Effectiveness of Inactivated COVID-19 Vaccines Against Illness Caused by the B.1.617.2 (Delta) Variant During an Outbreak in Guangdong, China : A Cohort Study.

BACKGROUND: Real-world evidence on inactivated COVID-19 vaccines against the highly transmissible B.1.617.2 (Delta) variant of SARS-CoV-2 is limited, leaving an important gap in the evidence base about inactivated COVID-19 vaccines for use by immunization programs. OBJECTIVE: To estimate inactivated vaccine effectiveness (VE) against the B.1.617.2 variant. DESIGN: Retrospective cohort study. SETTING: The study was based on the first outbreak of the B.1.617.2 variant in mainland China that was discovered and traced in Guangdong in May and June 2021. PARTICIPANTS: 10 805 adult case patients with laboratory-confirmed infection and close contacts. MEASUREMENTS: Participants were categorized as unvaccinated, partially vaccinated (1 dose), and fully vaccinated (2 doses). We estimated VE against the primary outcome of pneumonia and the secondary outcomes of infections, symptomatic infections, and severe or critical illness associated with the B.1.617.2 variant. RESULTS: Results are reported in the order of outcome severity. Of 10 805 participants, 1.3% contracted infections, 1.2% developed symptomatic infections, 1.1% had pneumonia, and 0.2% had severe or critical illness. The adjusted VEs of full vaccination were 51.8% (95% CI, 20.3% to 83.2%) against infection, 60.4% (CI, 31.8% to 88.9%) against symptomatic infection, and 78.4% (CI, 56.9% to 99.9%) against pneumonia. Also, full vaccination was 100% (CI, 98.4% to 100.0%) effective against severe or critical illness. By contrast, the adjusted VEs of partial vaccination against infection, symptomatic infection, and pneumonia were 10.7% (CI, -41.2% to 62.6%), 6.8% (CI, -47.4% to 61.0%), and 11.6% (CI, -42.6% to 65.8%), respectively. LIMITATION: Observational study with possible unmeasured confounders; insufficient data to do reliable subgroup analyses by age and vaccine brand. CONCLUSION: Full vaccination with inactivated vaccines is effective against the B.1.617.2 variant. Effort should be made to ensure full vaccination of target populations. PRIMARY FUNDING SOURCE: National Natural Science Foundation of China and Key-Area Research and Development Program of Guangdong Province.

Comparisons of microbiological characteristics and antibiotic resistance of Klebsiella pneumoniae isolates from urban rodents, shrews, and healthy people.

BACKGROUND: The comparisons of molecular characterization and antibiotic resistance of Klebsiella pneumoniae (KP) isolates from humans and other animal hosts are not well studied. Our goal was to compare the molecular epidemiology of KP strains that were isolated from urban rodents, shrews, and healthy people. RESULTS: K. pneumoniae (KP) isolates were isolated from fecal samples of rodents, shrews and healthy adults in 2015 in southern China. In total, 465 fecal samples were collected, of which 85 from rodents, 105 from shrews, and 275 from healthy adults. Antimicrobial susceptibility and production of extended-spectrum ß-lactamases (ESBL) of the isolates were tested. PCR-based methods were used to detect specific genes, including ESBL genes (blaTEM, blaSHV, and blaCTX-M) in ESBL-producing isolates, capsular serotypes (K1, K2, K5, K20, K54, and K57) in hypervirulent KPs (hvKPs), and virulence genes (magA, wcaG, rmpA, uge, kfu, and aerobactin) in hvKP isolates. Multilocus sequence type (MLST) and pulsed-field gel electrophoresis (PFGE) were performed to exclude the homology of these isolates. The carriage rate of KP in urban rodents and shrews (78.42%) was higher than that in healthy adults (66.18%) (χ2 = 8.206, P = 0.004). The prevalence rates of ESBL-producing isolates among rodents, shrews, and humans were 7.94, 12.79, and 17.03%, respectively. The positive rates of CTX-M, TEM and SHV types in ESBL-producing isolates were 29.79, 27.66, and 17.02%, respectively. Serotype K1, K5, K20, and K57 were detected in both small mammals and humans. PFGE typing revealed thirty-six clusters. PFGE cluster A was clustered by samples of shrews and healthy adult, with a similarity of 88.4%. MLST typing revealed thirty-eight types. ST23 and ST35 were detected in samples of shrews and healthy adults. ST37 was detected in samples of 2 rodents and a healthy adult. CONCLUSIONS: Overlapping serotypes of hvKP were observed in both the animals and humans. The same PFGE or MLST types were also found in isolates derived humans, rodents and shrews. Therefore, urban rodents and shrews might play a certain role in the transmission of drug-resistant and hypervirulent KP.

Composition of gut and oropharynx bacterial communities in Rattus norvegicus and Suncus murinus in China.

BACKGROUND: Rattus norvegicus and Suncus murinus are important reservoirs of zoonotic bacterial diseases. An understanding of the composition of gut and oropharynx bacteria in these animals is important for monitoring and preventing such diseases. We therefore examined gut and oropharynx bacterial composition in these animals in China. RESULTS: Proteobacteria, Firmicutes and Bacteroidetes were the most abundant phyla in faecal and throat swab samples of both animals. However, the composition of the bacterial community differed significantly between sample types and animal species. Firmicutes exhibited the highest relative abundance in throat swab samples of R. norvegicus, followed by Proteobacteria and Bacteroidetes. In throat swab specimens of S. murinus, Proteobacteria was the predominant phylum, followed by Firmicutes and Bacteroidetes. Firmicutes showed the highest relative abundance in faecal specimens of R. norvegicus, followed by Bacteroidetes and Proteobacteria. Firmicutes and Proteobacteria had almost equal abundance in faecal specimens of S. murinus, with Bacteroidetes accounting for only 3.07%. The family Streptococcaceae was most common in throat swab samples of R. norvegicus, while Prevotellaceae was most common in its faecal samples. Pseudomonadaceae was the predominant family in throat swab samples of S. murinus, while Enterobacteriaceae was most common in faecal samples. We annotated 33.28% sequences from faecal samples of S. murinus as potential human pathogenic bacteria, approximately 3.06-fold those in R. norvegicus. Potential pathogenic bacteria annotated in throat swab samples of S. murinus were 1.35-fold those in R. norvegicus. CONCLUSIONS: Bacterial composition of throat swabs and faecal samples from R. norvegicus differed from those of S. murinus. Both species carried various pathogenic bacteria, therefore both should be closely monitored in the future, especially for S. murinus.

Methicillin-resistant Staphylococcus aureus among urban rodents, house shrews, and patients in Guangzhou, Southern China.

BACKGROUND: The transmission of methicillin-resistant Staphylococcus aureus (MRSA) between humans and animals has been identified in a number of countries. In this study, MRSA in urban rodents and shrews in a community was investigated. Further, comparisons of MRSA isolates from rodents, shrews, and humans were conducted to evaluate the relationships of these isolates from different origins. RESULTS: Between 2015 and 2016, 397 oropharynx samples from 212 rodents and 185 shrews, and 8 MRSA isolates from hospital patients were collected. Twelve MRSA were isolated from the small mammals (3.0, 95%CI: 1.3-4.7%), including 11 isolates from rodents and one from a shrew. Three MRSA isolates from Rattus norvegicus were PVL-positive, and seven isolates were IEC-negative (one from Suncus murinus, five from Rattus norvegicus, and one from a patient). The spa type, MLST, and antimicrobial resistance patterns showed that the MRSA retrieved from rodents and shrews are likely related to human strains. CONCLUSION: MRSA derived from rodent shares similar antimicrobial resistance and molecular characteristics to those from humans, suggesting that urban rodents may play as maintenance host or vectors for MRSA which is important to human health.

Viral metagenomics of six bat species in close contact with humans in southern China.

Accumulating studies have shown that bats could harbor various important pathogenic viruses that could be transmitted to humans and other animals. Extensive metagenomic studies of different organs/tissues from bats have revealed a large number of novel or divergent viruses. To elucidate viral diversity and epidemiological and phylogenetic characteristics, six pooled fecal samples from bats were generated (based on bat species and geographic regions characteristic for virome analysis). These contained 500 fecal samples from six bat species, collected in four geographic regions. Metagenomic analysis revealed a plethora of divergent viruses originally found in bats. Multiple contigs from influenza A virus and coronaviruses in bats shared high identity with those from humans, suggesting possible cross-species transmission, whereas a number of contigs, whose sequences were taxonomically classifiable within Alphapapillomavirus, Betaretrovirus, Alpharetrovirus, Varicellovirus, Cyprinivirus, Chlorovirus and Cucumovirus had low identity to viruses in existing databases, which indicated possible evolution of novel viral species. None of the established caliciviruses and picornaviruses were found in the 500 fecal specimens. Papillomaviruses with high amino acid identity were found in Scotophilus kuhlii and Rhinolophus blythi, challenging the hypotheses regarding the strict host specificity and co-evolution of papillomaviruses. Phylogenetic analysis showed that four bat rotavirus A strains might be tentative G3 strains, according to the Rotavirus Classification Working Group classification.

The prevalence and genomic characteristics of hepatitis E virus in murine rodents and house shrews from several regions in China.

BACKGROUND: Urban rodents and house shrews are closely correlated in terms of location with humans and can transmit many pathogens to them. Hepatitis E has been confirmed to be a zoonotic disease. However, the zoonotic potential of rat HEV is still unclear. The aim of this study was to determine the prevalence and genomic characteristics of hepatitis E virus (HEV) in rodents and house shrews. RESULTS: We collected a total of 788 animals from four provinces in China. From the 614 collected murine rodents, 20.19% of the liver tissue samples and 45.76% of the fecal samples were positive for HEV. From the 174 house shrews (Suncus murinus), 5.17% fecal samples and 0.57% liver tissue samples were positive for HEV. All of the HEV sequences obtained in this study belonged to Orthohepevirus C1. However, we observed a lower percentage of identity in the ORF3 region upon comparing the amino acid sequences between Rattus norvegicus and Rattus losea. HEV derived from house shrews shared a high percentage of identity with rat HEV. Notably, the first near full-length of the HEV genome from Rattus losea is described in our study, and we also report the first near full-length rat HEV genomes in Rattus norvegicus from China. CONCLUSION: HEV is prevalent among the three common species of murine rodents (Rattus. norvegicus, Rattus. tanezumi, and Rattus. losea) in China. HEV sequences detected from house shrews were similar to rat HEV sequences. The high identity of HEV from murine rodents and house shrews suggested that HEV can spread among different animal species.

Ungulate bocaparvovirus 4 and rodent bocavirus are different genotypes of the same species of virus.

Bocaviruses are associated with many human infectious diseases, such as respiratory tract infections, gastroenteritis, and hepatitis. Rats are known to be reservoirs of bocaviruses, including rodent bocavirus and rat bocavirus. Recently, ungulate bocaparvovirus 4, a known porcine bocavirus, has also been found in rats. Thus, investigating bocaviruses in rats is important for determining the origin of the viruses and preventing and controlling their transmission. To the best of our knowledge, no study to date has investigated bocaviruses in the livers of rats. In this report, a total of 624 rats were trapped in southern China between 2014 and 2017. Liver and serum samples from rats were tested for the prevalence of bocaviruses using PCR. Sequences related to ungulate bocaparvovirus 4 and rodent bocavirus were detected in both liver and serum samples. Interestingly, the prevalence of ungulate bocaparvovirus 4 (reference strain: KJ622366.1) was higher than that of rodent bocavirus (reference strain: KY927868.1) in both liver (2.24% and 0.64%, respectively) and serum samples (2.19% and 0.44%, respectively). The NS1 regions of ungulate bocaparvovirus 4 and rodent bocavirus related sequences displayed over 84% and 88% identity at the nucleic acid and amino acid levels, respectively. Furthermore, these sequences had similar genomic structure, genomic features, and codon usage bias, and shared a common ancestor. These viruses also displayed greater adaptability to rats than pigs. Our results suggested that ungulate bocaparvovirus 4 and rodent bocavirus may originate from rats and may be different genotypes of the same bocavirus species.

Detection and Genetic Characterization of Seoul Virus in Liver Tissue Samples From Rattus norvegicus and Rattus tanezumi in Urban Areas of Southern China.

Rodents are important hosts of hantaviruses, and lungs and kidneys are known to be the preferred organs of these viruses. Recently, hantaviruses were detected in liver samples from wild rodents in Hungary and the United States, and feeder rats in the Netherlands. However, few studies have detected hantaviruses in the liver of rats from China. In this study, hantaviruses were investigated in liver samples from R. norvegicus and R. tanezumi trapped in urban areas of southern China. A total of 461 R. norvegicus and 64 R. tanezumi were trapped. Using a pan-hantavirus PCR method, hantaviruses were detected in liver, lung, and serum samples from these animals. About 7.43% of liver samples were positive for Seoul virus (SEOV). The detection rate of SEOV in liver samples from R. norvegicus (8.24%) was higher than that from R. tanezumi (1.56%), suggesting the predominant role of R. norvegicus in the transmission of SEOV in urban areas of China. Three R. norvegicus had SEOV RNA in their liver samples but not in their lung samples, suggesting that the liver might be one of the targeted organs of SEOV. The first full SEOV protein-coding sequences (CDS) of the S and M segments, and partial CDS of the L segment from R. tanezumi were amplified. Several full and partial CDS of the S, M, and L segments from R. norvegicus were also obtained. The SEOV sequences obtained from different animals were highly similar, suggesting the cross-species transmission potential of SEOV between R. norvegicus and R. tanezumi.

Risk factors associated with COVID-19 infection: a retrospective cohort study based on contacts tracing.

This study aimed to estimate the attack rates, and identify the risk factors of COVID-19 infection. Based on a retrospective cohort study, we investigated 11,580 contacts of COVID-19 cases in Guangdong Province from 10 January to 15 March 2020. All contacts were tested by RT-PCR to detect their infection of SARS-COV-2. Attack rates by characteristics were calculated. Logistic regression was used to estimate the risk factors of infection for COVID-19. A total of 515 of 11,580 contacts were identified to be infected with SARS-COV-2. Compared to young adults aged 20-29 years, the infected risk was higher in children (RR: 2.59, 95%CI: 1.79-3.76), and old people aged 60-69 years (RR: 5.29, 95%CI: 3.76-7.46). Females also had higher infected risk (RR: 1.66, 95%CI: 1.39-2.00). People having close relationship with index cases encountered higher infected risk (RR for spouse: 20.68, 95%CI: 14.28-29.95; RR for non-spouse family members: 9.55, 95%CI: 6.73-13.55; RR for close relatives: 5.90, 95%CI: 4.06-8.59). Moreover, contacts exposed to index case in symptomatic period (RR: 2.15, 95%CI: 1.67-2.79), with critically severe symptoms (RR: 1.61, 95%CI: 1.00-2.57), with symptoms of dizzy (RR: 1.58, 95%CI: 1.08-2.30), myalgia (RR: 1.49, 95%CI: 1.15-1.94), and chill (RR: 1.42, 95%CI: 1.05-1.92) had higher infected risks. Children, old people, females, and family members are susceptible of COVID-19 infection, while index cases in the incubation period had lower contagiousness. Our findings will be helpful for developing targeted prevention and control strategies to combat the worldwide pandemic.

Optical coherence tomography for the diagnosis of malignant skin tumors: a meta-analysis.

Optical coherence tomography (OCT) is an emergent imaging tool used for noninvasive diagnosis of skin diseases. The present meta-analysis was carried out to assess the accuracy of OCT for the diagnosis of skin cancer. We conducted a systematic literature search though EMBASE, Medline, PubMed, the Cochrane Library, and Web of Science database for relevant articles published up to June 6, 2017. The quality of the included studies was assessed using the QUADAS-2 tool and the Oxford Levels of Evidence Scale. Statistical analyses were conducted using the software Meta-Disc version 1.4 and STATA version 12.0. A total of 14 studies involving more than 813 patients with a total of 1958 lesions were included in our analyses. The pooled sensitivity and specificity of OCT for skin cancer diagnoses were 91.8% and 86.7%, respectively. Subgroup analysis showed that the pooled sensitivities of OCT for detecting basal cell carcinoma (BCC), squamous cell carcinoma (SCC), actinic keratosis, and malignant melanoma were 92.4%, 92.3%, 73.8%, and 81.0%, respectively. The pooled specificities were 86.9%, 99.5%, 91.5%, and 93.8%, respectively. OCT appears to be useful for the detection of BCC and SCC. It is a valuable diagnostic method when screening for early skin cancers.

The risk of human papillomavirus infection for male fertility abnormality: a meta-analysis.

Human papillomavirus (HPV) is the most common sexually transmitted virus in males and females worldwide; yet its impact upon male fertility remains unclear. The objective of this study was to evaluate the potential impact of HPV infection in semen on male fertility abnormality. A systematic literature search was performed in PubMed, Medline, Embase, Web of Science, and the Cochrane Library database for relevant publications up to May 6, 2017. The odds ratio (OR), and its corresponding 95% confidence interval (CI), was selected to represent the effect size. Statistical analysis was conducted using STATA 12.0. In total, eight articles, providing data on 1955 participants, were included in this meta-analysis. Collectively, the data suggested that HPV infection of semen was a risk factor for male fertility abnormality with an OR of 3.02 (95% CI: 2.11-4.32; I2 = 6.9%). Sensitivity analysis revealed that the results of this study were robust. In conclusion, HPV infection of semen represents a risk factor for male fertility abnormality.