The SARS-CoV-2 pandemic: remaining uncertainties in our understanding of the epidemiology and transmission dynamics of the virus, and challenges to be overcome

Factors associated with the worsening of COVID-19 symptoms among cohorts in community- or home-isolation care in southern Thailand

Introduction

This study aimed to investigate factors associated with time-to-referral due to worsening symptoms in patients with laboratory-confirmed COVID-19 in southern Thailand. While underlying diseases have been evaluated to assess COVID-19 severity, the influence of vaccinations and treatments is also crucial.

Methods

A cohort of 8,638 patients quarantined in home or community isolation with laboratory-confirmed COVID-19 was analyzed. Survival analysis and the Cox proportional hazard ratio were employed to assess factors influencing time-toreferral.

Results

Age ≥ 60 years, neurologic disorders, cardiovascular disease, and human immunodeficiency virus infection were identified as significant risk factors for severe COVID-19 referral. Patients who received full- or booster-dose vaccinations had a lower risk of experiencing severe symptoms compared to unvaccinated patients. Notably, individuals vaccinated during the Omicron-dominant period had a substantially lower time-to-referral than those unvaccinated during the Delta-dominant period. Moreover, patients vaccinated between 1 and 6 months prior to infection had a significantly lower risk of time-to-referral than the reference group.

Discussion

These findings demonstrate early intervention in high-risk COVID-19 patients and the importance of vaccination efficacy to reduce symptom severity. The study provides valuable insights for guiding future epidemic management strategies and optimising patient care during infectious disease outbreaks.

Impact of mAb-induced A475V substitution on viral fitness and antibody neutralization of SARS-CoV-2 omicron variants in the presence of monoclonal antibodies and human convalescent sera

The emergence and rapid evolution of SARS-CoV-2 variants have posed a major challenge to the global efforts to control the COVID -19 pandemic. In this study, we investigated the potential of two SARS-CoV-2 variants, BA.2 and BA.5, to evade neutralization by a human monoclonal antibody targeting the virus's spike RBD (mAb 1D1). By subjecting the viruses to serial propagation in the presence of the antibody, we found that BA.2 exhibited poor growth, whereas BA.5 regained robust growth with significantly higher kinetics than the parental virus. Genetic analysis identified a single mutation, A475V, in the spike protein of BA.5 that substantially reduced the neutralizing activities of monoclonal antibodies and convalescent sera. In addition, the A475V mutation alone in BA.2 moderately reduced the neutralizing activity but completely abolished the neutralizing effect of mAb 1D1 when F486V or L452R were also present. Our results shed light on the possible evolutionary development of SARS-CoV-2 variants under selection pressure by monoclonal antibodies and have implications for the development of effective antibody therapies and vaccines against the virus.

SARS-CoV-2 elicits non-sterilizing immunity and evades vaccine-induced immunity: implications for future vaccination strategies

Neither vaccination nor natural infection result in long-lasting protection against SARS-COV-2 infection and transmission, but both reduce the risk of severe COVID-19. To generate insights into optimal vaccination strategies for prevention of severe COVID-19 in the population, we extended a Susceptible-Exposed-Infectious-Removed (SEIR) mathematical model to compare the impact of vaccines that are highly protective against severe COVID-19 but not against infection and transmission, with those that block SARS-CoV-2 infection. Our analysis shows that vaccination strategies focusing on the prevention of severe COVID-19 are more effective than those focusing on creating of herd immunity. Key uncertainties that would affect the choice of vaccination strategies are: (1) the duration of protection against severe disease, (2) the protection against severe disease from variants that escape vaccine-induced immunity, (3) the incidence of long-COVID and level of protection provided by the vaccine, and (4) the rate of serious adverse events following vaccination, stratified by demographic variables.

Optimization of the Illumina COVIDSeq™ protocol for decentralized, cost-effective genomic surveillance

A decentralized surveillance system to identify local outbreaks and monitor SARS-CoV-2 Variants of Concern is one of the primary strategies for the pandemic's containment. Although next-generation sequencing (NGS) is a gold standard for genomic surveillance and variant discovery, the technology is still cost-prohibitive for decentralized sequencing, particularly in small independent labs with limited resources. We have optimized the Illumina COVIDSeq™ protocol for the Illumina MiniSeq instrument to reduce cost without compromising accuracy. We slashed the library preparation cost by half by using 50% of recommended reagents at each step and normalizing the libraries before pooling to achieve uniform coverage. Reagent-only cost (∼$43.27/sample) for SARS-CoV-2 variant analysis with this normalized input protocol on MiniSeq instruments is comparable to what is achieved on high throughput instruments such as NextSeq and NovaSeq. Using this modified protocol, we tested 153 clinical samples, and 90% of genomic coverage was achieved for 142/153 samples analyzed in this study. The lineage was correctly assigned to all samples (152/153) except for one. This modified protocol can help laboratories with constrained resources to contribute in decentralized COVID-19 surveillance in the post-vaccination era.

'Vaccinate my village' strategy in Malawi: an effort to boost COVID-19 vaccination

OBJECTIVES

To boost COVID-19 vaccine uptake, an innovative 'vaccinate my village' (VMV) strategy using door-to-door vaccination by Health Surveillance Assistants (HSA) was adopted. In this study, we assessed the impact of the 'vaccinate my village' strategy on COVID-19 vaccine uptake.

METHODS

This was a cross-sectional review of the data on COVID-19 vaccination obtained from the Ministry of Health, Malawi, from 11 March 2021 to September 2022.

RESULTS

From March 2021-4 September 2022,091,551 COVID-19 vaccine doses were administered, out of which 2,253,546 were administered over just six months as a part of VMV as compared to 1,838,005 doses were administered over 13 months as a part of other strategies. The proportion of Malawi's population receiving at least one dose of the COVID-19 vaccine increased substantially from 4.66 to 15.4 with the implementation of the VMV strategy (p = 0.0001). District-wise coverage of the COVID-19 vaccine also increased significantly after its implementation (p = 0.0001).

CONCLUSIONS

Door-to-door vaccination involving HSAs benefitted the COVID-19 vaccination program in Malawi by ensuring accessibility, availability, and acceptability.

Novel ACE2 fusion protein with adapting activity against SARS-CoV-2 variants in vitro

Despite the successful development of vaccines and neutralizing antibodies to limit the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerging variants prolong the pandemic and emphasize the persistent need to develop effective antiviral treatment regimens. Recombinant antibodies directed to the original SARS-CoV-2 have been successfully used to treat established viral disease. However, emerging viral variants escape the recognition by those antibodies. Here we report the engineering of an optimized ACE2 fusion protein, designated ACE2-M, which comprises a human IgG1 Fc domain with abrogated Fc-receptor binding linked to a catalytically-inactive ACE2 extracellular domain that displays increased apparent affinity to the B.1 spike protein. The affinity and neutralization capacity of ACE2-M is unaffected or even enhanced by mutations present in the spike protein of viral variants. In contrast, a recombinant neutralizing reference antibody, as well as antibodies present in the sera of vaccinated individuals, lose activity against such variants. With its potential to resist viral immune escape ACE2-M appears to be particularly valuable in the context of pandemic preparedness towards newly emerging coronaviruses.

Point-of-care detection of SARS-CoV-2 antigen among symptomatic vs. asymptomatic persons: Testing for COVID-19 vs. infectivity

Background

Management of the coronavirus disease 2019 (COVID-19) pandemic caused by a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) requires rapid and simple methods to detect COVID-19 patients and identify potential infectors. This study aimed to evaluate the utility of a point-of-care (PoC) rapid antigen diagnostic test (Ag-RDT) in these settings.

Patients and methods

Individuals who consecutively presented for SARS-CoV-2 testing at a tertiary care center in Buenos Aires, Argentina, underwent PoC Ag-RDT testing and real-time RT-PCR (qRT-PCR) on the same day during June 2021.

Results

Of 584 included subjects, 108 (18.5%) were symptomatic for COVID-19 while the remaining presented for miscellaneous reasons unrelated to possible or confirmed contact with a SARS-CoV-2-infected individual. A positive Ag-RDT result was obtained in 26 (24.1%) symptomatic and 7 (1.5%) asymptomatic persons (p < 0.001), which was concordant with qRT-PCR in 105/108 [97.2%, Cohen's kappa coefficient (κ) = 0.927] symptomatic and 467/476 (98.1% κ = 0.563) asymptomatic participants, with a positive percentage agreement (PPA; 95% confidence interval) of 89.7% (71.5-97.3%) and 42.9% (18.8-70.4%), respectively. None of the 11 false-negative diagnoses showed a C_t-value ≤20. Considering only failures with a C_t-value below 31 as hypothetical infectivity threshold of 10⁵ SARS-CoV-2 RNA copies/mL, concordance was observed in 98.1% (κ = 0.746) in the asymptomatic population, accounting for a PPA of 66.7% (30.9-91%).

Conclusions

PoC Ag-RDT accurately detected active SARS-CoV-2 infection and showed acceptable diagnostic performance in asymptomatic persons potentially spreading infectious virus. Ag-RDT may therefore be useful to slow down or stop transmission by enabling adequate decisions on isolation at a public health level.

Lessons Learned from the COVID-19 Pandemic and How Blood Operators Can Prepare for the Next Pandemic

Humans interact with virus-infected animal hosts, travel globally, and maintain social networks that allow for novel viruses to emerge and develop pandemic potential. There are key lessons-learned from the coronavirus diseases 2019 (COVID-19) pandemic that blood operators can apply to the next pandemic. Warning signals to the COVID-19 pandemic included outbreaks of Severe acute respiratory syndrome-related coronavirus-1 (SARS-CoV-1) and Middle East respiratory syndrome-related coronavirus (MERS-CoV) in the prior two decades. It will be critical to quickly determine whether there is a risk of blood-borne transmission of a new pandemic virus. Prior to the next pandemic blood operators should be prepared for changes in activities, policies, and procedures at all levels of the organization. Blood operators can utilize “Plan-Do-Study-Act” cycles spanning from: vigilance for emerging viruses, surveillance activities and studies, operational continuity, donor engagement and trust, and laboratory testing if required. Occupational health and donor safety issues will be key areas of focus even if the next pandemic virus is not transfusion transmitted. Blood operators may also be requested to engage in new activities such as the development of therapeutics or supporting public health surveillance activities. Activities such as scenario development, tabletop exercises, and drills will allow blood operators to prepare for the unknowns of the next pandemic.

Comparative Assessment of Severe Acute Respiratory Syndrome Coronavirus 2 Variants in the Ferret Model

The continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans necessitates evaluation of variants for enhanced virulence and transmission. We used the ferret model to perform a comparative analysis of four SARS-CoV-2 strains, including an early pandemic isolate from the United States (WA1), and representatives of the Alpha, Beta, and Delta lineages. While Beta virus was not capable of pronounced replication in ferrets, WA1, Alpha, and Delta viruses productively replicated in the ferret upper respiratory tract, despite causing only mild disease with no overt histopathological changes. Strain-specific transmissibility was observed; WA1 and Delta viruses transmitted in a direct contact setting, whereas Delta virus was also capable of limited airborne transmission. Viral RNA was shed in exhaled air particles from all inoculated animals but was highest for Delta virus. Prior infection with SARS-CoV-2 offered varied protection against reinfection with either homologous or heterologous variants. Notable genomic variants in the spike protein were most frequently detected following WA1 and Delta virus infection.

Incidence, Hospitalization, Mortality and Risk Factors of COVID-19 in Long-Term Care Residential Homes for Patients with Chronic Mental Illness

Long-term care residential homes (LTCRH) for patients with chronic mental illness have suffered the enormous impact of COVID-19. This study aimed to estimate incidence, hospitalization, mortality, and risk factors of COVID-19 to prevent future epidemics. From March 2020 to January 2021 and before vaccination anti-SARS-CoV-2 begins, cumulate incidence rate (CIR), hospitalization rate (HR), mortality rate (MR), and risk factors of COVID-19 in the 11 LTCRH of two Health Departments of Castellon (Spain) were studied by epidemiological surveillance and an ecological design. Laboratory tests confirmed COVID-19 cases, and multilevel Poisson regression models were employed. All LTCRH participated and comprised 346 residents and 482 staff. Residents had a mean age of 47 years, 40% women, and suffered 75 cases of COVID-19 (CIR = 21.7%), five hospitalizations (HR = 1.4%), and two deaths (MR = 0.6%) with 2.5% fatality-case. Staff suffered 74 cases of the disease (CIR = 15.4%), one hospitalization (HR = 0.2%), and no deaths were reported. Risk factors associated with COVID-19 incidence in residents were private ownership, severe disability, residents be younger, CIR in municipalities where LTCRH was located, CIR in staff, and older age of the facilities. Conclusion: COVID-19 incidence could be prevented by improving infection control in residents and staff and modernizing facilities with increased public ownership.

Nano-multilamellar lipid vesicles promote the induction of SARS-CoV-2 immune responses by a protein-based vaccine formulation

The development of safe and effective vaccine formulations against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents a hallmark in the history of vaccines. Here we report a COVID-19 subunit vaccine based on a SARS-CoV-2 Spike protein receptor binding domain (RBD) incorporated into nano-multilamellar vesicles (NMV) associated with monophosphoryl lipid A (MPLA). The results based on immunization of C57BL/6 mice demonstrated that recombinant antigen incorporation into NMVs improved antibody and T-cell responses without inducing toxic effects under both in vitro and in vivo conditions. Administration of RBD-NMV-MPLA formulations modulated antigen avidity and IgG subclass responses, whereas MPLA incorporation improved the activation of CD4⁺/CD8⁺ T-cell responses. In addition, immunization with the complete vaccine formulation reduced the number of doses required to achieve enhanced serum virus-neutralizing antibody titers. Overall, this study highlights NMV/MPLA technology, displaying the performance improvement of subunit vaccines against SARS-CoV-2, as well as other infectious diseases.

A prospective multicenter study on cutaneous reactions reported after Sinopharm COVID-19 vaccination

BACKGROUND

The new coronavirus COVID-19 pandemic has had an unprecedented impact on global health and economic growth. A widely used vaccine is the weakened inactivated severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) virus (Sinopharm). Following major SARS-CoV-2 vaccination campaigns, cutaneous symptoms are on the rise.

METHODS

This study is a prospective observational study evaluating cutaneous reactions and time of recovery after Sinopharm vaccination. The cases involved were over the age of 18. The data were anonymized. On the registry's vaccine section, we tracked vaccination dates, skin reactions, and recovery times. All respondents who reported only a cutaneous reaction to the first vaccination dose received a follow-up contact asking about a second vaccination dose cutaneous reaction.

RESULTS

The study included 4560 cases. The mean age of all studied cases was 41.2 ± 6.1 years. There were dermatologic complications in 1190 patients (26.1%). There was induration at the injection site in 495 patients (10.9%), urticaria in 210 patients (4.6%), morbilliform eruption in 375 patients (8.2%), flare of skin site in 105 patients (2.3%), and angioedema in 105 patients (2.3%). The mean recovery days in all studied patients were 2.92 ± 0.94 days with a minimum recovery period of 2 days and a maximum of 7 days.

CONCLUSIONS

Because Sinopharm's cutaneous reactions are frequently mild and self-limiting, vaccination should not be discouraged based on these findings. If the first vaccine dose creates a cutaneous reaction, there is no need to skip the second dose.

COVID-19 vaccine express strategy in Malawi: An effort to reach the un-reach

Objectives

To establish the impact of “Covid-19 Vaccination express” (CVE) on vaccine uptake in Malawi

Design

Retrospective cross-sectional study to compare the daily vaccine administration rate in CVE and routine covid vaccination (RCV). RCV data was collected from March 2021 to October 2021. The data regarding CVE was collected from 5 November 2021 to 31 December 2021. Data was collected regarding (1) the total number and type of vaccine doses administered and (2) Demographic details like age, gender, occupation, presence of comorbidities, the first dose, or the second dose of the people who received a vaccine.

Results

From March-December 2021, a total of 1,866,623 COVID-19 vaccine doses were administered, out of which 1,290,145 doses were administered at a mean daily vaccination rate of 1854 (95% CI: 1292-2415) doses as a part of RCV, and 576,478 doses were administered at a mean daily vaccination rate of 3312 (95% CI: 2377-4248) doses as a part of CVE.

Comparing the mean daily doses (Astra Zeneca, AZ doses 1 & 2) administered in the CVE and RCV showed that the mean daily doses of AZ vaccine administered were significantly higher in the CVE (p<0.05).

Conclusion

CVE successfully increased the uptake of the Covid-19 vaccine.

Addressing vaccine hesitancy and resistance for COVID-19 vaccines

The COVID-19 vaccine rollout has had various degrees of success in different countries. Achieving high levels of vaccine coverage is key to responding to and mitigating the impact of the pandemic on health and aged care systems and the community. In many countries, vaccine hesitancy, resistance, and refusal are emerging as significant barriers to immunisation uptake and the relaxation of policies that limit everyday life. Vaccine hesitancy/ resistance/ refusal is complex and multi-faceted. Individuals and groups have diverse and often multiple reasons for delaying or refusing vaccination. These reasons include: social determinants of health, convenience, ease of availability and access, health literacy understandability and clarity of information, judgements around risk versus benefit, notions of collective versus individual responsibility, trust or mistrust of authority or healthcare, and personal or group beliefs, customs, or ideologies. Published evidence suggests that targeting and adapting interventions to particular population groups, contexts, and specific reasons for vaccine hesitancy/ resistance may enhance the effectiveness of interventions. While evidence regarding the effectiveness of interventions to address vaccine hesitancy and improve uptake is limited and generally unable to underpin any specific strategy, multi-pronged interventions are promising. In many settings, mandating vaccination, particularly for those working in health or high risk/ transmission industries, has been implemented or debated by Governments, decision-makers, and health authorities. While mandatory vaccination is effective for seasonal influenza uptake amongst healthcare workers, this evidence may not be appropriately transferred to the context of COVID-19. Financial or other incentives for addressing vaccine hesitancy may have limited effectiveness with much evidence for benefit appearing to have been translated across from other public/preventive health issues such as smoking cessation. Multicomponent, dialogue-based (i.e., communication) interventions are effective in addressing vaccine hesitancy/resistance. Multicomponent interventions that encompasses the following might be effective: (i) targeting specific groups such as unvaccinated/under-vaccinated groups or healthcare workers, (ii) increasing vaccine knowledge and awareness, (iii) enhanced access and convenience of vaccination, (iv) mandating vaccination or implementing sanctions against non-vaccination, (v) engaging religious and community leaders, (vi) embedding new vaccine knowledge and evidence in routine health practices and procedures, and (vii) addressing mistrust and improving trust in healthcare providers and institutions via genuine engagement and dialogue. It is universally important that healthcare professionals and representative groups, as often highly trusted sources of health guidance, should be closely involved in policymaker and health authority decisions regarding the establishment and implementation of vaccine recommendations and interventions to address vaccine hesitancy.

Hematological- and Immunological-Related Biomarkers to Characterize Patients with COVID-19 from Other Viral Respiratory Diseases

COVID-19 has overloaded health system worldwide; thus, it demanded a triage method for an efficient and early discrimination of patients with COVID-19. The objective of this research was to perform a model based on commonly requested hematological variables for an early featuring of patients with COVID-19 form other viral pneumonia. This investigation enrolled 951 patients (mean of age 68 and 56% of male) who underwent a PCR test for respiratory viruses between January 2019 and January 2020, and those who underwent a PCR test for detection of SARS-CoV-2 between February 2020 and October 2020. A comparative analysis of the population according to PCR tests and logistic regression model was performed. A total of 10 variables were found for the characterization of COVID-19: age, sex, anemia, immunosuppression, C-reactive protein, chronic obstructive pulmonary disease, cardiorespiratory disease, metastasis, leukocytes and monocytes. The ROC curve revealed a sensitivity and specificity of 75%. A deep analysis showed low levels of leukocytes in COVID-19-positive patients, which could be used as a primary outcome of COVID-19 detection. In conclusion, this investigation found that commonly requested laboratory variables are able to help physicians to distinguish COVID-19 and perform a quick stratification of patients into different prognostic categories.

SARS-CoV-2: phenotype, genotype, and characterization of different variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19), a major international public health concern. Because of very similar amino acid sequences of the seven domain names, SARS-CoV-2 belongs to the Coronavirinae subfamily of the family Coronaviridae, order Nidovirales, and realm Riboviria, placed in exceptional clusters, but categorized as a SARS-like species. As the RNA virus family with the longest genome, the Coronaviridae genome consists of a single strand of positive RNA (25–32 kb in length). Four major structural proteins of this genome include the spike (S), membrane (M), envelope (E), and the nucleocapsid (N) protein, all of which are encoded within the 3′ end of the genome. By engaging with its receptor, angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 infects host cells. According to the most recent epidemiological data, as the illness spread globally, several genetic variations of SARS-CoV-2 appeared quickly, with the World Health Organization (WHO) naming 11 of them. Among these, seven SARS-CoV-2 subtypes have received the most attention. Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.617.2) are now designated as variations of concern (VOC) (B.1.1.529). Lambda (C.37) and Mu are variations of interest (VOI) (B.1.621). The remaining six are either being monitored or are no longer considered a threat. On the basis of studies done so far, antiviral drugs, antibiotics, glucocorticoids, recombinant intravenous immunoglobulin, plasma therapy, and IFN-α2b have been used to treat patients. Moreover, full vaccination is associated with lower infection and helps prevent transmission, but the risk of infection cannot be eliminated completely in vaccinated people.

Genome Sequences of 408 SARS-CoV-2 Strains Obtained from Nasopharyngeal Swabs in La Araucanía Region, Southern Chile

Here, we announce the genome sequences of 408 strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) obtained from nasopharyngeal swabs in the Araucanía Region, Southern Chile. The genomes obtained are valuable to expand the availability of useful genomic data for future epidemiological studies of SARS-CoV-2 in Chile and worldwide.

Significance of Immune Status of SARS-CoV-2 Infected Patients in Determining the Efficacy of Therapeutic Interventions

Coronavirus disease 2019 (COVID-19) is now being investigated for its distinctive patterns in the course of disease development which can be indicated with miscellaneous immune responses in infected individuals. Besides this series of investigations on the pathophysiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), significant fundamental immunological and physiological processes are indispensable to address clinical markers of COVID-19 disease and essential to identify or design effective therapeutics. Recent developments in the literature suggest that deficiency of type I interferon (IFN) in serum samples can be used to represent a severe progression of COVID-19 disease and can be used as the basis to develop combined immunotherapeutic strategies. Precise control over inflammatory response is a significant aspect of targeting viral infections. This account presents a brief review of the pathophysiological characteristics of the SARS-CoV-2 virus and the understanding of the immune status of infected patients. We further discuss the immune system’s interaction with the SARS-CoV-2 virus and their subsequent involvement of dysfunctional immune responses during the progression of the disease. Finally, we highlight some of the implications of the different approaches applicable in developing promising therapeutic interventions that redirect immunoregulation and viral infection.

SARS-CoV-2 vaccine protection and deaths among US veterans during 2021

We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine effectiveness against infection (VE-I) and death (VE-D) by vaccine type in 780,225 veterans in the Veterans Health Administration, covering 2.7% of the US population. From February to October 2021, VE-I declined for all vaccine types, and the decline was greatest for the Janssen vaccine, resulting in a VE-I of 13.1%. Although breakthrough infection increased risk of death, vaccination remained protective against death in persons who became infected during the Delta variant surge. From July to October 2021, VE-D for age <65 years was 73.0% for Janssen, 81.5% for Moderna, and 84.3% for Pfizer-BioNTech; VE-D for age ≥65 years was 52.2% for Janssen, 75.5% for Moderna, and 70.1% for Pfizer-BioNTech. Findings support continued efforts to increase vaccination, booster campaigns, and multiple additional layers of protection against infection.

Role of Probiotics in the Management of COVID-19: A Computational Perspective

Coronavirus disease 2019 (COVID-19) was declared a pandemic at the beginning of 2020, causing millions of deaths worldwide. Millions of vaccine doses have been administered worldwide; however, outbreaks continue. Probiotics are known to restore a stable gut microbiota by regulating innate and adaptive immunity within the gut, demonstrating the possibility that they may be used to combat COVID-19 because of several pieces of evidence suggesting that COVID-19 has an adverse impact on gut microbiota dysbiosis. Thus, probiotics and their metabolites with known antiviral properties may be used as an adjunctive treatment to combat COVID-19. Several clinical trials have revealed the efficacy of probiotics and their metabolites in treating patients with SARS-CoV-2. However, its molecular mechanism has not been unraveled. The availability of abundant data resources and computational methods has significantly changed research finding molecular insights between probiotics and COVID-19. This review highlights computational approaches involving microbiome-based approaches and ensemble-driven docking approaches, as well as a case study proving the effects of probiotic metabolites on SARS-CoV-2.