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Impact of the COVID-19 pandemic on the epidemiology and clinical course of tuberculosis: expected and paradoxical consequences
BMC Infectious Diseases volume 25, Article number: 417 (2025)
Abstract
Background
This study included tuberculosis (TB) patients from high-burden Russian regions of Siberia and Far East. We aimed to assess the impact of the COVID-19 pandemic on the genotypic structure of Mycobacterium tuberculosis population and on epidemiology and clinical course of tuberculosis in TB and TB/COVID-19 coinfected patients.
Methods
A total of 456 M. tuberculosis isolates were studied and submitted to drug susceptibility testing and genotyping. The modern Beijing genotype and its main Russian epidemic and endemic clusters (B0/W148 and Central Asian/Russian), and ancient Beijing sublineage were detected by PCR assays targeting specific molecular markers. Non-Beijing isolates were spoligotyped and compared to SITVIT2 database.
Results
More than 80% of strains belonged to the Beijing genotype. Among Beijing strains, genetic clusters B0/W148 and Central-Asian/Russian (94–32) accounted for 94.2% in the pre-pandemic period and 96.6% during the pandemic in the TB group, and 81.5% of TB/COVID-19 group. Moreover, in the pre-pandemic TB group, the ratio of B0/W148 and 94–32 was almost 1:1 (49.7:44.4%), during the pandemic—1.5:1.0 (57.9:38.8%), while in the TB/COVID-19 group, the ratio shifted in favor of the 94–32 cluster and became 1:2 (31.8:65.9%). In TB/COVID patients, the structure of clinical forms shifted from chronic forms (fibrous cavernous TB, tuberculoma) to forms with more active inflammatory and destructive-inflammatory reactions (infiltration, dissemination, cavernous TB). In TB (without COVID-19-coinfection) group, the effectiveness of TB treatment during the pandemic decreased by 20.6% (p = 0.002). In the TB/COVID-19 group, the effectiveness of treatment increased, likely due to the predominance of the less frequently MDR Beijing 94–32 cluster in this group. A statistically significant positive correlation was shown between the detection of the 94–32-cluster and the effectiveness of treatment of patients with TB/COVID-19 (Q = 0.56, p = 0.006).
Conclusions
Our results are consistent with the reportedly higher ability of Beijing B0/W148 strains (compared to Beijing 94–32) to acquire resistance to anti-TB drugs, their increased virulence and transmissibility. Thus, the seemingly paradoxical, milder clinical course of TB in patients who further developed COVID-19 is explained by a shift in the ratio of M. tuberculosis subtypes due to syndemic interaction between the two epidemics.
Background
According to the World Health Organization (WHO), in 2023, tuberculosis (TB) became the leading cause of death from infectious diseases, replacing COVID-19. Thus, mortality from coronavirus decreased to 400 thousand people, and tuberculosis claimed 1.2 million lives [1]. The highest number of tuberculosis cases was registered in India (26% of all cases), Indonesia (10%), China (6.8%), the Philippines (6.8%) and Pakistan (6.3%) [1]. In Russia, the incidence of tuberculosis continues to decline, and in 2023 this figure decreased by 4.7% compared to 2022—from 31.1 to 29.2 per 100,000 population [2]. Although WHO excluded Russia from the list of countries with high incidence rates, the country is among the top three in terms of the spread of drug-resistant tuberculosis. Russia has the highest number of patients with multidrug-resistant tuberculosis (MDR-TB (> 50% of previously treated cases in 2023) [1]. At the same time, approximately a third of MDR-TB cases are newly diagnosed patients, which indicates an active transmission of resistant strains of Mycobacterium tuberculosis.
Siberian and Far Eastern Federal Districts have the most unfavorable TB epidemic situation in Russia. In 2022, the TB incidence in Russia was 31.1, and the TB prevalence was 58.5 per 100,000 population, while in Siberia and the Far East these indicators were, respectively, for incidence of 58.7 and 57.7, and for prevalence—116.9 and 118.1 per 100,000 population. The prevalence of MDR-TB in 2022 in Russia, Siberia, and the Far East was 15.1, 33.4 and 30.2 per 100,000 population, respectively [3].
As a rule, at the level of a patient, combined infectious diseases, due to pathogenic interactions, aggravate each other or, much less often, make their course mutually milder. On the other hand, at the epidemic level, infections can interact syndemically, being influenced by dynamic factors of the biological and social environment, healthcare system, resource availability, administrative decisions, psychosocial relationships. During the COVID-19 pandemic, the availability of medical care against TB declined due to the redistribution of resources in favor of fighting the pandemic, the reduced activities of anti-TB services caused by limited mobility of self-isolated citizens, stopping of preventive X-ray and immunological examinations, interruptions in the supply of medicines and consumables for laboratories, etc. As a result, there was an under-detection of tuberculosis and a decrease in the effectiveness of its treatment [4,5,6].
In contrast, a mass X-ray examination of COVID-19 suspected persons could increase the detection rate of previously undiagnosed tuberculosis [7]. Furthermore, during the pandemic, the spread of TB infection could be reduced due to restrictions on social activity, isolation measures, and the general use of personal protective equipment, as well as the prescription of longer anti-TB chemotherapy regimens [8,9,10,11].
The real picture of the syndemic TB/COVID-19 relationship has not been analyzed either globally or in particular regions or countries [12,13,14]. Consequently, the following questions remain open: how epidemiological indicators for TB are changing in regions with different epidemic situations during the COVID-19 pandemic, is there any mutual influence of two pathogens on their transmissibility, and does the presence of one disease aggravate the course of the other. The use of molecular epidemiology methods may help to answer these questions.
The M. tuberculosis population in the Russian Federation is mainly represented by two genetic families or genotypes—the Beijing genotype (a major part of East Asian lineage) and the Latin-American Mediterranean (LAM) genotype [15,16,17]. The latter is one of many genotypes of the heterogeneous Euro-American lineage that also includes Ural, Haarlem, S, and other genotypes. The Beijing genotype isolates in Russia mostly belong to its modern sublineage, and, in particular, to the B0/W148-cluster and the heterogeneous Central-Asian/Russian clade (also designated 94–32-cluster) [18, 19]. Information on the phylogenetic position of these Beijing genotypes and their key characteristics are shown in Figure S1.
In this study, we aimed to evaluate potential changes in the genotypic structure of the M. tuberculosis population in Russian Siberia and the Far East during the COVID-19 pandemic. Additionally, we sought to determine whether the COVID-19 pandemic had any impact on the epidemiology and clinical course of tuberculosis in patients with TB alone and those coinfected with TB and COVID-19 within the surveyed region.
Methods
A prospective open cohort study was conducted from 2019 to 2021 (spanning both pre-pandemic and pandemic periods). The study included 455 patients with respiratory tuberculosis, aged 21 to 58 years, from regions within the Siberian and Far Eastern federal districts (15 regions in total), of whom 295 were men and 160 were women. The control group consisted of 255 men and 146 women, while the TB/COVID-19 group included 40 men and 14 women.
The inclusion criteria for the study were clinically diagnosed and bacteriologically confirmed respiratory tuberculosis, as well as clinically and PCR-confirmed COVID-19 (for the TB/COVID-19 group). Exclusion criteria included patients younger than 20 or older than 70 years.
According to the WHO classification, tuberculous pleurisy is categorized as extrapulmonary tuberculosis; however, the Russian classification considers it a form of pulmonary tuberculosis, and in this study, tuberculous pleurisy was classified as a form of pulmonary tuberculosis. The clinical forms of tuberculosis used in the study included focal TB, characterized by chronic fibro-focal or fresh, mildly focal, non-destructive inflammatory lesions less than 10–12 mm in diameter, localized within 1–2 lung segments; infiltrative TB, characterized by round, cloudy, or broncholobular infiltrates larger than 12 mm, which may progress to lobitis (extensive infiltrates occupying an entire lobe); disseminated pulmonary TB, characterized by bilateral, multiple (more than 5 in one segment) inflammatory lesions resulting from hematogenous or lymphogenous spread of mycobacteria; tuberculous pleurisy, involving inflammation of the pleural cavity, leading to intoxication and fluid accumulation; tuberculoma, a form of pulmonary TB characterized by dense, rounded inclusions or single foci in the lung containing caseous-necrotic masses, surrounded by productive inflammation and fibrosis, and encapsulated from adjacent lung tissue; cavernous TB, a chronic form of TB characterized by air-filled cavities in the lungs without significant inflammation in the surrounding tissue; fibrous cavernous TB, which is cavernous TB with pronounced fibrosis; caseous pneumonia, the most severe form of TB, with an acute, progressive course, necrotic zones in the lungs, and a tendency toward cavity formation; and cirrhotic TB, the final, irreversible stage of long-term tuberculosis, typically diffuse and bilateral, marked by extensive scarring in the lung parenchyma and pleura, with minimal activity of specific inflammation.
All patients underwent comprehensive clinical and radiological examinations and were prescribed chemotherapy in accordance with current clinical guidelines [20].
A total of 455 M. tuberculosis isolates were collected (Table S1). Of them, 401 isolates were obtained from patients with pulmonary TB (TB group; 198 in 2018–2019 and 203 in 2020–2021) and 54 samples were from patients with pulmonary TB who were infected with the SARS-CoV-2 virus and further developed COVID-19 disease (TB/COVID-19 group). Clinical isolates for the periods 2018–2019 and 2020–2021 were collected using stratification by gender, age, diagnosis, and medical history to ensure the representativeness of the sample from the same regions of the Siberian and Far Eastern federal districts. De-identified clinical data and treatment outcomes for all patients were collected using the Federal Tuberculosis Registry and patient medical records.
Cultivation of mycobacteria was carried out by inoculation on solid and liquid nutrient media (Loewenstein-Jensen medium, Bactec MGIT 960) followed by species identification. Phenotypic DST was carried out by the method of absolute concentrations on solid media, the method of proportions on liquid media using the automated Bactec MGIT960 system, the modified method of proportions on solid media, as well as the method of serial dilutions in 96-well TrecDiagnostic System plates. Detection of M. tuberculosis complex DNA and determination of drug resistance were carried out using GenXpert and GenoType MTBDRsl VER 1.0/2.0. All methods were performed according to the current national regulations [21,22,23,24].
M. tuberculosis DNA was extracted from cultured bacteria as described [25]. The initial differentiation of M. tuberculosis strains into Beijing and non-Beijing groups was carried out using PCR-based methods as described previously [26]. Further, Beijing genotype strains were tested for the presence of specific molecular markers to identify Beijing subtypes: B0/W148-cluster and Central-Asian/Russian (94–32) clade as described [27, 28]. Non-Beijing strains were spoligotyped as described [29] followed by comparison with the SITVIT2 database (http://www.pasteur-guadeloupe.fr:8081/SITVIT2/), for spoligotype international type (SIT) and clade assignment.
The Chi-square test was used to identify any significant differences between the two groups, and p-values were calculated with 95% confidence intervals. To assess the correlation, Yule's Q coefficient of association was used.
Results
Population structure of M. tuberculosis
The majority of the studied strains belonged to the Beijing genotype (90.1%; 410/455). The prevalence rate of the Beijing genotype in the three groups of patients (pre-pandemic TB group, pandemic TB group, and TB/COVID-19 group) did not differ significantly: 94.9%, 87.7%, and 81.5%, respectively.
The genetic clusters Beijing B0/W148 and 94–32 predominated in the total collection and accounted for 46.4% and 39.8%, respectively. During the pandemic, the percentages of the clusters changed sharply. In the pre-pandemic TB group, the ratio of B0/W148 and 94–32 was very close (49.7% and 44.4%, respectively). During the pandemic, the proportion of B0/W148 to 94–32 increased (57.9% vs 38.8%), while in the TB/COVID-19 group, on the contrary, the 94–32-cluster was double as prevalent compared to B0/W148 cluster (χ2 = 10.465, p = 0.002) (Fig. 1).
The number of non-Beijing isolates from TB patients during the pandemic increased compared to the pre-pandemic period from 5.1% to 12.3%, although overall their prevalence remained low. Furthermore, in the TB/COVID-19 group, non-Beijing strains were detected in 18.5% of isolates. All non-Beijing isolates belonged to Lineage 4 (Euro-American lineage). Spoligotyping revealed four non-Beijing genetic families: LAM, Ural, H, T (38 isolates), and 6 unclassified isolates. At the same time, the diversity of non-Beijing genotypes in the pandemic sample increased compared to the previous period 2018–2019.
During the pandemic, the ratio of the clusters did not change in the TB group. However, in the TB/COVID-19 group, the presence of 94–32-cluster in all territories except for the Tomsk region increased significantly.
HIV-coinfected patients accounted for 12.1% of all enrolled patients. These patients were evenly distributed between the TB and TB/COVID-19 groups. Regarding M. tuberculosis genotypes, the ratio of Beijing B0/W148 and Beijing 94–32 strains was approximately the same in the subgroups of TB patients with and without HIV coinfection. Therefore, HIV coinfection did not affect the population structure of M. tuberculosis in the TB and TB/COVID-19 groups.
Drug resistance of M. tuberculosis strains
In this study, only 34 (7.5%) of all 455 isolates were drug susceptible (DS). Irrespective of the genotype, drug-resistant strains made up 95% of the TB group in 2018–2019 and 94.5% in the TB group in 2020–2021. This was significantly higher than 73.6% of drug-resistant isolates in the TB/COVID-19 group (p = 0.001, χ2 = 16.835, Fig. 2). The high proportion of MDR isolates is due to the specific features of the studied collections biased towards patients with severe TB admitted at the National referral center in Novosibirsk.
In patients in the TB group infected with the Beijing genotype, before the pandemic, drug-resistant isolates were 24 times more frequent than drug-susceptible, during the pandemic—15.7 times, and in the TB/COVID group – only 5.3 times more prevalent. In all comparisons, the difference between the groups was significant (p < 0.001) (Fig. 3).
The decrease of drug-resistance appears to positively correlates with the decrease in the share of the B0/W148 cluster (Q = 0,73, p < 0,0001) in TB group and negatively correlates with the increase in the share of cluster 94–32 (Q = −0,44, p = 0,0012) in TB + COVID group.
The proportion of drug-resistant non-Beijing strains during the pandemic also decreased (3 times) compared to the pre-pandemic period (Fig. 3).
Clinical characteristics of TB
The following clinical forms of the disease were recorded: focal, infiltrative, tuberculoma, fibrous-cavernous, disseminated, cirrhotic, and caseous pneumonia (Fig. 4).
In the TB group in the pre-pandemic period, fibrous-cavernous tuberculosis (FCT) was the most common of all clinical forms; infiltrative forms and tuberculomas were in the 2nd and 3rd place in prevalence, followed by disseminated forms. In this group of TB patients, the pandemic had virtually no effect on the prevalence of these clinical forms. At the same time, in the TB/COVID group, the proportion of FCT decreased 3.5 times (p = 0,00036, χ2 = 12,73), and the proportion of tuberculomas fell to zero, the proportion of infiltrative TB, on the contrary, increased by 1.5 times (non-significantly), and the share of cavernous TB “jumped” from 0 to 27.8%. The pandemic itself had little effect on the structure of clinical forms of TB, but in patients with TB/COVID coinfection, this structure shifted away from chronic forms (FCT, tuberculomas) to forms with more active inflammatory and destructive-inflammatory reactions (infiltration, dissemination, cavernous TB).
Before the pandemic, FCT and tuberculomas were associated with B0/W148-cluster, respectively, 1.6 (p = 0,014, χ2 = 6,087) and 1.4 (p = 0,006, χ2 = 7,592) times more often than with 94 −32-cluster, infiltrative TB was distributed almost equally between these clones, and disseminated TB was associated 2.5 times more often with clone 94–32 (p = 0,013, χ2 = 6,250) (Table 1).
During the pandemic period, in TB patients without COVID-19 coinfection, this pattern was more pronounced: B0/W148 was found in FCT and tuberculomas groups even more often, exceeding 94–32, respectively, by 1.7 and 2.7 times, while in infiltrative and disseminated forms, 94–32 was more common. A positive correlation was revealed between active inflammatory and destructive-inflammatory processes (infiltrative, disseminated and cavernous tuberculosis) and the prevalence of strain 94–32 in the TB and TB/COVID-19 groups (Q = 0.59; p < 0.001), as well as a positive correlation was observed between chronic forms (tuberculoma and fibrous-cavernous tuberculosis) and B0/W148 strain in the TB group (Q = 0.68; p < 0.001).
During the pandemic, non-Beijing strains were associated with tuberculomas 2.7 times less often (p = 0,029, χ2 = 4,77), and with disseminated TB and FCT, respectively, 3.2 and 6.2 times more often (p = 0,05, χ2 = 3,730) than before the pandemic. This may suggest a relative severity of clinical forms caused by non-Beijing strains during the pandemic period.
Effectiveness of treatment
The criteria for the effectiveness of treatment in the study were the cessation of bacterial excretion, closure of foci of decay, and improvement of clinical parameters. The effectiveness of TB treatment during the pandemic decreased statistically significantly (p = 0.002) compared to the pre-pandemic period by 20.6%. The decrease in effectiveness during the pandemic may be explained by restrictive measures that reduce the availability of medical care, as well as the predominance during this period of a more pathogenic and drug-resistant cluster of M. tuberculosis—B0/W148. In the TB/COVID group, the effectiveness of treatment was higher than in the TB group during the pandemic by 14.1%, although it remained lower than in the pre-pandemic TB group. The seemingly paradoxical increase in the effectiveness of treatment in the group of patients with double pulmonary infection TB and COVID-19 may be associated with the predominance in this group of the M. tuberculosis Beijing 94–32 cluster, which is less pathogenic and more sensitive to anti-tuberculosis drugs. Indeed, while the proportions of effectively treated patients with tuberculosis caused by clusters B0/W148 and 94–32 in the period 2018–2021 differed slightly, then in the TB/COVID-19 group, the effectiveness of treatment of tuberculosis caused by cluster 94–32 was 5.3 times higher than the effectiveness of treatment of tuberculosis caused by B0/W148 (Fig. 5).
The effectiveness of TB treatment depended on the strain genotype. In patients infected with cluster 94–32, the number of ineffectively treated patients was only 14.2%, while among patients infected with cluster B0/W148, it was 60%. A statistically significant positive correlation was shown between cluster 94–32 and the effectiveness of treatment of patients with TB/COVID-19 (Q = 0.56, p = 0.006). Differences in treatment outcomes among patients infected with strains of different genotypes are influenced by multiple factors, including both external factors and internal factors related to the physio-pathological response to the two infections. However, the lack of detailed patient-specific information restricted the possibility of conducting a more in-depth analysis of this correlation.
Discussion
A wide prevalence of the Beijing M. tuberculosis strains especially the B0/W148 cluster has become one of the reasons for the high incidence of MDR/XDR-TB in Russia [15, 18, 30, 31]. Another important factor that had a serious impact on all aspects of healthcare control (both in Russia and throughout the world) became the COVID-19 pandemic [32,33,34,35]. This study analyzed trends of the changing population structure of M. tuberculosis (in particular when TB and TB/COVID groups were compared) that could be associated with the COVID-19 pandemic.
Before and during the pandemic, the Beijing genotype predominated in the M. tuberculosis population in all patient groups studied. The overall structure of the Beijing genotype was dominated by genetic clusters B0/W148 and 94–32. In the pre-pandemic period, the proportions of both clusters in the TB group were similar. However, during the pandemic, the prevalence rate of B0/W148 in the TB group increased and it was detected 1.5 times more frequently than in the 94–32-cluster. Regarding the TB/COVID group, on the contrary, the share of 94–32-cluster increased and it was detected 2 times more frequently than B0/W148. In our opinion, the increased rate of B0/W148 during the pandemic is well explained by the reported increased virulence and transmissibility of this strain [31, 36] and, as a result, its greater success/increased spread under restrictive measures. Contrary, the marked decrease in the prevalence rate of the B0/W148 subtype in the TB/COVID-19 group can be explained by a longer stay in the hospital and in self-isolation of such patients with more severe TB caused by B0/W148, and, accordingly, a decreased probability of infection with the SARS-CoV-2 virus. The role of restrictive measures in reducing the spread of COVID-19 was shown on the global dataset of 52 countries around the world [32].
The predominance of the less frequently drug-resistant 94–32-cluster strains in the TB/COVID-19 group can explain the more effective treatment of tuberculosis in such patients and consequently, less stringent restrictive measures and greater mobility – resulting in more frequent infection with SARS-CoV-2.
We also cannot exclude the possibility of interference between M. tuberculosis and SARS-CoV-2 caused by TB-mediated activation of the immune response (for example, interferon production) [37, 38]; the problem of “interpathogenic interference" has been studied very poorly. Changes in the M. tuberculosis population structure during the pandemic can be explained by both pathogenic and “syndemic” interepidemic interactions.
A comparison of the main Beijing subtypes showed that in patients infected with B0/W148 and 94–32, the pandemic reduced the proportion of drug resistance insignificantly, while in TB + COVID-19 patients the decrease in drug resistance was observed, which is largely explained by the decrease in the share of the cluster B0/W148 and an increase in the share of the 94–32-cluster. Thus, changes in the drug resistance in different groups of patients during the pandemic may be explained by the changes in the M. tuberculosis population structure.
The pandemic itself had little effect on the structure of clinical forms of TB. However, in TB patients with COVID-19, most of whom were affected by clone 94–32, this structure sharply shifts away from predominantly chronic forms (FCT, tuberculomas) to forms with more active inflammatory reactions (infiltration, dissemination) and phenomena of local destruction (cavernous tuberculosis). This is explained by the fact that in groups without COVID-19, patients with advanced forms of TB, such as FCT, were mainly affected by the B0/W148, which is less treatable and more often causes the progression of the disease. It is also possible that people in contact with COVID-19 infection and those suspected of having it were more likely to seek examination and, as a result, in the TB/COVID-19 group, TB was more often detected at earlier stages.
Limitations
The limitation of this study was that the studied M. tuberculosis samples were limited to the collections available at the National Referral Center and its clinics in Novosibirsk, where severe TB patients are admitted. However, all collections were based on the same criteria and thus are comparable.
Conclusions
This is the first study of the relationship between changes in the M. tuberculosis population structure and drug resistance, clinical forms of TB, and the effectiveness of TB treatment during the COVID-19 pandemic, including co-infection with M. tuberculosis and SARS-CoV-2. The simultaneous development of the epidemic processes caused by M. tuberculosis and the SARS-CoV-2 resulted in a complex syndemic interaction that took place, mutually influencing the provision of medical care, the clinical structure of morbidity, drug resistance, and the structure of pathogen populations. The disruptions in access to medical care caused by the pandemic were, on the one hand, important reasons for the decline in the effectiveness of treatment for TB patients. On the other hand, changes in the structure of M. tuberculosis genotypes, drug resistance, and clinical forms in the TB/COVID group, turned out to be factors in increasing this effectiveness. Our results show that during syndemics such as the TB epidemic combined with the COVID-19 pandemic, it is advisable to determine the ratio of the main clusters of M. tuberculosis as a prognostic criterion for the development of the epidemic process and the development of an optimal epidemic control strategy by national health authorities. These results emphasize that in large-scale epidemics of infectious diseases, epidemiological surveillance of the spread and diagnosis of tuberculosis infection must include methods for targeted detection of strains of different genotypes, in our case, strains of the Beijing B0/W148 and Beijing 94–32 subtypes.
Data availability
All data of this study are presented in the article and supplementary material.
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Acknowledgements
We thank Irina Felker for her participation in the preparation of primary material for the study.
Funding
This work was supported by the Russian Foundation for Basic Research grant No. 20-515-80006.
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Yakov Schwartz conceptualized the study, designed the experiments, performed project administration and data analysis and wrote the article; Anna Vyazovaya conceptualized the study, designed and performed experiments, Natalya Tursunova performed data analysis and wrote the article, Igor Mokrousov performed project administration and wrote the article. All authors have read and agreed to the submitted version of the manuscript.
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The study was approved by the Ethics Committee of the Federal Budgetary Institution “Novosibirsk Tuberculosis Research Institute” оf the Ministry of Health оf the Russian Federation (Protocol № 51 of 29 April 2021) and informed consent to participate was obtained from all of the participants in the study. All patient-related data were treated anonymously.
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Igor Mokrousov is Senior Editorial Board Member in BMC Microbiology. Other coauthors declare that no conflicts of interest exist.
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Schwartz, Y., Vyazovaya, A., Tursunova, N. et al. Impact of the COVID-19 pandemic on the epidemiology and clinical course of tuberculosis: expected and paradoxical consequences. BMC Infect Dis 25, 417 (2025). https://doi.org/10.1186/s12879-025-10793-x
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DOI: https://doi.org/10.1186/s12879-025-10793-x