Tag Archives: Severe Acute Respiratory

Microbiology

Candida auris infection without epidemiologic links to a prior outbreak

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Dr. Priyom Bose, Ph.D.By Dr. Priyom Bose, Ph.D.Mar 23 2023Reviewed by Danielle Ellis, B.Sc.

The Centers for Disease Control and Prevention (CDC) has classified Candida auris (C. auris) as an urgent public threat due to its role in elevating mortality, its ability to persist in hospital environments, and the high possibility of developing pan-drug resistance.

Notably, a recent study published in the journal Open Forum Infectious Diseases has pointed out that surfaces near patients with C. auris quickly become re-contaminated after cleaning.

Existing research has not adequately elucidated the environmental reservoirs of C. auris. Further, few studies have reported epidemiologic links associated with C. auris infection. 

Study: The Emergence and Persistence of Candida auris in Western New York with no Epidemiologic Links: A Failure of Stewardship?. Image Credit: Kateryna Kon / ShutterstockStudy: The Emergence and Persistence of Candida auris in Western New York with no Epidemiologic Links: A Failure of Stewardship? Image Credit: Kateryna Kon / Shutterstock

Background

C. auris is a species of fungus that grows as yeast. It is one of the few species of the genus Candida which cause candidiasis in humans. In the past, C. auris infection was primarily found in cancer patients or those subjected to feeding tubes.

In the United States (US), the emergence of C. auris was traced to New York, and surveillance for this fungal infection was focused mainly on New York City to detect outbreaks. Recently, scientists investigated the association between genomic epidemiology and C. auris infection in Western New York.

A Case Study

The study describes the emergence of C. auris in a patient hospitalized at a small community hospital in Genesee County, New York (NY). In January 2022, C. auris was isolated from the urine culture of a 68-year-old male on the 51st day of hospitalization.

This patient had no known epidemiological connections outside his immediate community. Before his hospitalization, he was not exposed to other patients or family members associated with C. auris infection.

This patient had no history of organ transplantation, decubitus ulcers, hemodialysis, feeding tubes, or nursing home stays. He had an active lifestyle with a history of mild vascular dementia. He was hospitalized due to pneumonia and was prescribed azithromycin treatment.

Post hospitalization, he tested positive for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and was treated with dexamethasone (6 mg) daily for 10 days and remdesivir (200 mg) once, followed by 100 mg daily for five days.

Since the patient’s chest radiograph showed left lobar consolidation, he was further treated with empiric ceftriaxone and azithromycin. As the respiratory symptoms deteriorated, he received non-invasive positive pressure ventilation, with subsequent endotracheal intubation for eight days. He was successfully extubated. He developed a fever and received antimicrobial therapy for 73 days. The patient had a urinary catheter and a peripherally inserted central line in his arm for 35 days. 

Microbiology culture test and serum procalcitonin levels remained negative and within normal levels. On the 22nd day of hospitalization, Candida albicans were isolated from respiratory samples. On the 51st day, the urine culture revealed the presence of azole-resistant C. auris.

The isolated C. auris (MRSN101498) was forwarded to the Multidrug-resistant organism Repository and Surveillance Network (MRSN), where genomic sequencing was performed. After the patient was discharged, the hospital room was cleaned using hydrogen peroxide and peracetic acid, followed by ultraviolet-C light. Other patients who shared rooms with the patient with C. auris were tested for infection.

Study Outcomes

C. auris was not detected in the Western NY community hospital in the past year. Physicians stated that the patient received excessive antibiotic treatment for a prolonged period. Genomic studies revealed that the MRSN101498 genome sequence was closely related to the 2013 Indian strain with minor genomic differences. Interestingly, the K143R mutation in ERG11 was found in MRSN101498, which is associated with triazole resistance in Candida albicans.

Whole genome single nucleotide polymorphism (SNP) analysis also highlighted that MRSN101498 was strongly genetically related to four other isolates, with marginal differences.

These isolates were linked to an outbreak in March 2017 in a hospital 47 miles northeast of Rochester, NY. Based on the current findings, it is highly likely that isolates from Western NY share a recent common ancestor.

Study Importance

This case study is important for several reasons, including the absence of epidemiologic links to C.auris infection. Since reports from rural sectors are rare, this study addresses a vital surveillance ‘blind spot.’ 

However, the current study failed to identify the potential reservoirs of MRSN101498 in Western NY. Sporicidal disinfectants were inefficient for both Clostridioides difficile and C. auris. However, terminal cleaning protocols that included UV irradiation and sporicidal cleaning agents were able to eradicate C. auris effectively.

The current study highlights the role of excessive antibiotic exposure in the emergence of C. auris. It also indicates the challenges in eliminating fungi from hospital settings. The authors recommend proper antibiotic treatment and cleaning procedures for drug-resistant pathogens.

Journal reference:
Microbiology

New SARS-CoV-2 Omicron XBB.1.5 variant has high transmissibility and infectivity, study finds

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Mar 20 2023Reviewed by Danielle Ellis, B.Sc.

COVID-19 has caused significant global panic after its rapid emergence more than 3 years ago. Although we now have highly effective vaccines against the SARS-CoV-2 virus, which causes COVID-19, scientists continue to study emerging SARS-CoV-2 variants in order to safeguard public health and devise global preventive strategies against emerging variants. A team led by Japanese researchers has recently discovered that the SARS-CoV-2 Omicron XBB.1.5 variant, prevalent in the Western hemisphere, has high transmissibility and infectivity.

New SARS-CoV-2 Omicron XBB.1.5 variant has high transmissibility and infectivity, study finds
New SARS-CoV-2 variant may jeopardize public health across the globe. The SARS-CoV-2 Omicron XBB.1.5 variant spreads rapidly and is more infectious than its historic precursor. Image Credit: The University of Tokyo

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for millions of deaths worldwide. Although scientists have designed novel vaccines to counter COVID-19, they are constantly on the lookout for emerging variants that can bypass vaccine resistance and potentially jeopardize global public health. A team led by Japanese researchers has recently been successful in characterizing the new SARS-CoV-2 Omicron XBB.1.5 variant, which was first detected in October 2022. Their findings were published on January 31, 2023 in volume 23 of The Lancet Infectious Diseases.​​​

Says senior author Prof. Kei Sato from the Division of Systems Virology, The Institute of Medical Science, The University of Tokyo, Japan, “Because the Omicron XBB.1.5 variant can spread more rapidly than previous variants and has a potential to cause the next epidemic surge, we should carefully monitor it to safeguard public health.”

While studying emerging variants of the SARs-CoV-2 Omicron lineage, the research team made a startling discovery: the SARS-CoV-2 Omicron XBB.1.5 variant has a novel mutation in the spike (S) protein—the protein that anchors the virus firmly to the human angiotensin converting enzyme-2 (ACE2) receptor, thus facilitating the invasion of human cells. The serine-to-proline amino acid mutation noted at residue no. 486 in the S protein is virologically concerning because of a variety of reasons.

Sharing his concerns, first author Keiya Uriu from the Division of Systems Virology, Department of Microbiology and Immunology, The University of Tokyo, Japan, says, “In late 2022, the SARS-CoV-2 Omicron BQ.1 and XBB lineages, characterized by amino acid substitutions in the S protein and increased viral fitness, had become predominant in the Western and Eastern Hemisphere, respectively. In 2022, we elucidated the characteristics of a variety of newly emerging SARS-CoV-2 Omicron subvariants. At the end of 2022, the XBB.1.5 variant, a descendant of XBB.1 that acquired the S:S486P substitution, emerged and was rapidly spreading in the USA.”

To gain mechanistic insights into the infectivity, transmissibility, and immune response associated with XBB.1.5, the team conducted a series of experiments. For instance, upon conducting epidemic dynamics analysis—statistical modeling that facilitates the analysis of the general characteristics of any epidemic—the team realized that the relative effective reproduction number (Re) of XBB.1.5 was 1.2-fold greater than that of the parental XBB.1. This indicated that an individual with the XBB.1.5 variant could infect 1.2 times more people in the population than someone with the parental XBB.1 variant. Moreover, the team also realized that, as of December 2022, XBB.1.5 was rapidly outcompeting BQ.1.1, the predominant lineage in the United States.

Co-first-author Jumpei Ito from the Division of Systems Virology, remarks, “Our data suggest that XBB.1.5 will rapidly spread worldwide in the near future.”

The team also studied the virological features of XBB.1.5 to determine how tightly the S protein of the new variant interacts with the human ACE2 receptor. To this end, the researchers conducted a yeast surface display assay. The results showed that the dissociation constant (KD) corresponding to the physical interaction between the XBB.1.5 S receptor-binding domain (RBD) and the human ACE2 receptor is significantly (4.3-fold) lower than that for XBB.1 S RBD. “In other words, the XBB.1.5 variant binds to human ACE2 receptor with very high affinity,” explains Shigeru Fujita from the Division of Systems Virology.

Further experiments using lentivirus-based pseudoviruses also showed that XBB.1.5 had approximately 3-fold higher infectivity than XBB.1. These results suggest that XBB.1.5 exhibits a remarkably strong affinity to the human ACE2 receptor, which can be attributed to the S486P substitution.

The study by Prof. Sato and his team led to another important discovery from an immunization perspective. The XBB.1.5 S protein was found to be highly resistant to neutralization antibodies elicited by breakthrough infection with the BA.2/BA.5 subvariants. In other words, patients with prior infection from the BA.2/BA.5 subvariants may not show robust immunity against XBB.1.5, increasing their chances of infection and disease.

The results of our virological experiments explain why the Omicron XBB.1.5 variant has a higher transmissibility than past variants: This variant acquired strong binding ability to human ACE2 while maintaining a higher ability to escape from neutralizing antibodies.”

​​​​​​​Yusuke Kosugi, Division of Systems Virology, Department of Microbiology and Immunology, The University of Tokyo, Japan

Contributing members of The Genotype to Phenotype Japan (G2P-Japan) Consortium conclude, “The SARS-CoV-2 Omicron XBB.1.5 variant does show enhanced transmissibility. Although few cases have been detected in the Eastern hemisphere, it could become a looming threat. Imminent prevention measures are needed.”

​​​​​​​Thanks to the research team for the early warning! Meanwhile, we must continue adopting safe practices to defend ourselves from XBB.1.5. 

Source:

The University of Tokyo

Journal reference:

Uriu, K., et al. (2023) Enhanced transmissibility, infectivity, and immune resistance of the SARS-CoV-2 omicron XBB.1.5 variant. The Lancet Infectious Diseases. doi.org/10.1016/S1473-3099(23)00051-8.

Microbiology

Real-world data on the effectiveness of Sotrovimab as a prophylactic against COVID-19

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Bhavana KunkalikarBy Bhavana KunkalikarMar 16 2023Reviewed by Danielle Ellis, B.Sc.

*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

In a recent study posted in the medRxiv* preprint server, scientists assessed the efficacy of sotrovimab for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) treatment.

Emerging SARS-CoV-2 variants have lowered the fold change in half maximal effective concentration (EC50) for the SARS-CoV-2 Omicron BA.2 sublineage and subsequent sublineages. Yet, the association between this decrease and clinical efficacy outcomes is unknown. With a lack of clinical trials evaluating the efficacy of sotrovimab against novel variants, real-world evidence becomes an essential data source.

Study: Real-world effectiveness of sotrovimab for the treatment of SARS-CoV-2 infection during Omicron BA.2 subvariant predominance: a systematic literature review. Image Credit: Cryptographer / ShutterstockStudy: Real-world effectiveness of sotrovimab for the treatment of SARS-CoV-2 infection during Omicron BA.2 subvariant predominance: a systematic literature review. Image Credit: Cryptographer / Shutterstock

About the study

In the present study, researchers assessed the efficacy of sotrovimab on severe coronavirus disease 2019 (COVID-19) outcomes throughout the period of the prevalence of the SARS-CoV-2 Omicron BA.2 subvariant.

This systematic literature review (SLR) comprised observational papers assessing clinical outcomes as well as the viral load in sotrovimab-treated patients, which were published between 1 January 2022 and 3 November 2022 in preprint articles, peer-reviewed journal publications, and conference abstracts. To identify data related to Omicron BA.2 and the following subvariants, the team chose a suitable publication period for the systematic review.

The following electronic databases were searched on 3 November 2022: MEDLINE, LitCovid, Embase, EcoLit, and Cochrane COVID-19 Study Registry. Further searches were undertaken in medRvix, bioRvix, arRvix, xhemRvix, Preprints.org, SSRN, and ResearchSquare for relevant preprints. In addition, relevant abstracts from the following conferences were indexed beginning in January 2022: Infectious Diseases Week, International Conference on Emerging Infectious Diseases, European Respiratory Society, and European Congress of Clinical Microbiology and Infectious Diseases.

Data extraction from the listed studies was conducted by a single extractor using a Microsoft Excel-designed data extraction file. Information extracted included the study’s title and citation, data source, study design and details, country, number of patients, study population, data collection period and circulating SARS-CoV-2 variants, duration of follow-up, key baseline features, and clinical outcomes. The clinical outcomes taken into account for the study included hospital admission, intensive care admission, respiratory support, emergency department visits, mortality, COVID-19 progression, the relative and absolute change in viral load observed during the acute phase after sotrovimab therapy, and the number of patients having undetectable viral load after sotrovimab treatment.

Results

Initial searches of electronic databases generated 257 studies. Another 263 studies were found by searching preprints, conference abstracts, and citation chasing from appropriate SLRs. After removing duplicates, 343 unique abstracts and titles were evaluated, of which 89 were deemed eligible for full-text review. Five observational trials reporting viral load or clinical outcome data associated with sotrovimab during the era of BA.2 predominance were deemed appropriate for inclusion in the present SLR.

Point estimates for hospitalization or mortality (as a composite endpoint) or clinical progression for sotrovimab-treated patients. a95 CIs calculated via Clopper-Pearson methods using reported data. bDefined as March through April 2022 in source and assumes homogeneity in the distribution of SARS-CoV-2 variants across all US states. cOnly COVID-19-specific outcome shown; all-cause outcome also reported in source. dHospitalizations were COVID-19-specific; deaths could be due to any cause. CI confidence interval

Point estimates for hospitalization or mortality (as a composite endpoint) or clinical progression for sotrovimab-treated patients. a95 CIs calculated via Clopper-Pearson methods using reported data. bDefined as March through April 2022 in source and assumes homogeneity in the distribution of SARS-CoV-2 variants across all US states. cOnly COVID-19-specific outcome shown; all-cause outcome also reported in source. dHospitalizations were COVID-19-specific; deaths could be due to any cause. CI confidence interval

The number of patients reporting hospitalization or fatality due to COVID-19 was consistently low for all investigations and periods of the prevalence of Omicron BA.1 and BA.2 variants. COVID-19-related hospital admission or mortality rates were between 1.0% and 3.1% for sotrovimab-treated patients during Omicron BA.1 prevalence and from 1.0% and 3.6% when BA.2 was predominant. The number of patients who reported hospitalization and mortality due to all causes ranged from 2.1% to 2.7% for the BA.1 predominance era, and from 1.7% to 2.0% for the BA.2 era. During Omicron BA.1 predominance, COVID-19-related mortality was projected to be 0.21% for the sotrovimab group versus 0.67% for the molnupiravir group, and 0.15% versus 0.96% for the BA.2 era, respectively.

During the BA.1 and BA.2 subvariant surges, sotrovimab was associated with a significantly decreased incidence of 28-day SARS-CoV-2-related hospital admission or fatality compared to molnupiravir. After statistical adjustment for demographics, vaccination status, high-risk cohort categories, body mass index, calendar time, and other comorbidities, the findings indicated that sotrovimab was associated with a significantly lower risk of COVID-19-related hospital admission or mortality compared to molnupiravir during the BA.1 and BA.2 periods.

During the BA.2 subvariant surge, sotrovimab was linked with a decreased risk of 30-day hospitalization or mortality from all causes compared to no mAb treatment. In March 2022, sotrovimab was considerably more successful than non-mAb-treated patients, with an adjusted reduction of 59% in relative risk and a propensity score-matched relative risk reduction of 64% with respect to 30-day all-cause hospital admission or mortality. Similar risks of hospitalization were associated with BA.1 and BA.2 patients treated with sotrovimab.

Conclusion

The study findings showed that sotrovimab continued to be clinically effective in mitigating severe clinical outcomes associated with SARS-CoV-2 infections during the period of SARS-CoV-2 Omicron BA.2 predominance compared to the control/comparator and relative to Omicron BA.1 predominance. During Omicron BA.1 and BA.2 subvariant predominance, the studies consistently reported low rates of poor clinical outcomes in individuals treated with sotrovimab.

*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Microbiology

Study finds community-onset bacterial coinfection in children with critical COVID-19 is infrequent but empiric antibiotics are commonly prescribed

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Pooja Toshniwal PahariaBy Pooja Toshniwal PahariaMar 8 2023Reviewed by Danielle Ellis, B.Sc.

In a recent study published in Open Forum Infectious Diseases, researchers evaluated the use of empiric antibiotics to determine the prevalence rates of community-acquired bacterial coinfections among hospitalized pediatric critical coronavirus disease 2019 (COVID-19) patients and to identify opportunities for de-escalating antibiotic usage in case of no bacteria-caused sepsis among high-risk individuals, and those presenting with shock.

Study: Community-onset bacterial coinfection in children critically ill with SARS-CoV-2 infection. Image Credit: nokwalai/Shutterstock
Study: Community-onset bacterial coinfection in children critically ill with SARS-CoV-2 infection. Image Credit: nokwalai/Shutterstock

Background

Community-acquired bacterial coinfections among hospitalized adult coronavirus disease 2019 (COVID-19) patients are uncommon; however, empiric antibiotic usage is reportedly high. Data on empiric antibiotic usage and bacterial coinfections among pediatric individuals with critical severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are limited.

The clinical manifestations of severe SARS-CoV-2 infections often include pulmonary distress and fever, findings that could be difficult to discriminate from serious bacterial infections, which might prompt the use of empiric antibiotics in the initial days of hospitalization, particularly among high-risk individuals.

About the study

In the present study, researchers investigated whether any radiographic, laboratory, or clinical features ascertainable during hospitalization were related to empiric antibiotic usage or were estimative of bacterial coinfections acquired in community settings.

The team evaluated individuals below 19.0 years and admitted to pediatric high-acuity units (HAU) or intensive care units (ICU) due to SARS-CoV-2 infections from March 2020 to December 2020. On the basis of microbiology reports from the initial 72 hours of hospitalization, the team adjudicated if patients had community-acquired bacterial coinfections.

Clinical and demographic variables of individuals with and without antibiotic prescriptions and bacterial coinfections in the initial days of hospitalization were compared. Poisson regression modeling was performed to assess factors related to the outcome, and the adjusted relative risk (aRR) values were calculated.

Data were obtained from patient electronic medical records and data from the nationwide overcoming COVID-19 population health active surveillance registry of patients hospitalized due to COVID-19-associated complications between 15 March 2020 and 31 December 2020 across >70.0 pediatric hospitals in 25 states.

COVID-19 diagnosis was confirmed using polymerase chain reaction (PCR). The team excluded multisystem inflammatory syndrome among children (MIS-C) patients diagnosed using the Centers for Disease Control and Prevention (CDC) criteria. Data were obtained on demographic parameters, clinical symptoms and signs, comorbidities, radiographical and laboratory investigations, and data on antibiotics prescribed at admission and the course of critical COVID-19, including clinical outcomes and hemodynamic and respiratory support needed.

The primary study outcome assessed was the prescriptions of empirical antimicrobials, for which enteral or intravenous antimicrobials administered in the initial two days of hospital admission were assessed. The second outcome evaluated community-acquired bacterial infection presence, for which relevant case report form (CRF) information from individuals with SARS-CoV-2-positive microbiological cultures, and PCR, were analyzed in the initial 72 hours of hospital admission.

Results

Out of 532 individuals, 63.0% were administered empiric antibiotics; however, only seven percent developed bacterial coinfections, of which only three percent were respiratory-type. Empirical antibiotics had a greater likelihood of being prescribed to immunosuppressed individuals (aRR of 1.3), requiring non-mechanical ventilator-type respiratory aid (aRR of 1.4), or requiring invasive-type mechanical ventilators (aRR of 1.8), than no respiratory aid.

The most frequently prescribed antimicrobials were ceftriaxone (41%) and vancomycin (28%), followed by cefepime (20%). Most individuals were prescribed multiple antimicrobials, with 21%, 10%, and 18% receiving 2.0, 3.0, and ≥4.0 antibiotics in the initial two days of hospital admission. More than 33% of individuals received antibiotics for ≥5.0 days, despite no evidence of bacterial coinfections. The median social vulnerability index (SVI) values were significantly greater among those who received antibiotics than those who did not.

The median C-reactive protein (CRP) levels were greater among those who received antibiotics versus those who did not (4.6 mg per dL vs. 2.2 mg per dL), as were the median procalcitonin levels (0.4 ng per mL vs. 0.1 ng per mL). The median leukocyte counts showed no significant differences between the two groups. Antibiotic usage was related to COVID-19 severity, indicated by greater median values for PEdiatric Logistic Organ Dysfunction-2 (PELOD-2) scores at hospitalization among individuals who received antibiotics than those who did not.

Seven percent (n=38) of individuals had true community-onset bacterial coinfections, of which 13, 16, 8.0, and 4.0 were bloodstream infections, respiratory infections, urinary tract infections, and bacterial infections at other sites (peritonitis, colitis, meningitis, and pharyngitis), respectively.

No particular pathogenic organism predominantly caused bacterial coinfections, although most pulmonary coinfections were caused by Staphylococcus aureus and/or Pseudomonas aeruginosa. Greater PELOD-2 scores at admission were associated with bacterial coinfections (aRR of 1.2), in addition to age, sex, and pulmonary conditions other than asthma (aRR 2.3).

Conclusion

Overall, the study findings showed that community-onset bacterial coinfections among children with critical COVID-19 are not frequent; however, empiric antibiotics are usually prescribed. The study findings inform antibiotic use and underpin swift de-escalation in case assessments indicating that coinfections are not likely.

Journal reference:
Microbiology

Maternal and perinatal outcomes of women infected with SARS-CoV-2 during the Omicron wave in Italy

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Bhavana KunkalikarBy Bhavana KunkalikarJan 25 2023Reviewed by Danielle Ellis, B.Sc.

In a recent study published in the Clinical Microbiology and Infection, researchers assessed the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination on pregnant women during the Omicron wave.

Study: Vaccination against SARS-CoV-2 in pregnancy during the Omicron wave: the prospective cohort study of the Italian obstetric surveillance system. Image Credit: GolF2532/Shutterstock
Study: Vaccination against SARS-CoV-2 in pregnancy during the Omicron wave: the prospective cohort study of the Italian obstetric surveillance system. Image Credit: GolF2532/Shutterstock

Background

During the coronavirus disease 2019 (COVID-19) pandemic, pregnant women were more likely than the general population to develop severe COVID-19. In utero mother-to-child viral transmission was shown to be uncommon, and infected mothers demonstrated a strong immune response with anti-SARS-CoV-2 antibodies passed on to newborns.

Despite many studies indicating a substantial maternal antibody response to SARS-CoV-2 immunization and the absence of safety issues, the vaccination rate among pregnant women remained lower than that of the general population. Only a few studies have been undertaken to date on the impact of the SARS-CoV-2 Omicron variant on unvaccinated and vaccinated pregnant women.

About the study

In the present study, researchers compared the perinatal and maternal outcomes of SARS-CoV-2-infected women in Italy during the SARS-CoV-2 Omicron variant wave based on their vaccination protection.

The current national prospective cohort research involved pregnant women who tested COVID-19-positive within seven days of hospitalization in any Italian maternity unit between January 1 and May 31 2022. In addition, women reported whether they had received the SARS-CoV-2 vaccine, as well as the when (before and/or at the time of pregnancy) and how many doses were received.

The primary outcome measure was SARS-CoV-2 disease severity, classified as mild, moderate, or severe. The two most severe severity categories, determined by pneumonia diagnosis, were grouped together for statistical analysis as “moderate or severe COVID-19 disease” (MSCD). Secondary outcomes comprised preterm birth, stillbirth, delivery mode, admission to the neonatal intensive care unit (NICU), and early neonatal mortality before hospital release.

MSCD protection was taken into account as an exposure variable. Women vaccinated with a minimum of one vaccine dose at the time of pregnancy, and those vaccinated with the full vaccine schedule and the first booster vaccine were protected against MSCD. On the other hand, unvaccinated women and participants who were vaccinated with either one or two vaccine doses prior to pregnancy and tested positive for SARS-CoV-2 at 22 or more gestational weeks were deemed unprotected. Women with incomplete vaccination information and those who were vaccinated with one or two doses prior to pregnancy and who tested positive for SARS-CoV-2 at less than 22 gestational weeks were deemed “unknown in terms of protective status.”

Results

Between January 1 and May 31, 2022, a total of 2,774 women who tested positive for SARS-CoV-2 within seven days of hospitalization were enrolled. Information was available about the protection status of 2147 women, while no significant clinical or socio-demographic variations were noted between these women and the entire cohort.

According to the study’s definition, almost 1,069 (49.8%) individuals were protected against MSCD. Of them, 74 were vaccinated with one vaccine during pregnancy, while 596 received two, including a minimum of one dose administered during pregnancy, while 327 received their first booster. In contrast, 1,078 women were deemed unprotected, including 989 women who were unvaccinated and 89 who tested positive for SARS-CoV-2 at 22 or more weeks of gestation after receiving one or two doses before pregnancy. All except 26 women were immunized with the conventional vaccinations alone or in conjunction with messenger ribonucleic acid (mRNA) vaccines.

Compared to protected women, unprotected women displayed a higher likelihood of being younger, less educated, of foreign nationality, and symptomatic. Also, 96.4% were hospitalized for childbirth or obstetrical causes, whereas 3.6% were hospitalized due to COVID-19. Eight of the latter acquired severe disease, 12 developed a moderate disease, and 58 developed a mild disease.

MSCD illness was uncommon overall but more prevalent among unprotected women than among protected women. Among the 41 MSCD cases, 27 of 29 unprotected women had not received any vaccine, while two were vaccinated with two doses prior to pregnancy. Three of the 12 protected women received the booster, while nine received two doses, among which the first was received before and the second was received during pregnancy.

Among unprotected women, seven out of eight severe infection cases and one maternal fatality occurred. COVID-19 pneumonia was deemed the cause of death, reported two weeks after delivery. Unprotected women had a greater incidence of MSCD compared to protected women, Asian women, and those with a history of comorbidities.

Sensitivity analysis revealed that unprotected women had considerably higher MSCD risk than protected women. Furthermore, 8.7% of newborns were born preterm, predominantly late preterm, with no significant variations between unprotected and protected women, but C-section was reported in 34.4% and 29.3% of women, respectively. The rate of preterm birth was greater among MSCD-infected women compared to those with milder cases and those with CS. Also, out of 619 CS cases, five were urgent/emergent due to COVID-19, and all involved MSCD-affected women.

Conclusion

Overall, the study findings documented a low prevalence of severe SARS-CoV-2 infection in pregnant women and considerable efficacy of the COVID-19 vaccine in providing protection. These statistics can serve as the foundation for informing pregnant women uncertain about the vaccine’s efficacy and demonstrating the importance of vaccination in protecting their newborns.

Journal reference:
Microbiology

What are the major findings of long COVID research?

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Pooja Toshniwal PahariaBy Pooja Toshniwal PahariaJan 17 2023Reviewed by Aimee Molineux

In a recent review published in Nature Reviews Microbiology, researchers explored existing literature on long coronavirus disease (COVID). They highlighted key immunological findings, similarities with other diseases, symptoms, associated pathophysiological mechanisms, and diagnostic and therapeutic options, including coronavirus disease 2019 (COVID-19) vaccinations.

Study: Long COVID: major findings, mechanisms and recommendations. Image Credit: Ralf Liebhold/Shutterstock
Study: Long COVID: major findings, mechanisms and recommendations. Image Credit: Ralf Liebhold/Shutterstock

Long COVID refers to a multisystemic disease among SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2)-positive individuals, with increasing prevalence rates by the day. Studies have reported on long COVID risk factors, symptoms, pathophysiology, diagnosis, and treatment options, with increasing similarities between long COVID and other diseases such as POTS (postural orthostatic tachycardia syndrome) and ME/CFS (myalgic encephalomyelitis/ chronic fatigue syndrome).

About the review

In the present review, researchers explored the existing data on long COVID immunology, symptoms, pathophysiology, diagnosis, and therapeutic options.

Key long COVID findings and similarities with other diseases

Studies have reported persistently reduced exhausted T lymphocytes, dendritic cells, cluster of differentiation 4+ (CD4+) lymphocyte and CD8+ lymphocyte counts, and greater PD1 (programmed cell death protein-1) expression. In addition, increase in innate cell immunological activities, non-classical monocytes, expression of interferons (IFNs)-β, λ1, and interleukins (IL)-1β, 4,6, tumor necrosis factor (TNF). Cytotoxic T lymphocyte expansion has been linked to gastrointestinal long COVID symptoms, and persistent increase in CCL11 (C-X-C motif chemokine 11) expression has been linked to cognitive dysfunction among long COVID patients.

Elevated autoantibody titers have been reported among long COVID patients, such as autoantibodies against ACE2 (angiotensin-converting enzyme 2), angiotensin II receptor type I (AT1) receptors, β2-adrenoceptors, angiotensin 1–7 Mas receptors, and muscarinic M2 receptors. Reactivation of Epstein-Barr virus (EBV) and human herpes virus-6 (HHV-6) has been reported in long COVID patients and ME/CFS. EBV reactivation has been linked to neurocognitive impairments and fatigue in long COVID.

SARS-CoV-2 persistence reportedly drives long COVID symptoms. SARS-CoV-2 proteins and/or ribonucleic acid (RNA) have been detected in cardiovascular, reproductive, cranial, ophthalmic, muscular, lymphoid, hepatic, and pulmonary tissues, and serum, breast, urine, and stool obtained from long COVID patients. Similar immunological patterns are noted between long COVID and ME/CFS, with elevated cytokine levels in the initial two to three years of disease, followed by reduction with time, without symptomatic improvements in ME/CFS. Lower cortisol levels, mitochondrial dysfunction, post-exertional malaise, dysautonomia, mast cell activation, platelet hyperactivation, hypermobility, endometriosis, menstrual alterations, and intestinal dysbiosis occur in both conditions.

Long COVID symptoms and underlying pathophysiological mechanisms

Long COVID-associated organ damage reportedly results from COVID-19-induced inflammation and associated immune responses. Cardiovascular long COVID symptoms such as chest pain and palpitations have been associated with endothelial dysfunction, micro-clotting, and lowered vascular density. Long COVID has been associated with an increased risk of renal damage and type 2 diabetes. Ophthalmic symptoms of long COVID, including altered pupillary responses to light, result from the loss of small nerve fibers in the cornea, increased dendritic cell density, and impaired retinal microvasculature. Respiratory symptoms such as persistent cough and breathlessness result from altered pulmonary perfusion, epithelial injury, and air entrapment in the airways.

Cognitive and neurological long COVID symptoms include loss of memory, cognitive decline, sleep difficulties, paresthesia, balancing difficulties, noise and light sensitivity, tinnitus, and taste and/or smell loss. Underlying pathophysiological mechanisms include kynurenine pathway activation, endothelial injury, coagulopathy, lower cortisol levels, loss of myelin, microglial reactivation, oxidative stress, hypoxia, and tetrahydrobiopterin deficiency.  Gastrointestinal symptoms such as pain in the abdomen, nausea, appetite loss, constipation, and heartburn have been associated with elevated Bacteroides vulgatus and Ruminococcus gnavus counts and lower Faecalibacterium prausnitzii counts. Neurological symptoms often have a delayed onset, worsen with time and persist longer than respiratory and gastrointestinal symptoms, and long COVID presents similarly in children and adults.

Diagnostic and therapeutic options for long COVID, including COVID-19 vaccines

The diagnosis and treatment of long COVID are largely symptom-based, including tilt tests for POTS, magnetic resonance imaging (MRI) to detect cardiovascular and pulmonary impairments, and electrocardiograms to detect QRS complex fragmentation. Salivary tests and serological tests, including red blood cell deformation, lipid profile, complete blood count, D-dimer, and C-reactive protein (CRP) evaluations, can be performed to assess immunological biomarker levels. PCR (polymerase chain reaction) analysis is used for SARS-CoV-2 RNA detection and quantification, and antibody testing is performed to assess humoral immune responses against SARS-CoV-2.

Pharmacological treatments include intravenous Ig for immune dysfunction, low-dosage naltrexone for neuronal inflammation, beta-blockers for POTS, anticoagulants for microclot formation, and stellate ganglion blockade for dysautonomia. Other options include antihistamines, paxlovid, sulodexide, and pycnogenol. Non-pharmacological options include cognitive pacing for cognitive impairments, diet limitations for gastrointestinal symptoms, and increasing salt consumption for POTS. COVID-19 vaccines have conferred minimal protection against long COVID, the development of which depends on the causative SARS-CoV-2 variant, and the number of vaccination doses received. Long COVID has been reported more commonly post-SARS-CoV-2 Omicron BA.2 subvariant infections.

Based on the review findings, long COVID is a multiorgan disease that has debilitated several lives worldwide, for which diagnostic and therapeutic options are inadequate. The findings underscored the need for future studies, clinical trials, improved education, mass communication campaigns, policies, and funding to reduce the future burden of long COVID.

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Microbiology

Study compares effectiveness of Pfizer vs. Moderna booster COVID vaccines after third dose

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Neha MathurBy Neha MathurJan 3 2023Reviewed by Emily Henderson, B.Sc.

In a recent scientific paper published in the journal Nature Microbiology, researchers reproduced two target trials using electronic health records (EHRs) of the Department of Veterans Affairs (VA) to compare the effectiveness of the third dose of BNT162b2 or messenger ribonucleic acid (mRNA)-1273 vaccine among United States (US) veterans.

Study: Comparative effectiveness of third doses of mRNA-based COVID-19 vaccines in US veterans. Image Credit: Steve Heap / ShutterstockStudy: Comparative effectiveness of third doses of mRNA-based COVID-19 vaccines in US veterans. Image Credit: Steve Heap / Shutterstock

Background

There is a lack of head-to-head comparative studies of the effectiveness of a third booster dose of different mRNA-technology-based coronavirus disease 2019 (COVID-19) vaccines. An ideal comparative effectiveness study of mRNA vaccines should cover racially diverse populations and evaluate possible differences in vaccine efficacy based on the time when an individual completed the primary vaccination series. Most importantly, these studies should account for the time windows of the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants.

During the current SARS-CoV-2-induced pandemic, vaccination effectively reduced the burden of severe disease and death from COVID-19. Especially, booster doses of BNT162b2 and mRNA-1273 vaccines countered waning immunity and broadened protection against novel, highly transmissible SARS-CoV-2 variants. In one of their previous work covering 439,684 US veterans, researchers found that both mRNA-1273 and BNT162b2 lowered the risk of SARS-CoV-2 infection and severe disease outcomes during SARS-CoV-2 Alpha variant prevalence.

About the study

In the present study, researchers matched recipients of  BNT162b2 or mRNA-1273 vaccines in a 1:1 ratio based on their risk factors to estimate their comparative effectiveness over 16 and nine weeks in the Delta-Omicron and Omicron period, respectively, for five COVID-19 outcomes:

  • reported SARS-CoV-2 infection,
  • reported symptomatic SARS-CoV-2 infection,
  • SARS-CoV-2 infection-related hospitalization,
  • intensive care unit (ICU) admission, and
  • death.

The veterans in the first emulated trial received the third dose of BNT162b2 or mRNA-1273 vaccines between 20 October 2021 and 8 February 2022. This period corresponded to SARS-CoV-2 Delta and Omicron variants prevalence. For each veteran in the primary analysis, the team started follow-up on the day of the third vaccination (baseline). It ended 16 weeks after baseline, death, or the end of study duration, i.e., 15 February 2022, as applicable.

The veteran population of the second emulated trial received the third dose of any of the two mRNA COVID-19 vaccines between 1 January and 1 March 2022, the period of only Omicron predominance. The median follow-up continued over nine weeks, during which the team documented 214 SARS-CoV-2 infections.

Study findings

In the first emulated trial, 147,553 and 214,728 veterans received the third dose of BNT162b2 and mRNA-1273, respectively. The baseline characteristics of 65,196 BNT162b2 recipients matched to an equal number of mRNA-1273 recipients were comparable compared to the eligible population. The median age of this veteran population was 70 years, 96% were males, and 24% were Blacks.

During the 16-week follow-up spanning Delta and Omicron prevalence, the researchers documented 2,994 SARS-CoV-2 infections, of which 200 were symptomatic COVID-19 cases, 194 sought hospitalization, 52 needed ICU admission, and 22 culminated in death. During this time, the estimated risk of reported infection for the BNT162b2 and mRNA-1273 third dose was 353.9 and 308.5 events per 10,000 individuals, respectively.

In the second emulated trial, 25,557 and 36,809 eligible veterans received the third dose of BNT162b2 mRNA-1273, respectively. Like in the first trial, the matched population comprised 7,894 BNT162b2 and an equal number of mRNA-1273 recipients with comparable baseline demographic and clinical characteristics relative to the eligible population. They had a higher proportion of men and White people.

During nine weeks of follow-up amid Omicron predominance, the estimated risk of documented SARS-CoV-2 infection was higher with a third dose of the BNT162b2 vaccine vs. mRNA-1273. Accordingly, the estimated risk ratio was 1.57, presented as events per 10,000 individuals.

Conclusions

The present study remarkably showed the comparative effect of the third (booster) dose of two mRNA vaccines, BNT162b2  and mRNA-1272, among a nationwide cohort of US veterans. Both vaccines reduced the absolute risks of breakthrough SARS-CoV-2 infections and severe COVID-19 outcomes. However, mRNA-1273 recipients had a lower risk of COVID-19-related adverse events over 16 weeks of follow-up than the mRNA-1273 vaccine recipients, particularly for reported SARS-CoV-2 infections. The findings remained comparable across periods spanning Delta and Omicron predominance and only Omicron predominance. The authors advocated continuous evaluation of the comparative effectiveness and safety of additional (booster) doses of COVID-19 mRNA vaccines in the future.

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Microbiology

Bacterial outer membrane vesicles: utility as vaccines and novel engineering approaches

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Dr. Sanchari Sinha Dutta, Ph.D.By Dr. Sanchari Sinha Dutta, Ph.D.Jan 3 2023Reviewed by Danielle Ellis, B.Sc.

In an article published in Frontiers in Microbiology, scientists have described the utility of gram-negative bacteria-derived outer membrane vesicles as vaccines and methods to expand their applications.

Study: Outer membrane vesicles: A bacterial-derived vaccination system. Image Credit: Maxx-Studio/Shutterstock
Study: Outer membrane vesicles: A bacterial-derived vaccination system. Image Credit: Maxx-Studio/Shutterstock

Background

Outer membrane vesicles (OMVs) are spherical lipid nanoparticles with a diameter of 20-300 nm. These vesicles are derived from the cell membrane of Gram-negative bacteria and are composed of bacterial proteins, lipids, nucleic acids, and other components.

OMVs derived from pathogenic or non-pathogenic bacteria play an essential role in bacterial pathogenesis, cell-to-cell communication, horizontal gene transfer, quorum sensing, and maintaining bacterial fitness. However, as a non-replicative component, OMVs cannot induce disease pathogenesis independently.  

Bacterial proteins and glycans make OMVs a potent immunogenic component that can be used as adjuvants to induce host immune response. Because of this property, OMVs are considered potential candidates for vaccine development.

Isolation of OMVs

Gram-negative bacteria release OMVs during growth or in stressful conditions. However, such spontaneous OMVs are released in low quantities and, thus, cannot be used for large-scale vaccine production.

Several strategies have been developed to increase OMV production. Sonication, vortexing, or EDTA-mediated extraction have been applied to mechanically disrupt the bacterial membrane, leading to the release of OMVs.

OMVs extracted by EDTA closely relate to the native bacterial membrane and induce comparable immune responses. In contrast, sonication and vortexing increase the amount of non-membrane components in the final product, resulting in increased antigenicity and reduced safety.

Detergent-based extraction is another well-documented method that produces OMVs with reduced levels of lipopolysaccharides (LPS), which are bacterial toxins. Despite reducing the risk of toxicity, this process leads to the loss of many bacterial proteins and lipoproteins, which in turn results in the suppression of OMV-stimulated immune responses.

Manipulating certain bacterial genes can increase vesiculation and, thus, can produce high levels of genetically-modified OMVs. The genes encoding bacterial lipoproteins Lpp and NlpI and the outer membrane protein OmpA are the major targets for genetic manipulation.

Heterologous OMVs

Non-pathogenic bacterial strains can express heterologous proteins to reduce toxicity and improve the immunogenicity of OMVs.

A protein of interest can be fused with a bacterial transmembrane protein, and the resulting plasmid can be introduced into the bacterial strain, which will subsequently produce recombinant OMVs expressing the desired protein on the surface.

Another potential strategy for expressing heterologous proteins is glycoengineering of the LPS O antigen. Glycosylated OMVs can be produced by expressing the O antigen gene of a pathogen in a non-pathogenic O-antigen mutant strain of bacteria.

OMV-induced immune response

The pathogen-associated molecular patterns present on the OMV outer membrane activate the pattern recognition receptors on the host cells, leading to the activation of innate immune signaling and the release of proinflammatory cytokines. The engulfment of OMVs by innate immune cells induces adaptive immune responses.

LPS acts as an adjuvant to induce an effective host immune response to the bacterial antigen expressed on the OMV surface. However, overexpression of LPS can lead to overstimulation of immune responses and induction of systemic toxic shock. Detergent-based preparations or genetic manipulations can be used to reduce the level of highly reactive LPS on the OMV surface.

OMV-based vaccines

OMVs expressing desired antigens can be administered into the body through various routes, including oral/intranasal, intramuscular, subcutaneous, intraperitoneal, and intradermal. It has recently been shown that OMV expressing the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces robust immune responses in hamsters when administered intranasally.

Two clinically-approved OMV vaccines, VA-MENGOC-BC™ and Bexsero™, are currently available against the invasive N. meningitidis serogroup B strain. The PorA protein expressed by this bacterium is highly variable between strains. The OMVs derived from the meningitis-causing strain have been used successfully to develop vaccines against this particular bacterial strain.

Many OMV vaccines are currently under development. These vaccine candidates have been designed to target N. gonorrhoeae, Shigella spp., Salmonella spp., extraintestinal pathogenic E. coli (EXPEC), V. cholerae, M. tuberculosis, and non-typeable H. influenzae.    

Besides anti-bacterial vaccines, OMVs have been used to produce vaccines against viruses, including influenza virus and coronavirus. Tumor-targeted OMVs containing therapeutic siRNA or tumor antigens have also been developed as therapeutic cancer vaccines.

Journal reference:
Microbiology

Exploring dynamics of emergence and spread of SARS-CoV-2 variants of concern

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Tarun Sai LomteBy Tarun Sai LomteDec 15 2022Reviewed by Aimee Molineux

In a recent study posted to the medRxiv* preprint server, researchers evaluated the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in Canada.

Study: Emergence and Spread of SARS-CoV-2 Variants of Concern in Canada: a Retrospective Analysis from Clinical and Wastewater Data. Image Credit: PHOTOCREO Michal Bednarek/Shutterstock
Study: Emergence and Spread of SARS-CoV-2 Variants of Concern in Canada: a Retrospective Analysis from Clinical and Wastewater Data. Image Credit: PHOTOCREO Michal Bednarek/Shutterstock

Wastewater-based epidemiology (WBE) can ascertain the proportion of viral RNA by applying polymerase chain reaction (PCR) or sequencing techniques. WBE helps inform the public and health officials about coronavirus disease 2019 (COVID-19) outbreaks and trends. As such, clinical and wastewater surveillance data can be leveraged to improve estimates of VOC prevalence.

About the study

In the present study, researchers retrospectively analyzed the dynamics of SARS-CoV-2 VOC emergence and spread using clinical and wastewater data in Canada. The Public Health Agency of Canada (PHAC) records clinical COVID-19 case data. Some entries have data on the infecting SARS-CoV-2 variant/lineage determined by genome sequencing or screening via a discriminatory assay.

The PHAC, Statistics Canada, and the National Microbiology Laboratory (NML) initiated a pilot program in October 2020 to test for SARS-CoV-2 in wastewater specimens collected twice/thrice a week 15 from sewage treatment plants in multiple cities, including Edmonton, Montreal, Vancouver, Halifax, and Toronto. Besides, wastewater sampling was performed five times a week from three plants in Winnipeg.

Samples from these cities were shipped to NML for quantitative PCR (qPCR) analysis. In addition, the researchers included qPCR data on wastewater sampled three times a week from Saskatoon by the University of Saskatchewan. The NML and the University of Saskatchewan quantified the proportion of VOCs in wastewater. The authors focused on four SARS-CoV-2 VOCs (Alpha, Gamma, Delta, and Omicron) in this study.

Using PHAC records, VOC-infected clinical cases were identified, and confidence intervals (CIs) for the proportions of each variant were computed. To compute the growth rate, the authors assumed that time-dependent proportions of SARS-CoV-2 VOCs followed a logistic growth model during each wave. A similar logistic growth model with a hierarchical structure was applied to aggregate province-level clinical surveillance data into national estimates.

VOC proportions measured in wastewater were the percentages of variant alleles detected by assays. Due to limited data, wastewater data were not used to derive CIs or fit logistic models. Therefore, the growth rate of each variant was assessed using clinical data alone. Nonetheless, VOC proportions in wastewater were compared to those from clinical surveillance to assess similarities.

Findings

Results from the following provinces with large sample sizes were reported – Alberta, British Columbia, Manitoba, Newfoundland and Labrador, Ontario, Quebec, and Saskatchewan. The authors observed similar trends in SARS-CoV-2 VOC proportions across all provinces in clinical and wastewater data. In the Summer of 2021, Alpha, Gamma, and Delta VOCs likely cocirculated in Alberta, Saskatchewan, and British Columbia.

SARS-CoV-2 VOC transitions appeared faster in Quebec and Ontario. The proportion of unidentified VOCs in clinical data in each province was less than 80%, except during the early Alpha wave and post-July 2021 in Manitoba and Quebec. The proportions of SARS-CoV-2 VOCs in wastewater exhibited trends similar to those measured by clinical surveillance, particularly for the Omicron variant.

The Gamma VOC significantly circulated only in British Columbia, whereas the other three VOCs of interest circulated in all provinces. The Delta VOC spread at similar speeds across provinces, with Newfoundland and Labrador being the only outlier, likely due to the small sample size. Likewise, the Omicron VOC spread at a similar rate in provinces. SARS-CoV-2 Delta became predominant within four months.

Contrastingly, the Omicron VOC was the major circulating variant within a month. Posterior estimates suggested that the Alpha, Delta, and Omicron VOCs were spread throughout Canada by early January 2021, July 2021, and January 2022, respectively. In contrast, the maximum national proportion of the Gamma variant, which failed to spread throughout Canada, was approximately 25%.

Conclusions

To summarize, the study reported the spread of SARS-CoV-2 Alpha, Gamma, Delta, and Omicron VOCs in seven provinces in Canada using wastewater and clinical surveillance data. The researchers observed synchrony in SARS-CoV-2 VOC introduction across jurisdictions with similar speeds for each variant. This was remarkable, given the differences between provinces in implementing public health measures for COVID-19 management.

SARS-CoV-2 Gamma and Delta, which harbor few mutations, required four months to become the dominant variant. By contrast, the Omicron variant, which carries several novel mutations, became predominant in less than a month. Overall, WBE can complement clinical surveillance and serve as a viable indicator of SARS-CoV-2 VOC circulation in communities.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Microbiology

Researchers explore the correlation between the dynamic shedding pattern of SARS-CoV-2 and viral load

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Neha MathurBy Neha MathurDec 7 2022Reviewed by Aimee Molineux

In a recent article published in Nature Reviews Microbiology, researchers attempted to establish an association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load, indicating its ribonucleic acid (RNA) levels, and the presence of infectious virions.

Study: SARS-CoV-2 viral load and shedding kinetics. Image Credit: CROCOTHERY/Shutterstock
Study: SARS-CoV-2 viral load and shedding kinetics. Image Credit: CROCOTHERY/Shutterstock

Additionally, they examined host and other biological factors that affect infectious virion(s) shedding by SARS-CoV-2. They also evaluated the strengths and limitations of diagnostic tools that might help precisely estimate viral load, a robust substitute for characterizing the shedding of infectious virions by SARS-CoV-2.

Background

SARS-CoV-2 shedding patterns have become unique and distinguished from that of its ancestral strain in three years of the coronavirus disease 2019 (COVID-19) pandemic. The emergence of SARS-CoV-2 variants of concern (VOCs) has likely further complicated this pattern.

A detailed understanding of viral shedding patterns is crucial for designing public health interventions to contain human-to-human SARS-CoV-2 transmission. Although multifactorial, biological characteristics of SARS-CoV-2 and its variants, host factors, and pre-existing immunity of the diseased individual affect the shedding of its infectious virions, which, in turn, determines its onward transmission.

Nevertheless, viral load is a key parameter for estimating SARS-CoV-2 infectiousness, and a higher viral load in an infected individual’s upper respiratory tract (URT) implies a greater risk for onward transmission. To date, no diagnostic test precisely identifies or distinguishes between replication-competent SARS-CoV-2 and its residual RNA.

Factors at play in SARS-CoV-2 viral load and infectious virion(s) shedding dynamics

Reverse transcription-polymerase chain reaction (RT-PCR) assay, for instance, only detects viral RNA with high sensitivity in the respiratory tract of an infected individual, which remains detectable even in the absence of infectious virions. It presents results as viral RNA copies per milliliter of swab sample or by the discretionary test-specific cycle threshold (CT) value. Then, there could be SARS-CoV-2 RNA in peripheral blood, urine, ocular secretions, and the patient’s stool. Yet again, diagnostic tests are unable to detect infectious viruses in these non-respiratory specimens.

Contrastingly, RT-PCR estimates infectiousness qualitatively or quantitatively by viral replication in cell culture. Clinical samples with lower viral load often show delayed development of a cytopathic effect (CPE). Likewise, there are other methods for infectious virion quantification, such as plaque assays and focus-forming assays, to name a few. If swab samples are not immediately submerged in a viral transport medium and stored at −80 °C after collection, it loses viability resulting in complete loss of infectious virions. Other factors influencing successful virus isolation include cell lines used for isolation. Most importantly, working with SARS-CoV-2 infectious virions requires adherence to biosafety level 3 conditions, and detection of the viable virus is restricted to research only, deemed unsuitable for diagnostics. Likewise, CT values are only a weak predictor of infectious virions in the first five days post-onset of symptoms (dpos).

Antigen-detecting (rapid) diagnostic tests (Ag-RDT) fetch faster results and are inexpensive. They show good harmony with RT-PCR positivity when CT values are below 25 to 30, a viral load suggesting the presence of infectious virions; however, they fetch unreliable results at higher CT values. Further, it remains unclear whether Ag-RDT positivity beyond 10 dpos correlates with infectious virion(s) shedding. With the increasing presence of mucosal antibodies and rising hybrid immunity, Ag-RDTs may further lose sensitivity.

It is worth noting that it is difficult to estimate the time for which a SARS-CoV-2-infected individual remains infectious. A patient’s age, gender, immunity, and infecting variant; all these factors and more influence viral shedding dynamics. Studies showing the difference in the infectious virus titers between Alpha and Delta VOCs and ancestral SARS-CoV-2 have consistently fetched conflicting results. Nevertheless, both VOCs generate higher viral RNA loads than the parental strain, with an increased probability of cell culture isolation.

Despite its high transmissibility, Omicron led to much lower RNA viral loads and cell culture isolation probability. Studies have observed different behaviors of Omicron sublineages concerning infectious virus titers, with Omicron BA.2 leading to higher RNA viral loads and taking more time to clear infection than Omicron BA.1.

Infectious virion shedding by the ancestral SARS-CoV-2 strain resolved faster in those under 18 year-olds compared to individuals >50 years of age. A study showed its higher RNA loads for prolonged times in men infected with Alpha or Delta VOCs than in women. Furthermore, population-scale analysis of viral RNA loads in different age groups showed minimal differences in the dissemination of SARS-CoV-2 RNA load between adults and children; however, it had diminished in those below five years.

Studies have estimated the average incubation period of ancestral SARS-CoV-2 between 4.6 and 6.4 days. However, as the time of infection is often unknown, researchers use dpos when analyzing viral load and infectious virions. However, findings concerning viral shedding patterns have shown considerable heterogeneity in symptomatic and asymptomatic COVID-19 patients. Regardless of clinical symptoms, studies have detected high viral loads in the URT of infected individuals, which makes clinical symptoms – a not-so-robust indicator of infectiousness.

Likewise, the viral load of an index case is an unreliable proxy for SARS-CoV-2 transmission. Viral load can substantially vary between two individuals due to susceptibility and immunity from previous infections or vaccination, which affects their disposition to transmit SARS-CoV-2. In the same way, some sites, in particular, represent a higher risk of transmission; accordingly, many SARS-CoV-2 superspreading events typically occurred indoors in crowded places, such as music auditoriums, cruise ships, care centers, and hospitals.

Researchers have been pursuing several approaches to find a proxy for infectiousness to guide SARS-CoV-2 isolation techniques. In this context, single guide RNAs, transcribed in SARS-CoV-2-infected cells but not packaged in their infectious virions, could serve as a good proxy of infectious virions. However, the assays devised to detect sgRNAs with specific RT-PCR assays have yet to be successfully incorporated into routine diagnostic tools owing to their lower sensitivity. Also, the absence of sgRNA does not necessarily indicate infectiousness but the absence of active SARS-CoV-2 replication.

Conclusions

To summarize, all the currently available diagnostic tools have limitations concerning infectious SARS-CoV-2 virion detection. Though they have not been able to contain every SARS-CoV-2 infection, they are indispensable components of the anti-COVID-19 public health arsenal that have helped reduce the number of infectious individuals in the community and, subsequently, the number of secondary transmissions. Concerted and continuous efforts to evaluate viral-shedding characteristics amid changing biological properties of emerging SARS-CoV-2 variants would remain highly significant and help inform global future public health policies.

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