pathogens Article Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level Malik Sallam 1,2,* and Azmi Mahafzah 1,2 1 Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan; [email protected] 2 Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan * Correspondence: [email protected]; Tel.: +962-79-184-5186 Abstract: The rapid evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is manifested by the emergence of an ever-growing pool of genetic lineages. The aim of this study was to analyze the genetic variability of SARS-CoV-2 in Jordan, with a special focus on the UK variant of concern. A total of 579 SARS-CoV-2 sequences collected in Jordan were subjected to maximum likelihood and Bayesian phylogenetic analysis. Genetic lineage assignment was undertaken using the Pango system. Amino acid substitutions were investigated using the Protein Variation Effect Analyzer (PROVEAN) tool. A total of 19 different SARS-CoV-2 genetic lineages were detected, with the most frequent being the first Jordan lineage (B.1.1.312), first detected in August 2020 (n = 424, 73.2%). This was followed by the second Jordan lineage (B.1.36.10), first detected in September 2020 (n = 62, 10.7%), and the UK variant of concern (B.1.1.7; n = 36, 6.2%). In the spike gene region, Citation: Sallam, M.; Mahafzah, A. the molecular signature for B.1.1.312 was the non-synonymous mutation A24432T resulting in a Molecular Analysis of SARS-CoV-2 deleterious amino acid substitution (Q957L), while the molecular signature for B.1.36.10 was the Genetic Lineages in Jordan: Tracking synonymous mutation C22444T. Bayesian analysis revealed that the UK variant of concern (B.1.1.7) the Introduction and Spread of COVID-19 UK Variant of Concern at a was introduced into Jordan in late November 2020 (mean estimate); four weeks earlier than its official Country Level. Pathogens 2021, 10, reporting in the country. In Jordan, an exponential increase in COVID-19 cases due to B.1.1.7 lineage 302. https://doi.org/10.3390/ coincided with the new year 2021. The highest proportion of phylogenetic clustering was detected pathogens10030302 for the B.1.1.7 lineage. The amino acid substitution D614G in the spike glycoprotein was exclusively present in the country from July 2020 onwards. Two Jordanian lineages dominated infections in the Academic Editor: country, with continuous introduction/emergence of new lineages. In Jordan, the rapid spread of the Robert Colebunders UK variant of concern should be monitored closely. The spread of SARS-CoV-2 mutants appeared to be related to the founder effect; nevertheless, the biological impact of certain mutations should be Received: 4 February 2021 further investigated. Accepted: 3 March 2021 Published: 5 March 2021 Keywords: COVID-19; epidemiology; middle-income country; variant; mutation; UK variant; variant of concern Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. 1. Introduction The evolutionary analysis of severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) is appealing for several reasons. First, this novel virus harbours a ribonucleic acid (RNA) genome, with replication Copyright: © 2021 by the authors. using RNA-dependent RNA polymerase. This replicase enzyme has a minimal proofread- Licensee MDPI, Basel, Switzerland. ing activity; the hallmark of rapidly-evolving viruses (e.g., influenza virus and hepatitis C This article is an open access article virus) [1,2]. distributed under the terms and conditions of the Creative Commons In addition, the pandemic nature of coronavirus disease 2019 (COVID-19), with more Attribution (CC BY) license (https:// than 100 million detected cases so far, translates into a huge pool of susceptible hosts with creativecommons.org/licenses/by/ varying selective pressure on the viral genome [3,4]. This resulted in rapid divergence of 4.0/). Pathogens 2021, 10, 302. https://doi.org/10.3390/pathogens10030302 https://www.mdpi.com/journal/pathogens Pathogens 2021, 10, 302 2 of 12 the novel virus from its common ancestor that crossed the species barrier, accompanied by a noticeable genetic diversity in less than a year [5–7]. Moreover, the evolutionary analysis of viruses is helpful for epidemiologic pur- poses [6,8]. Characterization of SARS-CoV-2 genetic variants (monophyletic clades des- ignated as genetic lineages herein) is valuable to track the dynamics of its introduction and dissemination within a certain region [6,9]. Additionally, a consensus on SARS-CoV- 2 nomenclature and classification is invaluable for correlating the genetic diversity of the virus with potential biological differences (e.g., antigenicity, transmissibility, viru- lence) [5,10]. Besides the aforementioned points, phylogenetic studies on SARS-CoV-2 are facilitated by the burgeoning availability of genetic sequences of the virus, as a result of advancement in sequencing technology [5]. As of 3 February 2021; the total number of full-genome SARS-CoV-2 sequences exceeded 400,000 in the global science initiative and primary source for genomic data of influenza viruses (GISAID) [11]. To characterize the genetic lineages of SARS-CoV-2, a comprehensive and dynamic nomenclature/classification scheme was proposed by Rambaut et al. and was referred to as “Pango nomenclature system (from the first-person Latin verb meaning ‘I set’, ‘I fix’ or ‘I record’)” [5,12]. In the Pango system, the following notable lineages have been described so far: (1) lineage A, which dates back to December 2019, and contains the root of COVID-19 pandemic; (2) lineage B, which has Chinese sequences in its base, with branching indicating global exports; (3) lineage B.1, which dates back to January 2020 corresponding to the Italian outbreak; (4) lineage B.1.1.7 (a.k.a. the UK variant of concern) that was detected in the UK in September 2020 with N501Y and P681H as the most notable amino acid substitutions; (5) lineage B.1.351 which dates back to December 2020 (the South African variant) with N501Y, K417N, and E484K as the most notable amino acid substitutions; and (6) lineage P.1 (the Brazilian variant) that was first detected in December 2020 with N501Y, and E484K as the most notable amino acid substitutions [5,13–17]. Amino acid substitutions have been described in SARS-CoV-2 isolates across the world, with possible biological value pending further evidence [18–21]. Substitutions in the surface (spike) glycoprotein is of particular concern considering its importance in receptor binding and being a target for neutralizing antibodies [22]. The most notable example of such substitutions is the replacement of aspartic acid by glycine at position 614 of the spike glycoprotein of the virus (D614G). The predominance of such substitution was observed in various regions including the Middle East and North Africa [23,24]. Another amino acid substitutions with potential significance include N501Y and E484K in the receptor binding domain of the spike glycoprotein [18,25]. In Jordan, the COVID-19 epidemic went through several phases. In March 2020, mitigation measures took place including travel restrictions, wide lockdowns and curfew, enforcement of masks and social distancing, and prohibition of large gatherings [26,27]. This resulted in clusters of cases during the first five months. However, the inevitable SARS- CoV-2 dissemination started in August/September 2020 when the first wave of community transmission took place [27,28]. Following the peak in active cases and mortality in November 2020, a decline in the number of newly diagnosed cases and deaths was reported in 20 December 2020 and January 2021. The first reporting of B.1.1.7 UK variant of concern dated back to 24 December 2020, and the start of COVID-19 vaccination in the country took place in mid-January 2021 [27]. Several challenges face the country amid the current COVID- 19 epidemic including the widespread prevalence of misinformation and conspiracy beliefs, in addition to vaccine hesitancy [26,29,30]. Additionally, the scarcity of molecular and epidemiologic studies on the virus in Jordan can hamper the control efforts in the country. Thus, the aims of the current study were: (1) to describe the genetic diversity of SARS-CoV-2 in Jordan by analysis of the virus lineages; (2) to analyze the proportion of phylogenetic clustering indicative of local virus spread among the major lineages in the Pathogens 2021, 10, 302 3 of 12 country; and (3) to estimate the timing of the introduction of the UK variant of concern (B.1.1.7) into the country. 2. Results 2.1. Characteristics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Jordanian Dataset The total number of GISAID SARS-CoV-2 sequences collected in Jordan and utilized in this study were 579 full-genome sequences. Stratified per month, the number of SARS- CoV-2 sequences collected in the country together with total number of COVID-19 cases and deaths in Jordan are shown in (Table1). The majority of SARS-CoV-2 sequences were collected in October 2020 (n = 344, 59.4%) and September (n = 103, 17.8%), which coincided with surge in number of newly diagnosed COVID-19 cases in the country. Table 1. The total number of coronavirus disease 2019 (COVID-19) new cases, deaths and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences in Jordan (March 2020–January 2021). Newly Diagnosed COVID-19 Related Number of SARS-CoV-2 2 Percentage of Sequences Month COVID-19 1 Cases Deaths Sequences Compared to New Cases March 2020 274 5 22 8.0292% April 2020 179 3 6 3.3520% May 2020 286 1 0 0 June 2020 393 0 4 1.0178% July 2020 61 2 2 3.2787% August 2020 841 4 15 1.7836% September 2020 9791 46 103 1.0520% October 2020 60,782 768 344 0.5660% November 2020 146,823 1922 43 0.0293% December 2020 75,064 1083 2 0.0027% January 2021 30,539 447 38 0.1244% 1 COVID-19: Coronavirus disease 2019; 2 SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2.