Throughout the coronavirus disease 2019 (COVID-19) pandemic, divergent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages have emerged continuously, mostly through the genomic accumulation of substitutions. We report the discovery of a SARS-CoV-2 variant with a novel genomic architecture characterized by absent ORF7a, ORF7b, and ORF8, and a C-terminally modified ORF6 product resulting from partial 5′-untranslated region (UTR) duplication and transposition.

We report the genome sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains from the clinical samples of three coronavirus disease 2019 (COVID-19) patients in Hong Kong. All the genome sequences showed a 370-nucleotide deletion resulting in the complete loss of ORF7a.

A post-COVID surge of Bordetella pertussis was observed globally. China has reported a high level of macrolide-resistant Bordetella pertussis (MRBP) in recent years; however, the epidemiology of MRBP in Hong Kong remains unknown. We retrieved archived B. pertussis isolates from respiratory samples collected at five regional public hospitals in Hong Kong between 2015 and 2024 and tested their minimum inhibitory concentration (MIC) for macrolides and other non-macrolide antibiotics using the Etest method. All isolates were also subjected to whole genome sequencing for genotypic resistance, Multi-locus Antigen Sequence Typing (MLST) and Multi-locus Variable Number of Tandem Repeat Analysis (MLVA) typing. Twenty-nine isolates of B. pertussis were included in the study. All isolates demonstrating phenotypic macrolide resistance harbored the A2047G mutation while showing low MIC to trimethoprim-sulfamethoxazole, doxycycline, levofloxacin, piperacillin-tazobactam and meropenem. In 2023 and 2024, 100% were MRBP and all belonged to the MT28 clone with the ptxP3 antigenic type. The MRBP isolates in Hong Kong were phylogenetically related to those from mainland China during the same period. There was no obvious correlation between macrolide resistance and clinical presentation, laboratory findings, management and outcome. Phylogenetic analysis suggests that MRBP isolates in Hong Kong and mainland China are closely related.

The emergence of carbapenem-resistant non-typhoidal Salmonella species (CR-NTS) has been observed in recent years, causing increasing challenges in the clinical management and control of Salmonella infections. However, CR-NTS had not been comprehensively studied in Hong Kong previously. We retrieved archived non-typhoidal Salmonella isolates demonstrating carbapenem resistance from five public hospitals in Hong Kong during January 2020–June 2025. The isolates were characterised by NG-TEST CARBA-5 and subjected to whole-genome sequencing (WGS) and phylogenetic analysis. Clinical information of CR-NTS cases was also reviewed. Fourteen CR-NTS isolates (0.3%, 14/4404) were identified during the study period. All 13 CR-NTS isolates (one isolate could not be recovered) were NDM (New Delhi metallo-β-lactamase)-positive, with the first case identified in March 2023. WGS revealed six Group B Salmonella monophasic variants of Salmonella enterica serovar Typhimurium ST34 harbouring the bla_NDM-5 gene. The most common plasmid replicon co-present among bla_NDM-5-positive isolates was IncHI2–IncHI2A (63.6%, 7/11). Among cases of CR-NTS in our study, self-limiting gastroenteritis was the most common presentation (84.6%, 11/13); none presented with invasive infections; travel history was present in 7.7% (1/13). Phylogenetic analysis showed the genotypic relatedness of the ST34 isolates identified in Hong Kong to those on the Chinese mainland, with the possibility of local CR-NTS acquisition via imported food sources. Our findings highlighted the importance of a One Health approach to the control of CR-NTS and the need for continuous antimicrobial resistance surveillance of Salmonella spp. in Hong Kong.