Clinical characteristics of 310 SARS-CoV-2 Omicron variant patients and comparison with Delta and Beta variant patients in China

Although the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has spread, data on the clinical characteristics of infected patients are limited. In this study, the demographic, clinical characteristics, and laboratory data of 310 SARS-CoV-2 Omicron variant patients treated at Haihe Hospital of Tianjin were collected and analyzed. Information on these patients was compared to 96 patients with the Delta variant of concern (VOC) and 326 patients with the Beta VOC during the previous coronavirus disease 2019 (COVID-19) outbreak in Harbin. Of the 310 patients infected with the Omicron variant, the median age was 35 years. Most patients were clinically classified as mild (57.74%), and the most common symptoms were cough (48.71%), fever (39.35%), and sore throat (38.26%). The results for different vaccination groups in the Omicron group showed that the median of “SARS-CoV-2 specific IgG” after 2 or 3 doses of vaccination was higher than the unvaccinated group (all Ps < 0.05). Older age was associated with a higher proportion of moderate cases and lower asymptomatic and mild cases based on clinical classifications. Compared to the Delta and Beta groups, the median age of the Omicron group was younger. The total number of asymptomatic patients and mild patients in the Omicron virus group was higher than the Delta and Beta groups (60.97% vs. 54.17% vs. 47.55%). This study presented the clinical characteristics of the first group of patients infected with the Omicron variant in Tianjin, China, and compared their clinical features with patients infected by the Delta and Beta variants, which would increase our understanding of the characteristics of SARS-CoV-2 Omicron variant.     

COVID-19: Omicron – the latest,the least virulent,but probably not the last variant of concern of SARS-CoV-2

The Omicron variant rapidly became the dominant SARS-CoV-2 strain in South Africa and elsewhere. This review explores whether this rise was due to an increased transmission of the variant or its escape from population immunity by an extensively mutated spike protein. The mutations affected the structure of the spike protein leading to the loss of neutralization by most, but not all, therapeutic monoclonal antibodies. Omicron also shows substantial immune escape from serum antibodies in convalescent patients and vaccinees. A booster immunization increased, however, the titre and breadth of antiviral antibody response. The cellular immune response against Omicron was largely preserved explaining a satisfying protection of boosted vaccinees against severe infections. Clinicians observed less severe infection with Omicron, but other scientists warned that this must not necessarily reflect less intrinsic virulence. However, in animal experiments with mice and hamsters, Omicron infections also displayed a lesser virulence than previous VOCs and lung functions were less compromised. Cell biologists demonstrated that Omicron differs from Delta by preferring the endocytic pathway for cell entry over fusion with the plasma membrane which might explain Omicron’s distinct replication along the respiratory tract compared with Delta. Omicron represents a distinct evolutionary lineage that deviated from the mainstream of evolving SARS-CoV-2 already in mid-2020 raising questions about where it circulated before getting widespread in December 2021. The role of Omicron for the future trajectory of the COVID-19 pandemic is discussed.     

Respiratory Syncytial Virus (RSV) RNA loads in peripheral blood correlates with disease severity in mice

Background

Respiratory Syncytial Virus (RSV) infection is usually restricted to the respiratory epithelium. Few studies have documented the presence of RSV in the systemic circulation, however there is no consistent information whether virus detection in the blood correlates with disease severity.

Methods

Balb/c mice were inoculated with live RSV, heat-inactivated RSV or medium. A subset of RSV-infected mice was treated with anti-RSV antibody 72 h post-inoculation. RSV RNA loads were measured by PCR in peripheral blood from day 1-21 post-inoculation and were correlated with upper and lower respiratory tract viral loads, the systemic cytokine response, lung inflammation and pulmonary function. Immunohistochemical staining was used to define the localization of RSV antigens in the respiratory tract and peripheral blood.

Results

RSV RNA loads were detected in peripheral blood from day 1 to 14 post-inoculation, peaked on day 5 and significantly correlated with nasal and lung RSV loads, airway obstruction, and blood CCL2 and CXCL1 expression. Treatment with anti-RSV antibody reduced blood RSV RNA loads and improved airway obstruction. Immunostaining identified RSV antigens in alveolar macrophages and peripheral blood monocytes.

Conclusions

RSV RNA was detected in peripheral blood upon infection with live RSV, followed a time-course parallel to viral loads assessed in the respiratory tract and was significantly correlated with RSV-induced airway disease.     

High Human Bocavirus Viral Load Is Associated with Disease Severity in Children under Five Years of Age

Human bocavirus (HBoV) is a parvovirus and detected worldwide in lower respiratory tract infections (LRTIs), but its pathogenic role in respiratory illness is still debatable due to high incidence of co-infection with other respiratory viruses. To determine the prevalence of HBoV infection in patients with LRTI in Shanghai and its correlation with disease severity, we performed a 3-year prospective study of HBoV in healthy controls, outpatients and inpatients under five years of age with X-ray diagnosed LRTIs. Nasopharyngeal aspirates were tested by PCR for common respiratory viruses and by real time PCR for HBoV subtypes 1–4. Nasopharyngeal swabs from healthy controls and serum samples and stools from inpatients were also tested for HBoV1-4 by real time PCR. Viral loads were determined by quantitative real time PCR in all HBoV positive samples. HBoV1 was detected in 7.0% of inpatients, with annual rates of 5.1%, 8.0% and 4.8% in 2010, 2011 and 2012, respectively. Respiratory syncytial virus (RSV) subtype A was the most frequent co-infection detected; HBoV1 and RSVA appeared to co-circulate with similar seasonal variations. High HBoV viral loads (>10⁶ copies/ml) were significantly more frequent in inpatients and outpatients than in healthy controls. There was a direct correlation of high viral load with increasing disease severity in patients co-infected with HBoV1 and at least one other respiratory virus. In summary, our data suggest that HBoV1 can cause LRTIs, but symptomatic HBoV infection is only observed in the context of high viral load.     

Continued antigenic variation of highly pathogenic avian influenza A (H7N9) virus in laying hens in China, 2020–2021

Highlights
1. 13 strains of H7N9 viruses from laying hens in 2020 and 2021 were identified.
2. H7N9 viruses in China comprised at least 11 genotypes.
3. H7N9 viruses are high pathogenic in chickens, not in ducks.
4. The most H7N9 viruses cross-reacted poorly with H7-Re3 antiserum.
5. The H7-Re3 vaccine was unable to prevent H7N9 infection.     

Severe acute hepatitis in children with unknown aetiology,etiology analysis and the next action

Highlights
1. MIS-C and severe acute hepatitis might share the common pathogenic mechanism;
2. SARS-CoV-2 persistence throughout multiorgan and tissues;
3. Relationship between COVID-19 vaccines and severe acute hepatitis worth investigating.     

Congenital cytomegalovirus infection and advances in murine models of neuropathogenesis

Highlights
· Congenital human cytomegalovirus (CMV) infection causes severe neuropathogenesis.
· Murine CMV failed to break through the placental barrier to transmit to fetus.
· Zhou et al. established a novel mouse system to model congenital HCMV infection.
· The mouse CMV system by Zhou et al can be used for drug screening.     

Development of stable,cold-adapted,temperature-sensitive/conditional lethal chimeric enterovirus A71 and coxsackievirus A16

Highlights
1 A stable EV-A71 virus vector was created to generate chimeric enterovirus strains expressing capsid protein genes of EV-A71 subgenogroup C5 and CA16.
2 Phenotypic and genetic stability of the generated chimeric EV-A71 and CA16 were analyzed.
3 The amino acids at the cleavage site between VP1 and 2A is crucial for stability.     

Screening for arboviruses in healthy blood donors: Experience from Karachi,Pakistan

Highlights:
1 Potential transfusion-related transmission of DENV, WNV and JEV was investigated in healthy blood donors from the blood bank of Aga Khan University during July to December 2018.
2 ELISA for DENV, WNV and JEV IgM antibodies and RT-PCR for viral RNA detection were performed.
3 Of the 360 blood donors screened, IgM antibodies for DENV and WNV were positive in 3.9% and JEV in 0.28% respectively while none of the blood donors tested positive for RT-PCR.
4 Majority of the seropositive donors were between 19 to 30 years of age and residents of urban areas, mainly from Karachi City.
5 DENV and WNV seropositivity were significantly associated with residence in Malir District of Karachi.     

HCV 6a was expanding and became the predominant subtype among blood donors between 2004 and 2019 in Guangdong,China

Highlights
1. Currently, HCV 6a has replaced 1b as the most prevalent subtype in blood donors in Guangdong.
2. HCV 6a was the predominant subtype in males and older donors, while 1b predominated in females and younger donors.
3. HCV 6a may expand from Guangdong to other districts of China, and is worthy of attention     

Identification of a novel hepacivirus in Mongolian gerbil (Meriones unguiculatus) from Shaanxi,China

Highlights:
1. The first hepacivirus detected in Mongolian gerbils from a plague zones in China.
2. A novel hepacivirus closely related to hepacivirus E and F.
3. Mongolian gerbils could be a potential animal model for hepacivirus pathogenicity.
4. Extending the genetic diversity and host range of hepaciviruses.     

Development of functional antibodies against influenza B virus by activation-induced cytidine deaminase in hybridoma cells

Highlights
1. Class-switch recombination was mimicked in hybridomas through a controllable expression system of activation-induced cytidine deaminase.
2. IgG antibodies were generated through this system in an anti-Flu B IgM hybridoma 7G1.
3. IgG1 and IgG2a subtypes of 7G1 present improved antiviral activity in vitro and in vivo.     

New discovery of high-affinity SARS-CoV-2 spike S2 protein binding peptide selected by PhIP-Seq

Highlights
1 A peptide Spep-1 targeting S2 of SARS-CoV-2 spike protein was selected by PhIP-Seq.
2 Spep-1 showed nanomolar affinity and high specificity to spike protein.
3 S-1 based immunoassay can detect femtomolar spike antigen in spiked serum samples.
4 Spep-1 can be used in future on S2 recognition, virus tracing and drug delivery.     

Cigarette smoke-promoted acquisition of bacterial pathogens in the upper respiratory tract leads to enhanced inflammation in mice

Background

Bacterial colonization and recurrent infections of the respiratory tract contribute to the progression of chronic obstructive pulmonary disease (COPD). There is evidence that exacerbations of COPD are provoked by new bacterial strains acquired from the environment. Using a murine model of colonization, we examined whether chronic exposure to cigarette smoke (CS) promotes nasopharyngeal colonization with typical lung pathogens and whether colonization is linked to inflammation in the respiratory tract.

Methods

C57BL/6 N mice were chronically exposed to CS. The upper airways of mice were colonized with nontypeable Haemophilus influenzae (NTHi) or Streptococcus pneumoniae. Bacterial colonization was determined in the upper respiratory tract and lung tissue. Inflammatory cells and cytokines were determined in lavage fluids. RT-PCR was performed for inflammatory mediators.

Results

Chronic CS exposure resulted in significantly increased numbers of viable NTHi in the upper airways, whereas NTHi only marginally colonized air-exposed mice. Colonization with S. pneumoniae was enhanced in the upper respiratory tract of CS-exposed mice and was accompanied by increased translocation of S. pneumoniae into the lung. Bacterial colonization levels were associated with increased concentrations of inflammatory mediators and the number of immune cells in lavage fluids of the upper respiratory tract and the lung. Phagocytosis activity was reduced in whole blood granulocytes and monocytes of CS-exposed mice.

Conclusions

These findings demonstrate that exposure to CS impacts the ability of the host to control bacterial colonization of the upper airways, resulting in enhanced inflammation and susceptibility of the host to pathogens migrating into the lung.     

Emergence of H5N8 avian influenza virus in domestic geese in a wild bird habitat,Yishui Lake,north central China

Highlights
1. H5N8 viruses emerged in the wild bird habitat at Yishui Lake.
2. The homology between HG12 and a Russian human strain was over 99%.
3. HG12 can be transmitted through direct contact between guinea pigs.     

A method for the synthesis of C-(2-deoxy-β-glycosyl) arenes

Full-size image

(2) was converted by a Wittig reaction into a mixture of (

Full-size image

(4,5). Selective deprotection of the 5,6-O-isopropylidene group in compounds 4 and 5 followed by selective silylation at position 6 afforded the separate

Full-size image

8a–d and the corresponding E-isomers (9a–d). Iodonium-ion-induced cyclization of compounds 8c and 9a-c furnished stereoselectively the

Full-size image

10a–c. Full deprotection of compounds 10a–c and the O-acetylation led to compounds 11a–c, which on treatment with tributyltin hydride-azobisisobutyromnitrile yielded and the title compounds (12a–c).     

Segregation of virulent influenza A(H1N1) variants in the lower respiratory tract of critically ill patients during the 2010-2011 seasonal epidemic

Background

Since its appearance in 2009, the pandemic influenza A(H1N1) virus circulated worldwide causing several severe infections.

Methods

Respiratory samples from patients with 2009 influenza A(H1N1) and acute respiratory distress attending 24 intensive care units (ICUs) as well as from patients with lower respiratory tract infections not requiring ICU admission and community upper respiratory tract infections in the Lombardy region (10 million inhabitants) of Italy during the 2010–2011 winter-spring season, were analyzed.

Results

In patients with severe ILI, the viral load was higher in bronchoalveolar lavage (BAL) with respect to nasal swab (NS), (p<0.001) suggesting a higher virus replication in the lower respiratory tract. Four distinct virus clusters (referred to as cluster A to D) circulated simultaneously. Most (72.7%, n = 48) of the 66 patients infected with viruses belonging to cluster A had a severe (n = 26) or moderate ILI (n = 22). Amino acid mutations (V26I, I116M, A186T, D187Y, D222G/N, M257I, S263F, I286L/M, and N473D) were observed only in patients with severe ILI. D222G/N variants were detected exclusively in BAL samples.

Conclusions

Multiple virus clusters co-circulated during the 2010–2011 winter-spring season. Severe or moderate ILI were associated with specific 2009 influenza A(H1N1) variants, which replicated preferentially in the lower respiratory tract.     

Genetic characterization and pathogenicity of a reassortant Eurasian avian-like H1N1 swine influenza virus containing an internal gene cassette from 2009 pandemic H1N1 virus

Highlights
1. Identification of a reassortant EA H1N1 SIV (SD/18) which isolated from a pig farm in Shandong, north China.
2. Phylogenetic analysis showed that SD/18 virus containing a complete internal gene cassette from pdm/09 virus.
3. The results of pathogenicity in mice showed that the mortality rate of SD/18 virus in mice could reach 100%.
4. The potential risk of EA lineage SIVs to humans is very high and we need to pay enough attention to the different reassortant EA H1N1 viruses.     

Development of rapid nucleic acid assays based on the recombinant polymerase amplification for monkeypox virus

Highlights
1. Two RPA methods (F-RPA and VF- RPA) have been developed for monkeypox virus rapid detection.
2. The limit of detection was 15.32 copies/μL for F-RPA and 8.53 copies/μL for VF-RPA,
3. No cross-reaction was found in 14 rash and fever-associated viruses.
4. The two RPA methods developed are simple and rapid, making them potentially useful for detection of MPXV in the field/clinic.