SARS-CoV-2 と COVID-19 に関する備忘録 Vol.8――再感染のリスク…etc.

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SARS-CoV-2 と COVID-19 に関するメモ・備忘録


◆Comprehensive analysis of long COVID in a Japanese nationwide prospective cohort study【nature　2023年9月30日】

Abstract

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly since 2019, and the number of reports regarding long COVID has increased. Although the distribution of long COVID depends on patient characteristics, epidemiological data on Japanese patients are limited. Hence, this study aimed to investigate the distribution of long COVID in Japanese patients. This study is the first nationwide Japanese prospective cohort study on long COVID.

Methods

This multicenter, prospective cohort study enrolled hospitalized COVID-19 patients aged ≥18 years at 26 Japanese medical institutions. In total, 1200 patients were enrolled. Clinical information and patient-reported outcomes were collected from medical records, paper questionnaires, and smartphone applications.

Results

We collected data from 1066 cases with both medical records and patient-reported outcomes. The proportion of patients with at least one symptom decreased chronologically from 93.9% (947/1009) during hospitalization to 46.3% (433/935), 40.5% (350/865), and 33.0% (239/724) at 3, 6, and 12 months, respectively. Patients with at least one long COVID symptom showed lower quality of life and scored higher on assessments for depression, anxiety, and fear of COVID-19. Female sex, middle age (41–64 years), oxygen requirement, and critical condition during hospitalization were risk factors for long COVID.

Conclusions

This study elucidated the symptom distribution and risks of long COVID in the Japanese population. This study provides reference data for future studies of long COVID in Japan.

Introduction

The first case of coronavirus disease (COVID-19) was reported in Wuhan, China, in December 2019; after that, it spread rapidly across the globe, including Japan. The development of vaccines and therapeutic drugs has reduced the mortality rate of COVID-19; however, as of September 10, 2022, more than 613 million people had been infected worldwide, and more than 6.5 million people had died. More than 20 million people in Japan have been infected, and 42,000 have died. Currently, the number of infected patients is still increasing. Since the latter half of 2020, various systemic symptoms have been reported to persist after the acute phase of COVID-19 and have been referred to as long COVID in the United Kingdom, post-acute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the United States, and post COVID-19 condition by the World Health Organization (WHO).

Large-scale studies on long COVID have been conducted worldwide. For example, a large cohort study of 1733 COVID-19 cases in Wuhan, China, discharged between January 2020 and May 2020, showed that at six months post-COVID, 63% of patients had fatigue or weakness, 26% had sleep disturbances, 22% had hair loss, and 23% had anxiety or depression. In the follow-up reports from Wuhan, the percentage of patients with at least one symptom decreased from 68% after six months to 49% after 12 months. By August 2022, multiple systematic reviews of long COVID had been published, most of which mentioned the limitations of individual studies, such as target patient bias concerning the disease severity, generation, presence or absence of vaccination, and the method of approaching participants. Previous reports have consistently pointed out that long COVID symptoms are found in severe and mild cases. Therefore, a comprehensive study on patients with a wide range of medical histories is necessary as patients show various symptoms related to multiple organs.

The number of studies on long COVID in Japan is still limited; most are small-scale studies. We have reported nationwide Japanese epidemiological data regarding racial differences in the acute phase of COVID-19, especially its symptoms, clinical course, and prognosis. Long COVID may differ among races and nations, considering that SARS-CoV-2 induces unique symptoms in the Japanese population due to their specific genetic backgrounds. Therefore, we conducted the first large cohort study to characterize long COVID in Japan.

 


◆Effect of hybrid immunity and bivalent booster vaccination on omicron sublineage neutralisation【LANCET　2022年12月5日】

Vaccination is the central strategy to control the COVID-19 pandemic. Vaccination-induced antibodies that target the viral spike (S) protein and neutralise SARS-CoV-2 are crucial for protection against infection and disease. However, most vaccines encode for the S protein of the virus that circulated early in the pandemic (eg, the B.1 lineage), and emerging SARS-CoV-2 variants have mutations in the S protein that reduce neutralisation sensitivity. In particular, the omicron variant (B.1.1.529 lineage and sublineages) is highly mutated and efficiently evades antibodies. Therefore, bivalent mRNA vaccines have been developed that include the genetic information for S proteins of the B.1 lineage and the currently dominating omicron BA.5 lineage. These vaccines have shown increased immunogenicity and protection in mice, but information on potential differences in the effectiveness of monovalent and bivalent vaccine boosters in humans is scarce.

We compared neutralisation of BA.1, BA.4 and BA.5 (identical S proteins, BA.4-5), BA.4.6, and the emerging omicron sublineages BA.2.75.2 (circulating mainly in India), BJ.1 (parental lineage of the currently expanding XBB recombinant), and BQ.1.1 (the incidence of which is increasing in the USA and Europe). We tested neutralisation by antibodies that were induced upon triple vaccination, vaccination and breakthrough infection during the BA.1 and BA.2 wave or BA.5 wave in Germany, triple vaccination plus monovalent or bivalent mRNA booster vaccination, or triple vaccination plus breakthrough infection (BA.1 and BA.2 wave) and a bivalent mRNA booster vaccination. For this, we used S protein bearing pseudotypes, which adequately model antibody-mediated neutralisation of SARS-CoV-2. We found that neutralisation of particles pseudotyped with the B.1 S protein (B.1pp) was highest for all cohorts, followed by neutralisation of BA.1pp and BA.4-5pp, which is in line with expectations (figure; appendix p 17).
Compared with BA.4-5pp, neutralisation of BA.4.6pp and BJ.1pp was moderately reduced (up to 2·2 times lower), whereas neutralisation of BA.2.75.2pp and BQ.1.1pp was strongly reduced (up to 15·5 times lower; figure; appendix p 8). These results suggest that omicron sublineages BA.2.75.2 and BQ.1.1 possess high potential to evade neutralising antibodies elicited upon diverse immunisation histories. We observed that BA.1 and BA.2 breakthrough infections and BA.5 breakthrough infections in individuals who had been triple vaccinated induced higher omicron sublineage neutralisation (on average 3·7–8·5 times higher compared with triple vaccinated individuals without breakthrough infection) than monovalent or bivalent booster vaccination (on average 1·9–2·2 times higher compared with triple vaccinated individuals without breakthrough infection; appendix p 17). Furthermore, the highest omicron sublineage neutralisation was obtained for individuals who were triple vaccinated and also had a BA.1 or BA.2 breakthrough infection plus a subsequent bivalent booster vaccination (on average 17·6 times higher compared with triple vaccinated individuals without breakthrough infection; appendix p 17). No notable differences were detected between the neutralisation activity induced upon monovalent or bivalent vaccine boosters (on average 2·0 times higher following monovalent vaccination and 2·1 times higher following bivalent vaccination compared with triple vaccinated individuals without breakthrough infection).


Collectively, our results show that the emerging omicron sublineages BQ.1.1 and particularly BA.2.75.2 efficiently evade neutralisation independent of the immunisation history. Although monovalent and bivalent vaccine boosters both induce high neutralising activity and increase neutralisation breadth, BA.2.75.2-specific and BQ.1.1-specific neutralisation activity remained relatively low. This finding is in keeping with the concept of immune imprinting by initial immunisation with vaccines targeting the ancestral SARS-CoV-2 B.1 lineage. Furthermore, the observation that neutralisation of BA.2.75.2pp and BQ.1.1pp was most efficient in the cohort that had a breakthrough infection during the BA.1 and BA.2 wave and later received a bivalent booster vaccination, but was still less efficient than neutralisation of B.1pp, implies that affinity maturation of antibodies and two-time stimulation with different omicron antigens might still not be sufficient to overcome immune imprinting. As a consequence, novel vaccination strategies have to be developed to overcome immune imprinting by ancestral SARS-CoV-2 antigen.

AK, IN, SP, and MH have done contract research (testing of vaccinee sera for neutralising activity against SARS-CoV-2) for Valneva unrelated to this work. GMNB served as advisor for Moderna. SP served as advisor for BioNTech, unrelated to this work. All other authors declare no competing interests. MH and GMNB are co-first authors of this study.

 


◆Resistance of Omicron subvariants BA.2.75.2, BA.4.6 and BQ.1.1 to neutralizing antibodies【bioRxiv　2022年12月5日】

Abstract

Convergent evolution of SARS-CoV-2 Omicron BA.2, BA.4 and BA.5 lineages has led to the emergence of several new subvariants, including BA.2.75.2, BA.4.6. and BQ.1.1. The subvariants BA.2.75.2 and BQ.1.1 are expected to become predominant in many countries in November 2022. They carry an additional and often redundant set of mutations in the spike, likely responsible for increased transmissibility and immune evasion. Here, we established a viral amplification procedure to easily isolate Omicron strains. We examined their sensitivity to 6 therapeutic monoclonal antibodies (mAbs) and to 72 sera from Pfizer BNT162b2-vaccinated individuals, with or without BA.1/BA.2 or BA.5 breakthrough infection. Ronapreve (Casirivimab and Imdevimab) and Evusheld (Cilgavimab and Tixagevimab) lost any antiviral efficacy against BA.2.75.2 and BQ.1.1, whereas Xevudy (Sotrovimab) remained weakly active. BQ.1.1 was also resistant to Bebtelovimab. Neutralizing titers in triply vaccinated individuals were low to undetectable against BQ.1.1 and BA.2.75.2, 4 months after boosting. A BA.1/BA.2 breakthrough infection increased these titers, which remained about 18-fold lower against BA.2.75.2 and BQ.1.1, than against BA.1. Reciprocally, a BA.5 breakthrough infection increased more efficiently neutralization against BA.5 and BQ.1.1 than against BA.2.75.2. Thus, the evolution trajectory of novel Omicron subvariants facilitated their spread in immunized populations and raises concerns about the efficacy of most currently available mAbs.

Introduction

Successive sub-lineages of Omicron have spread worldwide since the identification of BA.1 in November 2021. Probably more than 80% of the population were infected by one or another Omicron subvariant in less than one year, without efficient protection against infection conferred by vaccination. The incidence of breakthrough infections in vaccinated individuals has thus increased with Omicron. All Omicron lineages exbibit considerable immune evasion properties. BA.1 and BA.2 contained about 32 changes in the spike protein, promoting immune escape and high transmissibility. BA.5 was then predominant in many countries by mid-2022 and was responsible for a novel peak of contaminations. BA.4 and BA.5 bear the same spike, with 4 additional modifications when compared to BA.2. The neutralizing activity of sera from COVID-19 vaccine recipients was further reduced against BA.4/BA.5 by about 3-5 fold compared to BA.1 and BA.2. Novel sub-variants with enhanced transmissibility rates, derived from either BA.2 or BA.4/BA.5, rapidly emerged and should become prevalent in November 2022. Their geographical distribution is heterogeneous, but they carry an additional limited set of mutations in the spike. For instance, BA.2.75.2, derived from BA.2, was first noted in India and Singapore and comprises R346T, F486S and D1199N substitutions. BA.4.6 was detected in various countries, including USA and UK, and carries R346T and N658S mutations. As of November 2022, BQ.1.1 became the main circulating lineage in many countries. It also carries the R346T mutation found in BA.2.75.2, along with K444T and N460K substitutions. The R346T mutation has been associated with escape from monoclonal antibodies (mAbs) and from vaccine-induced antibodies. This convergent evolution of the spike suggests that the different circulating SARS-CoV-2 sub-lineages faced a similar selective pressure, probably exerted by preexisting or imprinted immunity. A characterization of these new viruses is needed to evaluate their potential impact.

A few recent articles and preprints reported an extensive escape of these Omicron subvariants to neutralization, studying sera from individuals who received three or four vaccine doses, including a bivalent booster. Most of these studies were performed with lentiviral or VSV pseudotypes. In one preprint, recombinant SARS-CoV-2 viruses carrying spikes from Omicron sublineages in an ancestral SARS-CoV-2 backbone were generated, but they might behave somewhat differently than authentic isolates.

Here, we identified and used a highly permissive cell line to amplify BA.2.75.2, BA.4.6. and BQ.1.1 isolates. We analyzed the sensitivity of these strains to approved mAbs, to sera from Pfizer BNT162b2 vaccine recipients, and to individuals with BA.1/BA.2 or BA.5 breakthrough infections.

 

◆Neutralisation of SARS-CoV-2 Omicron subvariants BA.2.86 and EG.5.1 by antibodies induced by earlier infection or vaccination【bioRxiv　2023年10月1日】

Abstract

Highly mutated SARS-CoV-2 Omicron subvariant BA.2.86 emerged in July 2023. We investigated the neutralisation of isolated virus by antibodies induced by earlier infection or vaccination. The neutralisation titres for BA.2.86 were comparable to those for XBB.1 and EG.5.1, by antibodies induced by XBB.1.5 or BA.4/5 breakthrough infection or BA.4/5 vaccination.

Introduction

In late July 2023, global SARS-CoV-2 surveillance programs identified a new, highly mutated Omicron subvariant, BA.2.86. This variant is a descendant of the Omicron BA.2 variant, with the most recent common ancestor estimated to be from between 9th April and 24th July 2023. Since the emergence of BA.2.86, multiple countries have reported its presence, primarily as sporadic BA.2.86 cases with no clear epidemiological link. From the first 12 BA.2.86 cases in Denmark, the estimated effective reproduction number (Re) of this variant was 1.29-fold greater than that of XBB.1.5 and at least comparable to that of EG.5.1, one of the most rapidly expanding XBB subvariants. This is consistent with an outbreak of BA.2.86 in a care home in the United Kingdom (UK) that experienced an attack rate above 85%, indicating high transmissibility in close contact situations.

The earliest cases of BA.2.86 in Denmark suggested a clinical presentation and disease severity no different from other SARS-CoV-2 variants circulating during July/August 2023, such as EG.5.1 and XBB.1.16. Symptoms included cough, shortness of breath, and fever; none were severely ill. Some of the early cases had an underlying disease or received immune-modulating treatment. Taken together with the care home outbreak in the UK, individuals of older age and with comorbidities appear to be more at risk of developing a symptomatic BA.2.86 infection that warrants medical attention.

The increasing numbers of BA.2.86 infections 1-2 years after 3-4 immunisations, with or without prior infection, suggests that waning immunity may contribute to the susceptibility to BA.2.86 infection. Moreover, the highly mutated spike protein of BA.2.86 is antigenically distinct from all other SARS-CoV-2 variants, including the XBB subvariants, as determined using mRNA-vaccinated mouse serum. This suggests that BA.2.86 may evade pre-existing humoral immunity, as well as the acquired immunity from the updated XBB.1.5-based vaccines. The care home outbreak data suggested limited vaccine effectiveness against infection with BA.2.86 four months after vaccination.

To estimate the cross-neutralisation of BA.2.86 by XBB.1.5-induced antibodies, we used serum or plasma samples from persons who had experienced an XBB.1.5 infection as a proxy for the humoral immune response generated by the updated XBB.1.5 vaccines. In contrast to assessing antibodies raised against single SARS-Cov-2 variants in vaccinated or infected animals, human XBB.1.5 breakthrough infections are more representative of the complex and diverse pre-existing immunity of future XBB.1.5-based vaccine recipients. As a representative of the 2022 SARS-CoV-2 variant vaccine, we assessed antibody responses in persons who had either experienced an Omicron BA.4/5 breakthrough infection or received the Comirnaty Original/Omicron BA.4-5 bivalent mRNA vaccine as a fourth vaccination.

 


◆High fusion and cytopathy of SARS-CoV-2 variant B.1.640.1【bioRxiv　2023年9月6日】

ABSTRACT

SARS-CoV-2 variants with undetermined properties have emerged intermittently throughout the COVID-19 pandemic. Some variants possess unique phenotypes and mutations which allow further characterization of viral evolution and spike functions. Around 1100 cases of the B.1.640.1 variant were reported in Africa and Europe between 2021 and 2022, before the expansion of Omicron. Here, we analyzed the biological properties of a B.1.640.1 isolate and its spike. Compared to the ancestral spike, B.1.640.1 carried 14 amino acid substitutions and deletions. B.1.640.1 escaped binding by some anti-NTD and -RBD monoclonal antibodies, and neutralization by sera from convalescent and vaccinated individuals. In cell lines, infection generated large syncytia and a high cytopathic effect. In primary airway cells, B.1.640.1 replicated less than Omicron BA.1 and triggered more syncytia and cell death than other variants. The B.1.640.1 spike was highly fusogenic when expressed alone. This was mediated by two poorly characterized and infrequent mutations located in the spike S2 domain, T859N and D936H. Altogether, our results highlight the cytopathy of a hyper-fusogenic SARS-CoV-2 variant, supplanted upon the emergence of Omicron BA.1.

Importance Our results highlight the plasticity of SARS-CoV-2 spike to generate highly fusogenic and cytopathic strains with the causative mutations being uncharacterized in previous variants. We describe mechanisms regulating the formation of syncytia and the subsequent consequences in cell lines and a primary culture model, which are poorly understood.

INTRODUCTION

Over the timespan of the COVID-19 pandemic, SARS-CoV-2 has been subjected to selection pressures, leading to emerging variants carrying their own repertoire of mutations and to temporal waves of epidemiological resurgence. The most successful variants evolved to evade the immune response displaying differing abilities to form syncytia in cell culture systems. During the period of co-circulation, the disease severity of Omicron (BA.1) was reduced in comparison to Delta. Proposed explanations for this include background immunity, different tissue tropisms – with BA.1 preferentially replicating in the upper respiratory tract – and reduced cell-cell fusogenicity of BA.1 spike. Therefore, the mechanisms surrounding SARS-CoV-2 pathogenicity and Omicron’s attenuation are still debated.

SARS-CoV-2 fuses with the cell plasma membrane to transfer its genome into the cytoplasm and instigate replication. This process is initiated through the binding of the spike to its receptor angiotensin-converting enzyme 2 (ACE2). Spike is comprised of two subunits, S1 and S2, separated by a polybasic furin cleavage site (FCS) cleaved during viral production in the trans-Golgi network. Certain mutations in spike, such as P681H/R, allow for this process to occur more readily, subsequently improving viral fusion. During entry, spike is cleaved at the S2’ site by host proteases, mainly TMPRSS2 at the cell surface or cathepsins in endosomes, to allow the conformational changes necessary to project the fusion peptide into the host membrane, leading to membrane fusion. Thus, a series of proteolytic events regulate SARS-CoV-2 entry and tropism prior to replication of the viral RNA.

The later stages of the SARS-CoV-2 replication cycle occur in the endoplasmic reticulum (ER) and Golgi network. Here, the host protein COPI binds to the spike cytoplasmic tail and traffics it to the packaging site of SARS-CoV-2 virions. However, sub-optimal spike binding to COPI results in leakage to the plasma membrane. Consequently, spike at the cell surface may interact with ACE2 on neighbouring cells leading to cell-cell fusion and syncytia formation.

Histological studies of lung tissue from severe COVID-19 patients describe the presence of abnormal pneumocytes and large, multinucleated syncytia. Syncytia are also observed in the lungs of long-COVID patients who eventually succumb to the disease up to 300 days after their last negative PCR test. Syncytia could thus facilitate persistent infection, as seen in RSV infection, or contribute to pathogenesis. Syncytia formation by SARS-CoV-2 has also been demonstrated in various cell lines and in human iPSC derived cardiomyocytes. Spike mutations can impact fusogenicity. Notably, D215G and P681R/H increase fusion, with the latter promoting furin S1/S2 cleavage. Conversely, N856K and N969K in Omicron decrease fusogenicity. Nevertheless, the role of syncytia in SARS-CoV-2 replication and the impact on disease severity has yet to be fully explored.

Minor SARS-CoV-2 variants harbouring uncharacterized mutations represent opportunities in understanding certain viral processes. Variant B.1.640.1 was first identified in Republic of the Congo in April 2021 and found circulating in France in October 2021. As of May 2023, 1107 genome sequences of B.1.640.1 are available on the GISAID database, 895 from France, with the most recent dating to January 2022. Here, we isolated a B.1.640.1 strain and investigated the humoral immune response, replication, fusogenicity and cytopathy of this variant.