR. Overall, 53 out of 507 (10.5%) samples were positive for norovirus-RNA, and a wide variety of strains were found. Two novel genetic clusters were detected, which could indicate novel human or animal norovirus strains. However, whether these two new clusters are of human or animal origin is not known. Thirteen outbreaks, in which oysters were implicated as the source of infection were investigated: Norovirus RNA sequences could be detected in oysters from six outbreaks, but only in one outbreak the strains isolated from patients and oysters matched (>98% homology). Therefore, RT-PCR was of use in detecting norovirus contamination of oysters implicated in an outbreak, but was less useful in demonstrating an actual molecular epidemiological link with human cases. It was shown that contamination by noroviruses could be demonstrated in oysters worldwide, and therefore oysters may serve as an important vehicle for introducing novel norovirus strains.