Characterization and antiviral susceptibility of SARS-CoV-2 Omicron BA.2.

The recent emergence of SARS-CoV-2 Omicron (B.1.1.529 lineage) variants possessing numerous mutations has raised concerns of decreased effectiveness of current vaccines, therapeutic monoclonal antibodies and antiviral drugs for COVID-19 against these variants1,2. The original Omicron lineage, BA.1, prevailed in many countries, but more recently, BA.2 has become dominant in at least 68 countries3. Here we evaluated the replicative ability and pathogenicity of authentic infectious BA.2 isolates in immunocompetent and human ACE2-expressing mice and hamsters. In contrast to recent data with chimeric, recombinant SARS-CoV-2 strains expressing the spike proteins of BA.1 and BA.2 on an ancestral WK-521 backbone4, we observed similar infectivity and pathogenicity in mice and hamsters for BA.2 and BA.1, and less pathogenicity compared with early SARS-CoV-2 strains. We also observed a marked and significant reduction in the neutralizing activity of plasma from individuals who had recovered from COVID-19 and vaccine recipients against BA.2 compared to ancestral and Delta variant strains. In addition, we found that some therapeutic monoclonal antibodies (REGN10987 plus REGN10933, COV2-2196 plus COV2-2130, and S309) and antiviral drugs (molnupiravir, nirmatrelvir and S-217622) can restrict viral infection in the respiratory organs of BA.2-infected hamsters. These findings suggest that the replication and pathogenicity of BA.2 is similar to that of BA.1 in rodents and that several therapeutic monoclonal antibodies and antiviral compounds are effective against Omicron BA.2 variants.

Seroprevalence of severe acute respiratory syndrome coronavirus 2 N antibodies between December 2021 and march 2023 in Japan.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 in China and rapidly spread worldwide, leading to a pandemic. The threat of SARS-CoV-2 is subsiding as most people have acquired sufficient antibodies through vaccination and/or infection to prevent severe COVID-19. After the emergence of the omicron variants, the seroprevalence of antibodies against the N protein elicited by SARS-CoV-2 infection ranged from 44.4% to 80.2% in countries other than Japan. Here, we assessed the seroprevalence in Japan before and after the appearance of omicron variants. Serosurveillance of antibodies against N was conducted between December 2021 and March 2023 in Japan. In total, 7604 and 3354 residual serum or plasma samples were collected in the Tokyo metropolitan area and Sapporo, respectively. We found that the seroprevalence in representative regions of Japan increased approximately 3% to 23% after the emergence of the omicron variants. We also found higher seroprevalence among the young compared with the elderly. Our findings indicate that unlike other countries, most of the Japanese population has not been infected, raising the possibility of future SARS-CoV-2 epidemics in Japan.

Characterization of a new SARS-CoV-2 variant that emerged in Brazil.

The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a key role in viral infectivity. It is also the major antigen stimulating the host's protective immune response, specifically, the production of neutralizing antibodies. Recently, a new variant of SARS-CoV-2 possessing multiple mutations in the S protein, designated P.1, emerged in Brazil. Here, we characterized a P.1 variant isolated in Japan by using Syrian hamsters, a well-established small animal model for the study of SARS-CoV-2 disease (COVID-19). In hamsters, the variant showed replicative abilities and pathogenicity similar to those of early and contemporary strains (i.e., SARS-CoV-2 bearing aspartic acid [D] or glycine [G] at position 614 of the S protein). Sera and/or plasma from convalescent patients and BNT162b2 messenger RNA vaccinees showed comparable neutralization titers across the P.1 variant, S-614D, and S-614G strains. In contrast, the S-614D and S-614G strains were less well recognized than the P.1 variant by serum from a P.1-infected patient. Prior infection with S-614D or S-614G strains efficiently prevented the replication of the P.1 variant in the lower respiratory tract of hamsters upon reinfection. In addition, passive transfer of neutralizing antibodies to hamsters infected with the P.1 variant or the S-614G strain led to reduced virus replication in the lower respiratory tract. However, the effect was less pronounced against the P.1 variant than the S-614G strain. These findings suggest that the P.1 variant may be somewhat antigenically different from the early and contemporary strains of SARS-CoV-2.

[Analysis of anti-SARS-CoV-2 IgG antibody titers after mRNA booster vaccination in patients with nonmalignant hematological disorders].

In our facility, anti-SARS-CoV-2 mRNA vaccines were given to 21 patients, including 8 with aplastic anemia (AA), 3 with pure red cell aplasia (PRCA), and 10 with immune thrombocytopenic purpura (ITP), and IgG antibody titers were assessed one month after vaccinations. After receiving both a second vaccine and a booster shot, all patients with AA/PRCA treated with cyclosporine A aside from one, had IgG titers that were lower than the median levels of healthy controls. Even if prednisolone (PSL) doses did not go over 10 mg/day, ITP patients receiving PSL therapy were unable to achieve adequate levels of IgG after booster immunizations.

Age-Stratified Seroprevalence of SARS-CoV-2 Antibodies before and during the Vaccination Era, Japan, February 2020-March 2022.

Japan has reported a relatively small number of COVID-19 cases. Because not all infected persons receive diagnostic tests for COVID-19, the reported number must be lower than the actual number of infections. We assessed SARS-CoV-2 seroprevalence by analyzing >60,000 samples collected in Japan (Tokyo Metropolitan Area and Hokkaido Prefecture) during February 2020-March 2022. The results showed that ≈3.8% of the population had become seropositive by January 2021. The seroprevalence increased with the administration of vaccinations; however, among the elderly, seroprevalence was not as high as the vaccination rate. Among children, who were not eligible for vaccination, infection was spread during the epidemic waves caused by the SARS-CoV-2 Delta and Omicron variants. Nevertheless, seroprevalence for unvaccinated children <5 years of age was as low as 10% as of March 2022. Our study underscores the low incidence of SARS-CoV-2 infection in Japan and the effects of vaccination on immunity at the population level.

[SARS-CoV2 anti-spike IgG response following COVID-19 mRNA vaccination (BNT162b2) in patients with hematological disorders].

This is a prospective study conducted to determine the level of anti-spike IgG to SARS-CoV-2 2-6 weeks following the BNT162b2 vaccination in 125 patients with hematological disorders. Compared with healthy controls, patients with malignant lymphoma had lower rates of seropositivity and lower levels of antibody titer. Furthermore, patients who received rituximab (R)-containing chemotherapy had lower antibody titers than those who were not treated with R or who had completed R-containing chemotherapy more than 9 months earlier. Despite having 71% IgG-seropositivity, patients with multiple myeloma had lower antibody titers than the control group. Furthermore, patients receiving daratumumab-containing chemotherapy had lower antibody titers than those not receiving treatment. Moreover, patients with acute myeloid leukemia or myelodysplastic syndrome had lower antibody titers than the control group. Overall, the number of peripheral blood lymphocytes was significantly correlated with IgG titers, with seropositive patients having more peripheral blood lymphocytes than seronegative patients. Patients with severe immunosuppression, such as those with hematological disorders, often have impaired seroconversion with COVID-19 vaccination that should be taken into consideration by clinicians.

Epidemiology of macrolide-resistant Mycoplasma pneumoniae by age distribution in Japan.

INTRODUCTION: Mycoplasma pneumoniae (M. pneumoniae) is the major pathogen involved in community-acquired pneumonia in all age groups. Resistance to macrolides, the first-line treatment for M. pneumoniae infection, is a major global public health concern. However, studies evaluating macrolide-resistant M. pneumoniae infection simultaneously in all ages are limited. This study aimed to determine the prevalence and clinical characteristics of macrolide-resistant M. pneumoniae infection in terms of age distribution. METHODS: We enrolled 292 patients in Tokyo, Japan, who visited Eiju General Hospital or Zama Children's Clinic in 2015-2016. Patients were tested using real-time PCR for M. pneumoniae DNA. PCR-positive patients (n = 151) were further selected and sequentially divided into preschool-aged children (≤5 years, n = 31), school-aged children (6-15 years, n = 101), adolescents (16-19 years, n = 5), and adults (≥20 years, n = 14). We then analyzed the M. pneumoniae infection clinical characteristics, prevalence of macrolide-resistant infection, and 23S rRNA domain V resistance-associated mutation status. RESULTS: We found insignificant differences in the prevalence of macrolide-resistant M. pneumoniae infection among all groups, clinical characteristics, and resistance-associated mutation status in patients with macrolide-resistant M. pneumoniae infection. We also found statistically higher prevalence of mutation-positive (n = 85) M. pneumoniae in patients previously treated with macrolide compared to the mutation-negative group (n = 66); 63.8% vs 11.1% (p < 0.001), respectively. CONCLUSIONS: We found no significant differences in both clinical characteristics and prevalence of macrolide-resistant M. pneumoniae infection among all ages. Also, previous macrolide treatment contributes to drug-resistance.

Clinical usefulness of a rapid molecular assay, ID NOW™ influenza A & B 2, in adults.

INTRODUCTION: ID NOW™ Influenza A & B 2 (ID NOW 2) is a rapid molecular assay that combines two characteristics, namely the rapidness of rapid antigen detection test (RADT) and the high sensitivity of molecular assay. METHODS: The clinical performance of ID NOW 2 compared with real-time RT-PCR was evaluated in adults. RESULTS: The sensitivity of ID NOW 2 over multiple seasons from 2016/2017 to 2019/2020 was 97.3% (95% CI: 90.7-99.7) for Type A, 100% (95% CI: 81.9-100) for Type B, and 97.8% (95% CI: 92.2-99.7) for influenza (Type A + Type B), and it was significantly higher than the sensitivity of RADT, which was 80.0% (95% CI: 69.2-88.4) for Type A, 73.3% (95% CI: 44.9-92.2) for Type B, and 78.9% (95% CI: 69.0-86.8) for influenza. The sensitivity of RADT tended to be lower in patients in the particularly early period, within 12 h from disease onset; however, the sensitivity of ID NOW 2 remained high, increasing the difference between the sensitivity of RADT and ID NOW 2. The viral loads were low within 12 h from onset, and it was considered this affected the sensitivity of RADT due to its low analytical sensitivity. The specificity of ID NOW 2 was 98% or greater in all groups. CONCLUSIONS: Since ID NOW 2 has a high sensitivity and specificity in adults, it is anticipated to be used in clinical practice, particularly in patients who require early and accurate diagnosis.

Clinical evaluation of ID NOW influenza A & B 2, a rapid influenza virus detection kit using isothermal nucleic acid amplification technology - A comparison with currently available tests.

In this study, we evaluated the performance of ID NOW Influenza A & B 2 (ID NOW 2), a rapid molecular point-of-care test for influenza within 13 min, in comparison with currently available tests. A total of 254 nasopharyngeal swabs (NPS) and 271 nasopharyngeal aspirates (NPA) collected from 373 children and 152 adults with influenza-like illness were tested using ID NOW 2, viral culture, rapid antigen detection test, and loop-mediated isothermal amplification test to evaluate the sensitivity and specificity compared with real-time reverse transcription polymerase chain reaction as the reference method. The sensitivities of ID NOW 2 for influenza A were 95.9% and 95.7% in NPS and NPA, respectively, and for influenza B were 100% and 98.7% in NPS and NPA, respectively. The specificity was 100% for both influenza A and influenza B in NPS and NPA. Sensitivity of each test method reflected the difference of analytical sensitivity among the tests, and ID NOW 2 was not affected by time after illness onset and patient age. In conclusion, ID NOW 2 demonstrated a high sensitivity and specificity that is useful for diagnosis of influenza in the clinical setting and infection control.

[Analysis of anti-SARS-CoV-2 IgG antibodies in hematologic patients with asymptomatic or mildly symptomatic COVID-19 infections].

At our institution, an outbreak of hospital-acquired coronavirus infection (COVID-19) occurred in the hematology department. We used immunochromatography to examine the anti-COVID-19 IgG antibody level in 10 COVID-19 positive patients who exhibited little or no symptoms. Six patients were negative for IgG antibody at an average of 26 days (range: 11-39 days) after the COVID-19 diagnosis. Among them, two had been negative on PCR twice and were discharged but subsequently became positive on PCR 2-4 weeks later and developed pneumonia. These patients were also positive for IgG antibody after the confirmed diagnosis based on PCR accompanied with the development of pneumonia. Our findings suggest an immune response delay to COVID-19 in immunocompromised patients, such as those with hematologic disorders. Thus, follow-up examinations with antibody testing are important in these patients.

Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019.

In 2019, influenza A(H3N2) viruses carrying an I38T substitution in the polymerase acidic gene, which confers reduced susceptibility to baloxavir, were detected in Japan in an infant without baloxavir exposure and a baloxavir-treated sibling. These viruses' whole-genome sequences were identical, indicating human-to-human transmission. Influenza virus isolates should be monitored for baloxavir susceptibility.

Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019.

In January 2019, two influenza A(H3N2) viruses carrying an I38T substitution in the polymerase acidic subunit (PA), which confers reduced susceptibility to baloxavir, were detected from epidemiologically unrelated hospitalised children in Japan. The viruses exhibited reduced susceptibility to baloxavir but were susceptible to neuraminidase inhibitors. Only one of the two children had been treated with baloxavir. An epidemiological analysis suggests possible transmission of the PA I38T mutant A(H3N2) virus among humans.

Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018.

The novel cap-dependent endonuclease inhibitor baloxavir marboxil was approved for the treatment of influenza virus infection in Japan in February 2018. Two influenza A(H3N2) viruses carrying an I38T substitution in the polymerase acidic subunit (PA) were detected in baloxavir-treated children in December 2018. This mutation is known to confer reduced susceptibility to baloxavir, and the two mutant viruses exhibited 76- and 120-fold reduced susceptibility to baloxavir.

Trivalent inactivated influenza vaccine effective against influenza A(H3N2) variant viruses in children during the 2014/15 season, Japan.

The 2014/15 influenza season in Japan was characterised by predominant influenza A(H3N2) activity; 99% of influenza A viruses detected were A(H3N2). Subclade 3C.2a viruses were the major epidemic A(H3N2) viruses, and were genetically distinct from A/New York/39/2012(H3N2) of 2014/15 vaccine strain in Japan, which was classified as clade 3C.1. We assessed vaccine effectiveness (VE) of inactivated influenza vaccine (IIV) in children aged 6 months to 15 years by test-negative case-control design based on influenza rapid diagnostic test. Between November 2014 and March 2015, a total of 3,752 children were enrolled: 1,633 tested positive for influenza A and 42 for influenza B, and 2,077 tested negative. Adjusted VE was 38% (95% confidence intervals (CI): 28 to 46) against influenza virus infection overall, 37% (95% CI: 27 to 45) against influenza A, and 47% (95% CI: -2 to 73) against influenza B. However, IIV was not statistically significantly effective against influenza A in infants aged 6 to 11 months or adolescents aged 13 to 15 years. VE in preventing hospitalisation for influenza A infection was 55% (95% CI: 42 to 64). Trivalent IIV that included A/New York/39/2012(H3N2) was effective against drifted influenza A(H3N2) virus, although vaccine mismatch resulted in low VE.

In vitro and in vivo characterization of new swine-origin H1N1 influenza viruses.

Influenza A viruses cause recurrent outbreaks at local or global scale with potentially severe consequences for human health and the global economy. Recently, a new strain of influenza A virus was detected that causes disease in and transmits among humans, probably owing to little or no pre-existing immunity to the new strain. On 11 June 2009 the World Health Organization declared that the infections caused by the new strain had reached pandemic proportion. Characterized as an influenza A virus of the H1N1 subtype, the genomic segments of the new strain were most closely related to swine viruses. Most human infections with swine-origin H1N1 influenza viruses (S-OIVs) seem to be mild; however, a substantial number of hospitalized individuals do not have underlying health issues, attesting to the pathogenic potential of S-OIVs. To achieve a better assessment of the risk posed by the new virus, we characterized one of the first US S-OIV isolates, A/California/04/09 (H1N1; hereafter referred to as CA04), as well as several other S-OIV isolates, in vitro and in vivo. In mice and ferrets, CA04 and other S-OIV isolates tested replicate more efficiently than a currently circulating human H1N1 virus. In addition, CA04 replicates efficiently in non-human primates, causes more severe pathological lesions in the lungs of infected mice, ferrets and non-human primates than a currently circulating human H1N1 virus, and transmits among ferrets. In specific-pathogen-free miniature pigs, CA04 replicates without clinical symptoms. The assessment of human sera from different age groups suggests that infection with human H1N1 viruses antigenically closely related to viruses circulating in 1918 confers neutralizing antibody activity to CA04. Finally, we show that CA04 is sensitive to approved and experimental antiviral drugs, suggesting that these compounds could function as a first line of defence against the recently declared S-OIV pandemic.

Evaluation of new immunochromatographic assay kit for adenovirus detection in throat swab: comparison with culture and real-time PCR results.

A new immunochromatographic (IC) assay kit, BD Veritor System Adeno was evaluated to comparing with commercial available kit, BD Adeno Examan, cell culture, and real-time PCR using throat swab samples. Specimens were collected from 146 pediatric patients between July 2011 and January 2012. Mean age of patients was 4 years (8 months-15 years old). Patients were diagnosed with pharyngitis (n = 67), tonsillitis (n = 45), pharyngoconjunctival fever (n = 26), upper respiratory tract infection (n = 6), conjunctivitis (n = 1), or bronchitis (n = 1). Thirty-one of the patients (21.2%) had more than one disease. Among all samples, 61 (41.8%) were positive for adenovirus with BD Veritor System Adeno; 68 (46.6%) with BD Adeno Examan; 63 (43.2%) with real-time PCR; and 65 (44.5%) with cell culture. Serotype 3 (n = 41; 63.1%) was predominant among the 65 adenovirus isolates, followed by serotype 2 (n = 12; 18.5%), 1 (n = 6; 9.2%), 5 (n = 4; 6.2%), and 4 (n = 2; 3.1%). Relative sensitivity and specificity of BD Veritor System Adeno, BD Adeno Examan, and real-time PCR were 93.8% and 98.7%, 96.9% and 93.8%, and 96.9% and 100%, respectively. Positive predictive and negative predictive values for these methods were 98.4% and 95.1%, 92.6% and 97.4%, and 100% and 97.6%, respectively. The sensitivity and specificity of real-time PCR was greater than that of IC assay kits. However, IC assay kits also showed high sensitivity and specificity appropriate for clinical use.

Clinical Evaluation of the Accuracy of the Panbio™ COVID-19/Flu A&B Rapid Panel: A Combination Antigen Rapid Diagnostic Test for the Omicron Variant and Influenza A Virus.

It is difficult to differentiate between coronavirus disease 2019 (COVID-19) and influenza based on the symptoms. In the present study, a newly developed antigen rapid diagnostic test (Ag-RDT) called Panbio™ COVID-19/Flu A&B that can simultaneously detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A/B virus was evaluated. Its accuracy was evaluated using 235 pairs of nasopharyngeal samples collected from patients with respiratory symptoms and fever (>37.5°C). Reverse transcription polymerase chain reaction was used as a reference method to evaluate the accuracy of the SARS-CoV-2 detection. We confirmed the accuracy of the developed Ag-RDT against the Omicron variant where the sensitivity and specificity were 94.8% and 100%, respectively. In addition, to identify the influenza A virus, a noninferiority test was conducted using a commercial Ag-RDT, which has a sensitivity and specificity in comparison with viral culture of 94.8% and 98.4%, respectively. The positive and negative predictive values for influenza A virus were 98.5% and 98.1%, respectively, for the Panbio COVID-19/Flu A&B test. The evaluation of this newly developed Ag-RDT using clinical samples suggests that it has a high efficacy in clinical settings.

Evaluation of a new immunochromatographic assay for rapid identification of influenza A, B, and A(H1N1)2009 viruses.

We evaluated Clearline Influenza A/B/(H1N1)2009, a new multi-line immunochromatographic assay for rapid detection of antigens of influenza A (Flu A), B (Flu B), and A(H1N1)2009 viruses. Clearline detected Flu A, Flu B, and A(H1N1)2009 viruses with a detection limit of 4.6 × 10(3) to 7.5 × 10(4) pfu/assay. The sensitivity and specificity of detection of influenza virus by Clearline, using RT-PCR as reference standard, were determined for A(H1N1)2009, Flu A, and Flu B, in nasopharyngeal aspirate, nasopharyngeal swab, and self-blown nasal discharge specimens. Sensitivity for nasopharyngeal aspirate specimens was: A(H1N1)2009 = 97.3 %, Flu A = 94.5 %, and Flu B = 96.8 %, and specificity was Flu A = 99.1 % and Flu B = 100 %. Sensitivity for nasopharyngeal swab specimens was: A(H1N1)2009 = 91.9 %, Flu A = 92.8 %, and Flu B = 100 %, and specificity was Flu A = 98.2 % and Flu B = 100 %. Sensitivity for self-blown nasal discharge specimens was: A(H1N1)2009 = 75.7 %, Flu A = 86.5 %, and Flu B = 76.2 %, and specificity was Flu A = 98.4 % and Flu B = 100 %. Sensitivity and specificity of Clearline were sufficient for nasopharyngeal aspirate and swab specimens. For self-blown nasal discharge specimens, sensitivity was lower than for nasopharyngeal aspirates and nasopharyngeal swabs. The sensitivity of Clearline for A(H1N1)2009 was good even 6 h after the onset of symptoms. These findings suggest that Clearline may be useful for early clinical diagnosis of influenza.

Multi-omics of NET formation and correlations with CNDP1, PSPB, and L-cystine levels in severe and mild COVID-19 infections.

The detailed mechanisms of COVID-19 infection pathology remain poorly understood. To improve our understanding of SARS-CoV-2 pathology, we performed a multi-omics and correlative analysis of an immunologically naïve SARS-CoV-2 clinical cohort from blood plasma of uninfected controls, mild, and severe infections. Consistent with previous observations, severe patient populations showed an elevation of pulmonary surfactant levels. Intriguingly, mild patients showed a statistically significant elevation in the carnosine dipeptidase modifying enzyme (CNDP1). Mild and severe patient populations showed a strong elevation in the metabolite L-cystine (oxidized form of the amino acid cysteine) and enzymes with roles in glutathione metabolism. Neutrophil extracellular traps (NETs) were observed in both mild and severe populations, and NET formation was higher in severe vs. mild samples. Our correlative analysis suggests a potential protective role for CNDP1 in suppressing PSPB release from the pulmonary space whereas NET formation correlates with increased PSPB levels and disease severity. In our discussion we put forward a possible model where NET formation drives pulmonary occlusions and CNDP1 promotes antioxidation, pleiotropic immune responses, and vasodilation by accelerating histamine synthesis.

Successful Elimination of SARS-CoV-2 Following Vaccination with BNT162b2 after Prolonged Viral Infection in an Immunocompromised Lymphoma Patient.

A 52-year-old man with mantle cell lymphoma treated with bendamustine and rituximab developed prolonged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Despite elevated titers of anti-spike IgG antibody, protracted pancytopenia persisted for more than six months. Finally, the anti-SARS CoV-2 vaccine, BNT162b2, was administered, which improved his blood cell count and eliminated the virus. The increased anti-spike IgG titer and lymphocyte count after vaccination suggested that both humoral and cellular immunity acted in coordination to eliminate the virus.