Epidemiology, clinical characteristics, and virologic features of COVID-19 patients in Kazakhstan: A nation-wide retrospective cohort study

Abstract

Background: The earliest coronavirus disease-2019 (COVID-19) cases in Central Asia were announced in March 2020 by Kazakhstan. Despite the implementation of aggressive measures to curb infection spread, gaps remain in the understanding of the clinical and epidemiologic features of the regional pandemic.

Methods: We did a retrospective, observational cohort study of patients with laboratory-confirmed COVID-19 hospitalized in Kazakhstan between February and April 2020. We compared demographic, clinical, laboratory and radiological data of patients with different COVID-19 severities on admission. Logistic regression was used to assess factors associated with disease severity and in-hospital death. Whole-genome SARS-CoV-2 analysis was performed in 53 patients.

Findings: Of the 1072 patients with laboratory-confirmed COVID-19 in March-April 2020, the median age was 36 years (IQR 24-50) and 484 (45%) were male. On admission, 683 (64%) participants had asymptomatic/mild, 341 (32%) moderate, and 47 (4%) severe-to-critical COVID-19 manifestation; 20 in-hospital deaths (1•87%) were reported by 5 May 2020. Multivariable regression indicated increasing odds of severe disease associated with older age (odds ratio 1•05, 95% CI 1•03-1•07, per year increase; p<0•001), the presence of comorbidities (2•34, 95% CI 1•18-4•85; p=0•017) and elevated white blood cell count (WBC, 1•13, 95% CI 1•00-1•27; p=0•044) on admission, while older age (1•09, 95% CI 1•06-1•13, per year increase; p<0•001) and male sex (5•63, 95% CI 2•06-17•57; p=0•001) were associated with increased odds of in-hospital death. The SARS-CoV-2 isolates grouped into seven phylogenetic lineages, O/B.4.1, S/A.2, S/B.1.1, G/B.1, GH/B.1.255, GH/B.1.3 and GR/B.1.1.10; 87% of the isolates were O and S sub-types descending from early Asian lineages, while the G, GH and GR isolates were related to lineages from Europe and the Americas.

Interpretation: Older age, comorbidities, increased WBC count, and male sex were risk factors for COVID-19 disease severity and mortality in Kazakhstan. The broad SARS-CoV-2 diversity suggests multiple importations and community-level amplification predating travel restriction.

Funding: Ministry of Education and Science of the Republic of Kazakhstan.

Keywords: COVID-19; Central Asia; Clinical characteristics; Disease risk factors; Disease severity; Kazakhstan; Molecular epidemiology; SARS-CoV-2; SARS-CoV-2 genomics.

Figure 1

A. The retrospective cohort study profile, B. The SARS-CoV-2 genomic study profile.

Figure 2

Epidemic curve of the confirmed COVID-19 cases in the current study compared to the official statistics on confirmed COVID-19 cases in Kazakhstan in March-April 2020 according to the Republican Centre for Health Development and World Health Organization (WHO). Official statistics were obtained from the WHO website .

Figure 3

Distribution of patients with laboratory-confirmed COVID-19 across Kazakhstan. Based on data for 573 patients, for whom the site of initial diagnosis was known in the current study.

Figure 4

Regions of travel and transportation used by laboratory-confirmed COVID-19 patients with a recent history of international travel.

Figure 5

A. Phylogenetic tree depicting the Kazakhstan (“Kaz”) virus isolates in the context of globally circulating SARS-CoV-2 lineages. Each clade is denoted by a corresponding Global Initiative on Sharing All Influenza Data (GISAID) clade name; the Pangolin lineage names are given in brackets. Branch lengths measured in units of substitutions per site. Tree is coloured based on the GISAID nomenclature (see legend). B. Phylodynamic analysis of the Kazakhstan SARS-CoV-2 sequences in the international context. Maximum likelihood tree of Kazakhstan viral sequences and a subset of international sequences (see Methods), coloured by region of origin.