Background and Aims The safety and antibody responses of coronavirus disease 2019 (COVID‐19) vaccination in patients with chronic hepatitis B (CHB) virus infection is still unclear, and exploration in safety and antibody responses of COVID‐19 vaccination in CHB patients is significant in clinical practice. Methods 362 adult CHB patients and 87 healthy controls at an interval of at least 21 days after a full‐course vaccination (21–105 days) were enrolled. Adverse events (AEs) were collected by questionnaire. The antibody profiles at 1, 2 and 3 months were elucidated by determination of anti‐spike IgG, anti‐receptor‐binding domain (RBD) IgG, and RBD‐angiotensin‐converting enzyme 2 blocking antibody. SARS‐CoV‐2 specific B cells were also analysed. Results All AEs were mild and self‐limiting, and the incidence was similar between CHB patients and controls. Seropositivity rates of three antibodies were similar between CHB patients and healthy controls at 1, 2 and 3 months, but CHB patients had lower titers of three antibodies at 1 month. Compared to healthy controls, HBeAg‐positive CHB patients had higher titers of three antibodies at 3 months (all P < .05) and a slower decline in antibody titers. Frequency of RBD‐specific B cells was positively correlated with titers of anti‐RBD IgG (OR = 1.067, P = .004), while liver cirrhosis, antiviral treatment, levels of HBV DNA, alanine aminotransferase (ALT) and aspartate aminotransferase (AST) and total bilirubin (TB) were not correlated with titers of anti‐RBD IgG. Conclusions Inactivated COVID‐19 vaccines were well tolerated, and induced effective antibody response against SARS‐CoV‐2 in CHB patients.

Motivation The growing number of microbial reference genomes enables the improvement of metagenomic profiling accuracy but also imposes greater requirements on the indexing efficiency, database size, and runtime of taxonomic profilers. Additionally, most profilers focus mainly on bacterial, archaeal, and fungal populations, while less attention is paid to viral communities. Results We present KMCP, a novel k-mer-based metagenomic profiling tool that utilizes genome coverage information by splitting the reference genomes into chunks and stores k-mers in a modified and optimized COBS index for fast alignment-free sequence searching. KMCP combines k-mer similarity and genome coverage information to reduce the false positive rate of k-mer-based taxonomic classification and profiling methods. Benchmarking results based on simulated and real data demonstrate that KMCP, despite a longer running time than all other methods, not only allows the accurate taxonomic profiling of prokaryotic and viral populations but also provides more confident pathogen detection in clinical samples of low depth. Availability The software is open-source under the MIT license and available at https://github.com/shenwei356/kmcp. Supplementary information Supplementary data are available at Bioinformatics online.

Given the pandemic of severe acute respiratory syndrome coronavirus 2 Omicron variants, booster vaccination (BV) using inactivated virus vaccines (the third dose) has been implemented in China. However, the immune responses after BV, especially those against Omicron, in patients with chronic hepatitis B virus (HBV) infection (CHB) are unclear. In this prospective longitudinal study, 114 patients with CHB and 68 healthy controls (HCs) were recruited after receiving inactivated vaccination. The anti-receptor-binding domain (RBD) immunoglobulin G (IgG), neutralizing antibodies (NAbs), neutralization against Omicron (BA2.12.1, BA.4/5), and specific B/T cells were evaluated. In patients, anti-RBD IgG was elevated significantly after BV; the titers were as high as those in HCs. Similar results were obtained for the NAbs. However, compared with that against wild type (WT), the neutralization against Omicron was compromised after BV. The frequency of RBD + atypical memory B cells increased, but spike-specific cluster of differentiation 4 + /8 + T cells remained unchanged after BV. Moreover, no serious adverse events or HBV reactivation were observed after BV. These results suggest that BV significantly enhanced antibody responses against WT; however, it resulted in compromised antibody responses against Omicron in patients with CHB. Hence, new all-in-one vaccines and optimal vaccination strategies should be studied promptly.

A growing number of microbial reference genomes enable better metagenomic profiling accuracy yet put higher requirements on the indexing efficiency, database size, and runtime of taxonomic profilers. Besides, most profilers focused mainly on bacterial, archaeal, and fungal populations with less attention on viral communities. We present KMCP, a novel k-mer based metagenomic profiling tool that introduces genomic positions to k-mers by splitting the reference genomes into chunks. Benchmarking results on both simulated and real data demonstrate that KMCP not only allows for accurate taxonomic profiling of archaea, bacteria, and viral populations from metagenomic shotgun sequence data, but also provides confident pathogen detection for infectious clinical samples of low depth. KMCP is implemented in Go and is available as open-source software, under MIT, at https://github.com/shenwei356/kmcp.

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